installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.5Mb
Running ‘testthat.R’ [29s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(adegenet))
  > test_check("adegenet")
  
   *** caught segfault ***
  address 6000000, cause 'memory not mapped'
Package suggested but not available for checking: ‘microbenchmark’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    R  35.4Mb
Running ‘allFormats.R’
Running the tests in ‘tests/allFormats.R’ failed.
Complete output:
  > options(digits.secs=6, width=70)
  > 
  > library(anytime)
  > 
  > ref <- format(as.POSIXct(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"),
  +                          "%Y-%m-%d %H:%M:%0S"))
  Warning messages:
  1: In strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
    unknown timezone '%Y-%m-%d %H:%M:%0S'
  2: In as.POSIXct.POSIXlt(x) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  3: In strptime(x, f, tz = tz) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  4: In as.POSIXct.POSIXlt(as.POSIXlt(x, tz, ...), tz, ...) :
    unknown timezone '%Y-%m-%d %H:%M:%0S'
  5: In as.POSIXlt.POSIXct(x, tz) : unknown timezone '%Y-%m-%d %H:%M:%0S'
  > 
  > 
  > stopifnot(ref == format(anytime(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"))))
  Error: ref == format(anytime(c("2016-09-01 10:11:12", "2016-09-01 10:11:12.345678"))) are not all TRUE
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-67 (performance.Rmd) 
Error: processing vignette 'performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Package suggested but not available for checking: ‘kebabs’
Package required but not available: ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘AR1seg-Ex.R’ failed
The error most likely occurred in:

> ### Name: AR1seg-package
> ### Title: Segmentation of an AR(1) Gaussian process
> ### Aliases: AR1seg-package AR1seg
> 
> ### ** Examples
> 
> library(AR1seg)
> data(y)
> res=AR1seg_func(y,Kmax=15,rho=TRUE)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: AR1seg_func -> Segmentor -> Segmentor.default
Execution halted
Package suggested but not available for checking: ‘pdInfoBuilder’
Packages suggested but not available for checking:
  ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
installed size is 70.1Mb
  sub-directories of 1Mb or more:
    java  70.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Package suggested but not available for checking: ‘mzR’
Packages suggested but not available for checking: ‘geoR’ ‘BayesXsrc’
Package unavailable to check Rd xrefs: ‘BayesXsrc’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-27 (Benchmarks.Rmd) 
Error: processing vignette 'Benchmarks.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bayesImageS.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-14 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-14 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'MCMC-diagnostics.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BCSub.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 117.7Mb
  sub-directories of 1Mb or more:
    include  117.6Mb
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), lambda = lambda, 
+                          numthreads = 1, memory_size = 512, seed = 1, 
+                          use_ram = TRUE)

 *** caught segfault ***
address fffffff8, cause 'memory not mapped'

Traceback:
 1: .Call("BigQuic_BigQuicHelper", PACKAGE = "BigQuic", argvPasser)
 2: BigQuicHelper(argvPasser = c("-l", lambda[i], "-n", numthreads,     "-t", maxit, "-e", epsilon, "-k", k, "-m", memory_size, "-q",     verbose, "-r", isnormalized, inputFileName, outputFileName))
 3: BigQuic(inputFileName = paste(path.package("BigQuic"), "/extdata/testInput",     sep = ""), lambda = lambda, numthreads = 1, memory_size = 512,     seed = 1, use_ram = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
File ‘BMN/libs/BMN.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/bootTimeInference.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 67-80 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
Installation failed.
See ‘/home/ripley/R/packages/tests32/CampaR1.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data     1.8Mb
    models   2.3Mb
Package required but not available: ‘V8’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Found the following significant warnings:
  "cec_r.c", line 192: warning: improper pointer/integer combination: op "="
  "cec_r.c", line 267: warning: improper pointer/integer combination: op ":"
See ‘/home/ripley/R/packages/tests32/CEC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    data  60.0Mb
Package suggested but not available for checking: ‘js’
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
Running ‘testthat.R’ [29s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ClusterR)
  Loading required package: gtools
  > 
  > test_check("ClusterR")
  Error in simpleError(msg, call) : 
    R_Reprotect: only 160 protected items, can't reprotect index 252
  Calls: test_check ... <Anonymous> -> o_apply -> lapply -> FUN -> <Anonymous>
  Warning: stack imbalance in '$', 113 then 114
  Warning: stack imbalance in 'length', 112 then 65
  Warning: stack imbalance in '>', 110 then 55
  Warning: stack imbalance in 'while', 108 then 53
  Warning: stack imbalance in '$', 58 then 57
  Warning: stack imbalance in '{', 180 then 50
  Warning: stack imbalance in '{', 172 then 86
  Warning: stack imbalance in 'lapply', 154 then 62
  Warning: stack imbalance in '{', 147 then 55
  Warning: stack imbalance in '$', 88 then 80
  
   *** caught segfault ***
  address 0, cause 'memory not mapped'
  
   *** caught
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: mclust
Package 'mclust' version 5.2.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: BMA
Loading required package: survival
Loading required package: leaps
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:survival':

    heart

Loading required package: inline
Loading required package: rrcov
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Loading required package: foreach
Loading required package: iterators
Package 'clustvarsel' version 2.3
Type 'citation("clustvarsel")' for citing this R package in publications.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data     3.8Mb
    exdata   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    app   2.9Mb
    doc   2.2Mb
Package suggested but not available for checking: ‘RandomFields’
Package unavailable to check Rd xrefs: ‘RandomFields’
Running examples in ‘CompRandFld-Ex.R’ failed
The error most likely occurred in:

> ### Name: Covariogram
> ### Title: Computes covariance, variogram and extremal coefficient
> ###   functions
> ### Aliases: Covariogram
> ### Keywords: Composite
> 
> ### ** Examples
> 
> library(CompRandFld)
> library(RandomFields)
Error in library(RandomFields) : 
  there is no package called ‘RandomFields’
Execution halted
Missing or unexported objects:
  ‘htmlTable::htmlTableWidget’ ‘htmlTable::htmlTableWidgetOutput’
  ‘htmlTable::renderHtmlTableWidget’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Package required but not available: ‘RandomFields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MonetDBLite’
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-109 (cubature.Rmd) 
Error: processing vignette 'cubature.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/CuCubes.Rcheck/00install.out’ for details.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    extdata  32.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot48c546b16795.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot48c546b16795.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot625429334c8a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot625429334c8a.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Loading pre-compiled model from /home/ripley/R/Lib32/DeLorean/extdata/exact-sizes.rds
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.9Mb
    help   1.3Mb
Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’
Package unavailable to check Rd xrefs: ‘Rmosek’
Running ‘has-devel.R’
  Running ‘test-that.R’ [251s/253s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) -
  invalid 'times' argument
  1: expect_true(!is.null(find_topic("foofoo"))) at testthat/test-help.r:45
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: find_topic("foofoo")
  7: find_pkg_topic(path, topic)
  8: topic_index(pkg)
  9: build_topic_index(pkg)
  10: invert(lapply(rds, aliases))
  
  Updating collate directive in  /tmp/RtmpcPaiVD/testCollateOrder/DESCRIPTION 
  
  testthat results ================================================================
  OK: 377 SKIPPED: 10 FAILED: 1
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Packages suggested but not available for checking: ‘DiagrammeRsvg’ ‘rsvg’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata       2.5Mb
    htmlwidgets   5.0Mb
    img           3.4Mb
Package required but not available: ‘deTestSet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    include  18.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.2Mb
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/framework.Rmd’
(Is a VignetteBuilder field missing?)
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: cOde
Loading required package: trust
Loading required package: ggplot2
Loading required package: stringr

Attaching package: 'dMod'

The following object is masked from 'package:stats':

    profile

"jak-stat.c", line 6: zero or negative subscript
"jak-stat.c", line 7: zero or negative subscript
cc: acomp failed for jak-stat.c
make: Fatal error: Command failed for target `jak-stat.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jak-stat.c' had status 1 and error message 'Illegal seek'
"jak-stat_s.c", line 6: zero or negative subscript
"jak-stat_s.c", line 7: zero or negative subscript
cc: acomp failed for jak-stat_s.c
make: Fatal error: Command failed for target `jak-stat_s.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jak-stat_s.c' had status 1 and error message 'Illegal seek'
Quitting from lines 71-81 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
unable to load shared object '/home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes/jak-stat_s.so':
  ld.so.1: R: fatal: /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes/jak-stat_s.so: open failed: No such file or directory
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/DNAprofiles.Rcheck/00install.out’ for details.
Running examples in ‘docopulae-Ex.R’ failed
The error most likely occurred in:

> ### Name: rowmatch
> ### Title: Row Matching
> ### Aliases: rowmatch
> 
> ### ** Examples
> 
> a = as.matrix(expand.grid(as.double(2:3), as.double(3:6)))
> a = a[sample(nrow(a)),]
> a
     Var1 Var2
[1,]    2    4
[2,]    3    6
[3,]    3    4
[4,]    2    5
[5,]    2    3
[6,]    2    6
[7,]    3    3
[8,]    3    5
> 
> b = as.matrix(expand.grid(as.double(3:4), as.double(2:5)))
> b = b[sample(nrow(b)),]
> b
     Var1 Var2
[1,]    4    4
[2,]    3    2
[3,]    4    2
[4,]    3    5
[5,]    3    3
[6,]    4    5
[7,]    4    3
[8,]    3    4
> 
> i = rowmatch(a, b)
Error in ordt[i] : subscript too large for 32-bit R
Calls: rowmatch
Execution halted
Running ‘testthat.R’ [127s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(docopulae)
  > 
  > test_check("docopulae")
  1. Error: rowmatch works in trivial cases (@test_base.R#255) -------------------
  subscript too large for 32-bit R
  1: expect_equal(rowmatch(b, a), as.integer(c(NA, NA))) at testthat/test_base.R:255
  2: compare(object, expected, ...)
  3: rowmatch(b, a)
  
  2. Error: rowmatch works for a random example (@test_base.R#279) ---------------
  subscript too large for 32-bit R
  1: rowmatch(x, s) at testthat/test_base.R:279
  
  testthat results ================================================================
  OK: 142 SKIPPED: 0 FAILED: 2
  1. Error: rowmatch works in trivial cases (@test_base.R#255) 
  2. Error: rowmatch works for a random example (@test_base.R#279) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rgbif’
Packages suggested but not available for checking:
  ‘RMySQL’ ‘microbenchmark’
Packages unavailable to check Rd xrefs: ‘microbenchmark’, ‘RMySQL’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/dynamichazard.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    models   4.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/dynsbm.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/RtmpAcaWk3"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    examples   4.9Mb
Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)

 *** caught segfault ***
address f02bc, cause 'invalid permissions'
Running ‘testthat.R’ [150s/150s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(emdi)
  Loading required package: maptools
  Loading required package: sp
  Checking rgeos availability: FALSE
   	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
   	which has a restricted licence. It is disabled by default;
   	to enable gpclib, type gpclibPermit()
  > 
  > test_check("emdi")
  
   Bootstrap started                                                                        
   Bootstrap completed                                                                      1. Failure: Does parametric_bootstrap return the benchmark results? (@test_mse_estimation.R#44) 
  MSE[, "Quantile_10"] not equal to as.numeric(as.character(ebp_MSE_bc[, "quant10"])).
  5/5 mismatches (average diff: 0.0552)
  [1]  187158 -  187158 == -0.011422
  [2]   94721 -   94721 ==  0.000952
  [3]  610685 -  610685 == -0.048113
  [4]  355750 -  355750 ==  0.024758
  [5] 1737092 - 1737092 == -0.190909
  
  
  testthat results ================================================================
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: Does parametric_bootstrap return the benchmark results? (@test_mse_estimation.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynIRT
> ### Title: Dynamic IRT estimation via Variational Inference
> ### Aliases: dynIRT
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> ### Replication of Martin-Quinn Judicial Ideology Scores
> ### Based on July 23, 2014 (2014 Release 01) release of the Supreme Court Database
> ### Start values and priors based on replication code provided by Kevin Quinn
> 
> data(mq_data)
> 
> ## Estimate dynamic variational model using dynIRT()
> lout <- dynIRT(.data = mq_data$data.mq,
+                     .starts = mq_data$cur.mq,
+                     .priors = mq_data$priors.mq,
+                     .control = {list(
+                     threads = 1,
+                     verbose = TRUE,
+                     thresh = 1e-6,
+ 		    maxit=500
+                     )})

==================== 
dynIRT: Dynamic IRT via Variational Inference


error: 
error: Mat::init(): size is fixed and hence cannot be changedMat::init(): size is fixed and hence cannot be changedterminate called recursively
terminate called after throwing an instance of 'std::logic_error'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    xsd   5.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: +RTS:  not found
Quitting from lines 315-317 (creating-EML.Rmd) 
Error: processing vignette 'creating-EML.Rmd' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘ggtree’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 129-154 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Package unavailable to check Rd xrefs: ‘geoR’
Package suggested but not available for checking: ‘spocc’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    Sweave   6.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.3Mb
Package suggested but not available for checking: ‘RCytoscape’
Package suggested but not available for checking: ‘RMySQL’
Package unavailable to check Rd xrefs: ‘RMySQL’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    exiftool  11.5Mb
Running examples in ‘expm-Ex.R’ failed
The error most likely occurred in:

> ### Name: logm
> ### Title: Matrix Logarithm
> ### Aliases: logm
> ### Keywords: algebra math
> 
> ### ** Examples
> 
> m <- diag(2)
> logm(m)
     [,1] [,2]
[1,]    0    0
[2,]    0    0
> expm(logm(m))
     [,1] [,2]
[1,]    1    0
[2,]    0    1
> 
> ## Here, logm() is barely defined, and Higham08 has needed an amendment
> ## in order for not to loop forever:
> D0 <- diag(x=c(1, 0.))
> (L. <- logm(D0))
Warning in logm.Higham08(x) :
  Inverse scaling did not work (t = 1).
The matrix logarithm may not exist for this matrix.Setting m = 3 arbitrarily.
     [,1]     [,2]
[1,]    0        0
[2,]    0 -9576994
> stopifnot( all.equal(D0, expm(L.)) )
> 
> ## A matrix for which clearly no logm(.) exists:
> (m <- cbind(1:2, 1))
     [,1] [,2]
[1,]    1    1
[2,]    2    1
> (l.m <- logm(m)) ## all NA
Warning in sqrt(S[ij, ij]) : NaNs produced
Error in solve.default(X[ii, ii] + X[ij, ij], S[ii, ij] - sumU) : 
  system is computationally singular: reciprocal condition number = 0
Calls: logm ... logm.Higham08 -> rootS -> solve -> solve -> solve.default
Execution halted
Running examples in ‘ExtDist-Ex.R’ failed
The error most likely occurred in:

> ### Name: eval.estimation
> ### Title: Parameter Estimation Evaluation.
> ### Aliases: eval.estimation
> 
> ### ** Examples
> 
> eval.estimation(rdist=rNormal,edist=eNormal,n = 100, rep.num = 50,
+ params = list(mean = 1,sd = 5))
Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error : Hessian function might be wrong - check it! 

Error in eval(expr, envir, enclos) : object 'value' not found
Calls: eval.estimation ... edist -> wmle -> with -> with.default -> eval -> eval
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/FactoRizationMachines.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Package required but not available: ‘devEMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘fheatmap-Ex.R’ failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Package suggested but not available for checking: ‘devEMF’
Packages suggested but not available for checking:
  ‘microbenchmark’ ‘multipanelfigure’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FLSSS.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: forecast

Attaching package: 'forecastHybrid'

The following object is masked from 'package:forecast':

    accuracy

Quitting from lines 88-91 (forecastHybrid.Rmd) 
Error: processing vignette 'forecastHybrid.Rmd' failed with diagnostics:
do not know how to convert 'time(x$x)' to class "Date"
Execution halted
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘fractaldim-Ex.R’ failed
The error most likely occurred in:

> ### Name: fd.estim.method
> ### Title: Estimation of Fractal Dimension via Specific Methods
> ### Aliases: fd.estim.method fd.estim.variation fd.estim.variogram
> ###   fd.estim.madogram fd.estim.rodogram fd.estim.genton fd.estim.incr1
> ###   fd.estim.hallwood fd.estim.boxcount fd.estim.periodogram
> ###   fd.estim.dctII fd.estim.wavelet fd.estim.transect.var
> ###   fd.estim.transect.incr1 fd.estim.isotropic fd.estim.squareincr
> ###   fd.estim.filter1
> ### Keywords: ts spatial
> 
> ### ** Examples
> 
> library(RandomFields)
Error in library(RandomFields) : 
  there is no package called ‘RandomFields’
Execution halted
Running ‘run_tests.R’
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(fractaldim)
  Loading required package: abind
  > library(RandomFields)
  Error in library(RandomFields) : 
    there is no package called 'RandomFields'
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Package unavailable to check Rd xrefs: ‘RMark’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 90-102 (sparse_matrices.Rmd) 
Error: processing vignette 'sparse_matrices.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘geoR’
Package suggested but not available for checking: ‘R2BayesX’
Running examples in ‘gamsel-Ex.R’ failed
The error most likely occurred in:

> ### Name: gamsel
> ### Title: Fit Regularization Path for Gaussian or Binomial Generalized
> ###   Additive Model
> ### Aliases: gamsel
> ### Keywords: regression smooth nonparametric
> 
> ### ** Examples
> 
> data=gendata(n=500,p=12,k.lin=3,k.nonlin=3,deg=8,sigma=0.5)
> attach(data)
> bases=pseudo.bases(X,degree=10,df=6)
> # Gaussian gam
> gamsel.out=gamsel(X,y,bases=bases)
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)
> gamsel.cv=cv.gamsel(X,y,bases=bases)
> par(mfrow=c(1,1))
> plot(gamsel.cv)
> par(mfrow=c(3,4))
> plot(gamsel.out,newx=X,index=20)
> # Binomial model
> gamsel.out=gamsel(X,yb,family="binomial")
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)

 *** caught segfault ***
address 1000, cause 'memory not mapped'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data    3.8Mb
    doc     3.1Mb
    tests   2.6Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
Package unavailable to check Rd xrefs: ‘gcmr’
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(sp)
  > library(gstat)
  > library(geoR)
  Error in library(geoR) : there is no package called 'geoR'
  Execution halted
Running ‘testthat.R’ [23s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GeneralTree)
  Loading required package: R6
  > 
  > test_check("GeneralTree")
  1. Error: plotting a tree works (@test_plot.R#64) ------------------------------
  'create_nodes' is not an exported object from 'namespace:DiagrammeR'
  1: expect_identical(plot(tree)$x$diagram, diagram) at testthat/test_plot.R:64
  2: identical(object, expected)
  3: plot(tree)
  4: plot.GeneralTree(tree)
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'create_nodes' is not an exported object from 'namespace:DiagrammeR'
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    exdata   5.3Mb
Package suggested but not available for checking: ‘reactome.db’
Packages suggested but not available for checking: ‘geoR’ ‘geoRglm’
Package suggested but not available for checking: ‘geojsonlint’
Package unavailable to check Rd xrefs: ‘geojsonlint’
Running examples in ‘geojson-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.geojson
> ### Title: Geojson class
> ### Aliases: as.geojson as.geojson,SpatialLines-method
> ###   as.geojson,SpatialLinesDataFrame-method
> ###   as.geojson,SpatialPoints-method
> ###   as.geojson,SpatialPointsDataFrame-method
> ###   as.geojson,SpatialPolygons-method
> ###   as.geojson,SpatialPolygonsDataFrame-method
> ###   as.geojson,character-method as.geojson,geojson-method
> ###   as.geojson,json-method
> 
> ### ** Examples
> 
> # character
> as.geojson(geojson_data$featurecollection_point)
<geojson> 
  type:  FeatureCollection 
Warning: 'geojsonlint' not installed, skipping GeoJSON linting
Error in if (checkforpkg("geojsonlint")) { : 
  argument is not interpretable as logical
Calls: <Anonymous> ... geo_bbox.geojson -> geo_bbox -> geo_bbox.character -> hint_geojson
Execution halted
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojson")
  
  Attaching package: 'geojson'
  
  The following object is masked from 'package:graphics':
  
      polygon
  
  > test_check("geojson")
  1. Error: geo_bbox works - Point input (@test-geo_bbox.R#5) --------------------
  argument is not interpretable as logical
  1: point(x) at testthat/test-geo_bbox.R:5
  2: point.character(x)
  3: hint_geojson(x)
  
  2. Error: geo_bbox works - Point input (@test-geo_bbox.R#16) -------------------
  argument is not interpretable as logical
  1: multipoint(x) at testthat/test-geo_bbox.R:16
  2: multipoint.character(x)
  3: hint_geojson(x)
  
  Error in if (checkforpkg("geojsonlint")) { : 
    argument is not interpretable as logical
  Calls: test_check ... eval -> eval -> point -> point.character -> hint_geojson
  In addition: Warning message:
  'geojsonlint' not installed, skipping GeoJSON linting 
  testthat results ================================================================
  OK: 36 SKIPPED: 0 FAILED: 2
  1. Error: geo_bbox works - Point input (@test-geo_bbox.R#5) 
  2. Error: geo_bbox works - Point input (@test-geo_bbox.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'geojson'

The following object is masked from 'package:graphics':

    polygon

Warning: 'geojsonlint' not installed, skipping GeoJSON linting
Quitting from lines 30-44 (geojson-operations.Rmd) 
Error: processing vignette 'geojson-operations.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages required but not available: ‘constrainedKriging’ ‘RandomFields’

Package suggested but not available for checking: ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RandomFields’

Package suggested but not available for checking: ‘geoRglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘geoR’ ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Packages unavailable to check Rd xrefs: ‘RandomFields’, ‘geoR’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/ggdmc.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘readr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Warning: Ignoring unknown aesthetics: data_id, tooltip
Warning: Ignoring unknown aesthetics: data_id, tooltip
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot2fa132805e4b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2fa132805e4b.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1a3e52981b9f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1a3e52981b9f.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [133s/133s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  1. Failure: inherits timezone from data (@test-scale-date.R#18) ----------------
  sc$timezone not equal to NULL.
  Types not compatible: character vs NULL
  
  
  testthat results ================================================================
  OK: 778 SKIPPED: 0 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
Process terminated
Execution halted
Packages which this enhances but not available for checking:
  ‘geoRglm’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘geoRglm’
Running ‘testthat.R’ [505s/505s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmmsr)
  > 
  > test_check("glmmsr")
  1. Error: nSL = 0 gives similar result to Laplace (@test_fit.R#116) ------------
  std::bad_alloc
  1: glmm(response ~ covariate + (1 | cluster) + (1 | group), data = three_level, family = binomial, 
         method = "SR", control = list(nSL = 0), verbose = 0) at testthat/test_fit.R:116
  2: find_lfun_glmm_internal(modfr, method = method, control = con)
  3: find_lfun_SR(modfr, devfun_lme4, nSL = control$nSL, nAGQ = control$nAGQ)
  4: (function (value) 
     {
         if (missing(value)) {
             calibration_parameters__n_sparse_levels__get(self)
         }
         else {
             calibration_parameters__n_sparse_levels__set(self, value)
         }
     })(quote(0))
  5: calibration_parameters__n_sparse_levels__set(self, value)
  
  testthat results ================================================================
  OK: 76 SKIPPED: 0 FAILED: 1
  1. Error: nSL = 0 gives similar result to Laplace (@test_fit.R#116) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lme4
Loading required package: Matrix
Quitting from lines 373-389 (glmmsr-vignette.Rmd) 
Error: processing vignette 'glmmsr-vignette.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
Running ‘AAAtest-all.R’ [90m/90m]
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
  > if(require("testthat")) {
  +     pkg <- "glmmTMB"
  +     require(pkg, character.only=TRUE)
  +     print(sessionInfo())
  +     test_check(pkg)
  +     print(warnings()) # TODO? catch most of these by expect_warning(..)
  + } else {
  +     warnings("Package 'testthat' not available, cannot run unit tests for package",
  + 	     sQuote(pkg))
  + }
  Loading required package: testthat
  Loading required package: glmmTMB
  R version 3.3.2 Patched (2017-02-19 r72213)
  Platform: sparc-sun-solaris2.10 (32-bit)
  Running under: Solaris 10
  
  locale:
  [1] /en_GB.UTF-8/C/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] glmmTMB_0.1.1  testthat_1.0.2
  
  loaded via a namespace (and not attached):
   [1] minqa_1.2.4     MASS_7.3-45     Matrix_1.2-8    magrittr_1.5   
   [5] R6_2.2.0        TMB_1.7.8       Rcpp_0.12.9     crayon_1.3.2   
   [9] splines_3.3.2   nlme_3.1-131    grid_3.3.2      nloptr_1.0.4   
  [13] lme4_1.1-12     lattice_0.20-34
  Loading required package: lme4
  Loading required package: Matrix
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Installation failed.
See ‘/home/ripley/R/packages/tests32/gmwm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pdftools’
Installation failed.
See ‘/home/ripley/R/packages/tests32/goldi.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in genoud(fn = criterion, nvars = d, max = TRUE, pop.size = optimcontrol$pop.size,  :
  Stopped because hard maximum generation limit was hit.
##  rgenoud (Version 5.7-12.4, Build Date: 2015-07-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

This is randtoolbox. For overview, type 'help("randtoolbox")'.
Package suggested but not available for checking: ‘Sxslt’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:tidyr':

    expand

Loading required package: lme4

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

The following object is masked from 'package:stats':

    step

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Quitting from lines 293-301 (introduction_to_groupdata2.Rmd) 
Error: processing vignette 'introduction_to_groupdata2.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Running examples in ‘gsl-Ex.R’ failed
The error most likely occurred in:

> ### Name: multimin
> ### Title: Function minimization
> ### Aliases: Multimin multimin multimin.init multimin.iterate
> ###   multimin.restart multimin.fminimizer.size
> ### Keywords: array
> 
> ### ** Examples
> 
> # The Rosenbrock function:
> x0 <- c(-1.2, 1)
> f <- function(x) (1 - x[1])^2 + 100 * (x[2] - x[1]^2)^2
> df <- function(x) c(-2*(1 - x[1]) + 100 * 2 * (x[2] - x[1]^2) * (-2*x[1]),
+                     100 * 2 * (x[2] - x[1]^2))
> 
> # The simple way to call multimin.
> state <- multimin(x0, f, df)
> print(state$x)
[1] 0.999997 0.999994
> 
> # The fine-control way to call multimin.
> state <- multimin.init(x0, f, df, method="conjugate-fr")
> for (i in 1:200)
+ 	state <- multimin.iterate(state)

 *** caught segfault ***
address 20, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [63s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gsrc)
  > 
  > test_check("gsrc")
  1. Failure: cnv returns correct output (@test_cnv.R#18) ------------------------
  dim(dat$cnv) not equal to c(12, 100).
  1/2 mismatches
  [1] 10 - 12 == -2
  
  
  2. Failure: segm returns correct output (@test_segm.R#17) ----------------------
  dim(dat$cna) not equal to c(104, 6).
  1/2 mismatches
  [1] 103 - 104 == -1
  
  
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: cnv returns correct output (@test_cnv.R#18) 
  2. Failure: segm returns correct output (@test_segm.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    java  61.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘haven-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_dta
> ### Title: Read and write Stata DTA files.
> ### Aliases: read_dta read_stata write_dta
> 
> ### ** Examples
> 
> path <- system.file("examples", "iris.dta", package = "haven")
> read_dta(path)
Error in df_parse_dta_file(spec, encoding) : 
  Failed to parse /home/ripley/R/Lib32/haven/examples/iris.dta: Invalid file, or file has unsupported features.
Calls: read_dta -> df_parse_dta_file -> .Call
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/hBayesDM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /usr/local/share/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-4 
trying URL 'ftp://ftp.bafg.de/pub/REFERATE/GRDC/ltdata/europe.zip'
ftp data connection made, file length 0 bytes
==================================================
downloaded 4.6 MB

Station has monthly records
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Quitting from lines 252-254 (hddtools_vignette.Rmd) 
Error: processing vignette 'hddtools_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis

---------------------
Welcome to heatmaply version 0.7.0
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(heatmaply))
---------------------

Quitting from lines 83-85 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc          13.9Mb
    htmlwidgets   2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 45-46 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Running examples in ‘HLSM-Ex.R’ failed
The error most likely occurred in:

> ### Name: HLSMrandomEF
> ### Title: Function to run the MCMC sampler in random effects model (and
> ###   HLSMfixedEF for fixed effects model)
> ### Aliases: HLSMrandomEF HLSMfixedEF print.HLSM print.summary.HLSM
> ###   summary.HLSM getIntercept getAlpha getLS getLikelihood getBeta
> 
> ### ** Examples
> 
> 
> library(HLSM)
> 
> #Set values for the inputs of the function
> priors = NULL
> tune = NULL
> initialVals = NULL
> niter = 10
> 
> #Random effect HLSM on Pitt and Spillane data
> random.fit = HLSMrandomEF(Y = ps.advice.mat,FullX = ps.edge.vars.mat,
+ 	initialVals = initialVals,priors = priors,
+ 	tune = tune,tuneIn = FALSE,dd = 2,niter = niter,
+ 	intervention = 0)

 *** caught segfault ***
address 82000000, cause 'memory not mapped'

Traceback:
 1: base::.Call(.NAME, ...)
 2: .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode),     PACKAGE = "igraph")
 3: graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted,     diag = diag)
 4: graph.adjacency(Y[[tt]])
 5: FUN(X[[i]], ...)
 6: lapply(1:KK, function(tt) {    g = graph.adjacency(Y[[tt]])    ss = shortest.paths(g)    ss[ss > 4] = 4    Z0 = cmdscale(ss, k = dd)    dimnames(Z0)[[1]] = dimnames(YY[[tt]])[[1]]    return(Z0)})
 7: HLSMrandomEF(Y = ps.advice.mat, FullX = ps.edge.vars.mat, initialVals = initialVals,     priors = priors, tune = tune, tuneIn = FALSE, dd = 2, niter = niter,     intervention = 0)
An irrecoverable exception occurred. R is aborting now ...
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.7Mb
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(htmltools)
  > 
  > test_check("htmltools")
  Error in grepl("\n", lines, fixed = TRUE) : invalid multibyte string at '<f0><9f><98><8e>', making sure it's UTF-8 encoded on all platforms.'
  Calls: test_check ... with_reporter -> force -> source_file -> srcfilecopy -> grepl
  testthat results ================================================================
  OK: 146 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 79-82 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'pdftools'
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.9Mb
    doc    2.3Mb
Running examples in ‘icenReg-Ex.R’ failed
The error most likely occurred in:

> ### Name: simIC_weib
> ### Title: Simulates interval censored data from regression model with a
> ###   Weibull baseline
> ### Aliases: simIC_weib
> 
> ### ** Examples
> 
> set.seed(1)
> sim_data <- simIC_weib(n = 500, b1 = .3, b2 = -.3, model = 'ph', 
+                       shape = 2, scale = 2, inspections = 6, 
+                       inspectLength = 1)
> #simulates data from a cox-ph with beta weibull distribution.
> 
> diag_covar(Surv(l, u, type = 'interval2') ~ x1 + x2, 
+            data = sim_data, model = 'po')
> diag_covar(Surv(l, u, type = 'interval2') ~ x1 + x2,
+            data = sim_data, model = 'ph')
Error in ans[isOk] <- log(-log(x[isOk])) : 
  NAs are not allowed in subscripted assignments
Calls: diag_covar -> diag_covar -> s_trans
Execution halted
Running examples in ‘icesSAG-Ex.R’ failed
The error most likely occurred in:

> ### Name: getStandardAssessmentGraps
> ### Title: Get graphs of stock assessment output
> ### Aliases: getFishMortality getFishingMortalityGraph
> ###   getFishingMortalityHistoricalPerformance getLandingsGraph
> ###   getRecruitmentGraph getRecruitmentHistoricalPerformance
> ###   getSSBHistoricalPerformance getSpawningStockBiomassGraph
> ###   getStandardAssessmentGraps getYSSB getstock_recruitment
> 
> ### ** Examples
> 
> keys <- findKey("had", 2015)
> landings_img <- getLandingsGraph(keys[1])
Warning in download.file(fileurl, tmp, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://sg.ices.dk/StandardGraphsWebServices/Download/LandingsGraph8065_1_fol5em02demjwasrc2yqsnnn2017-01-14_10_30_50.png': HTTP status was '404 Not Found'
Error in download.file(fileurl, tmp, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://sg.ices.dk/StandardGraphsWebServices/Download/LandingsGraph8065_1_fol5em02demjwasrc2yqsnnn2017-01-14_10_30_50.png'
Calls: getLandingsGraph -> lapply -> FUN -> download.file
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address 9, cause 'memory not mapped'

Traceback:
 1: grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Quitting from lines 1343-1398 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   5.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/imager.Rcheck/00install.out’ for details.
Running examples in ‘IntegratedMRF-Ex.R’ failed
The error most likely occurred in:

> ### Name: CombPredict
> ### Title: Integrated Prediction of Testing samples using Combination
> ###   Weights from integrated RF or MRF model
> ### Aliases: CombPredict
> 
> ### ** Examples
> 
> library(IntegratedMRF)
> data(Dream_Dataset)
> Tree=1
> Feature=1
> Leaf=5
> Confidence=80
> finalX=Dream_Dataset[[1]]
> Cell=Dream_Dataset[[2]]
> Y_train_Dream=Dream_Dataset[[3]]
> Y_train_cell=Dream_Dataset[[4]]
> Y_test=Dream_Dataset[[5]]
> Y_test_cell=Dream_Dataset[[6]]
> Drug=c(1,2,3)
> Y_train_Drug=matrix(Y_train_Dream[,Drug],ncol=length(Drug))
> Result=Combination(finalX,Y_train_Drug,Cell,Y_train_cell,Tree,Feature,Leaf,Confidence)

 *** caught segfault ***
address 27a000, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Loading required package: gdistance
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:raster':

    union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: Matrix

Attaching package: 'gdistance'

The following object is masked from 'package:igraph':

    normalize


Error: processing vignette 'ipdw.Rnw' failed with diagnostics:
 chunk 2 (label = ipdw-1) 
Error in library("geoR") : there is no package called 'geoR'
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred QSPRpred-class
> 
> ### ** Examples
> 
> data(qspr.data)
> smis <- paste(qspr.data[,1])
> ty <- qspr.data[,c(2,5)]
> trainidx <- sample(1:nrow(qspr.data), 5000)
> testidx <- (1:nrow(qspr.data))[-trainidx][1:100]
> 
> data(qsprpred_EG_5k) 
> ## same as run => qsprpred_EG_5k <- 
> 
> #-----arguments
> #smis: SMILES string set (character vector) for training
> #y: property sets (matrix) for training  
> #v_ymin: minimum value of target properties
> #v_ymax: maximum value of target properties
> #v_descriptor: function transforming SMILES strings to feature matrix 
> #v_fpnames: character vectors indicating finger print used in the descriptor
> #w0: matrix representing prior mean of coeffients in linear regression model
> #V0_inv: matrix representing the prior variance of coeffients in linear regression model
> #a0: numeric value representing the location parameter in gamma prior 
> #b0: numeric value representing the shape parameter in gamma prior 
> #------
> 
> predictions <- qsprpred_EG_5k$qspr_predx(smis[testidx])  

get fingerprint graph from SMILES strings          
Error in .jcall("org/guha/rcdk/util/Misc", "Ljava/lang/Object;", "getProperty",  : 
  RcallMethod: cannot determine object class
Calls: <Anonymous> ... lapply -> FUN -> get.property -> .jcall -> .External
Execution halted
Package required but not available: ‘Fgmutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘itree/libs/itree.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘xval.o’, ‘xval_penalty.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 114-116 (JacobiEigen.Rmd) 
Error: processing vignette 'JacobiEigen.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: MASS
Loading required package: boot

Attaching package: 'boot'

The following object is masked from 'package:survival':

    aml

Loading required package: lattice

Attaching package: 'lattice'

The following object is masked from 'package:boot':

    melanoma

Loading required package: statmod
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
Running examples in ‘lakemorpho-Ex.R’ failed
The error most likely occurred in:

> ### Name: lakeMajorAxisLength
> ### Title: Calculate the length of the major axis for lake
> ### Aliases: lakeMajorAxisLength
> 
> ### ** Examples
> 
> data(lakes)
> lakeMajorAxisLength(inputLM)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘coordinates’ for signature ‘"numeric"’
Calls: lakeMajorAxisLength ... lapply -> Lines -> is -> Line -> coordinates -> <Anonymous>
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    2.6Mb
    help   1.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/largeVis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/LatentREGpp.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
Running examples in ‘leafletCN-Ex.R’ failed
The error most likely occurred in:

> ### Name: demomap
> ### Title: Show the basic shape of the data
> ### Aliases: demomap
> 
> ### ** Examples
> 
> demomap("china")
Error in loadNamespace(name) : there is no package called ‘rgeos’
Calls: demomap ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.1Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     23.8Mb
Package suggested but not available for checking: ‘EBImage’
Running examples in ‘lidR-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.raster.lasmetrics
> ### Title: Transform a 'lasmetrics' object into a spatial 'RasterLayer'
> ###   object
> ### Aliases: as.raster.lasmetrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
Error: ERROR: '%s' after %u of %u points> 
> meanHeight = grid_metrics(lidar, mean(Z))
Error: First argument is not a LAS object
Execution halted
Error in re-building vignettes:
  ...

 *** caught segfault ***
address 1c00000, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 134-135 (lingtypology.Rmd) 
Error: processing vignette 'lingtypology.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/liquidSVM.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        2.1Mb
    testdata   1.7Mb
Package suggested but not available for checking: ‘Rsymphony’
Packages required but not available: ‘geoR’ ‘RandomFields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 60-67 (quick-start.Rmd) 
Error: processing vignette 'quick-start.Rmd' failed with diagnostics:
error reading from connection
Execution halted
Running ‘testthat.R’ [110s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) ---------------
  invalid 'tz' value
  1: expect_equal(interval(t1, t2), new("Interval", 18316800, start = as.POSIXct("2007-01-01", 
         tz = "UTC"), tzone = "UTC")) at testthat/test-intervals.R:86
  2: compare(object, expected, ...)
  3: interval(t1, t2)
  4: as.POSIXct(start, tz = tzone)
  5: as.POSIXct.POSIXlt(start, tz = tzone)
  
  testthat results ================================================================
  OK: 2152 SKIPPED: 0 FAILED: 1
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lav2lvnet
> ### Title: Convert lavaan model to lvnet model matrices
> ### Aliases: lav2lvnet
> 
> ### ** Examples
> 
> library("lavaan")
This is lavaan 0.5-22
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

The following object is masked from ‘package:OpenMx’:

    vech

> 
> # Load dataset:
> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # lavaan model
> HS.model <- '
+ visual  =~ x1 + x2 + x3
+ textual =~ x4 + x5 + x6
+ speed   =~ x7 + x8 + x9 '
> 
> # fit via lavaan:
> lavFit <- cfa(HS.model, HolzingerSwineford1939[7:15],std.lv=TRUE)
> 
> # Fit via lvnet:
> mod <- lav2lvnet(HS.model, HolzingerSwineford1939[7:15])
> lvnetFit <- lvnet(Data, lambda = mod$lambda, psi = mod$psi)
Error: The job for model 'model' exited abnormally with the error message: Non-conformable matrices [(9 x 3) and (9 x 3)] in Matrix Multiply.
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot50a13dc81c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot50a13dc81c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot26a13d645564.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot26a13d645564.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    mapdata  32.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 72-86 (matchingR-performance.Rmd) 
Error: processing vignette 'matchingR-performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Running examples in ‘mcglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: anova.mcglm
> ### Title: Anova Tables
> ### Aliases: anova.mcglm
> 
> ### ** Examples
> 
> x1 <- seq(-1, 1, l = 100)
> x2 <- gl(5, 20)
> beta <- c(5, 0, -2, -1, 1, 2)
> X <- model.matrix(~ x1 + x2)
> set.seed(123)
> y <- rnorm(100, mean = X%*%beta, sd = 1)
> data = data.frame("y" = y, "x1" = x1, "x2" = x2)
> fit.anova <- mcglm(c(y ~ x1 + x2), list(mc_id(data)), data = data)
Automatic initial values selected. 
Error in rep(1:n_resp, information$n_betas) : invalid 'times' argument
> anova(fit.anova)
Error in UseMethod("anova") : 
  no applicable method for 'anova' applied to an object of class "try-error"
Calls: anova
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
----------------------------------------------------------------------
  mcglm: Multivariate Covariance Generalized Linear Models

  For support, collaboration or bug report, visit: 
    https://github.com/wbonat/mcglm

  mcglm version 0.3.0 (build on 2016-06-06) is now loaded.
----------------------------------------------------------------------
Loading required package: Matrix
Error in rep(1:n_resp, information$n_betas) : invalid 'times' argument
Quitting from lines 116-118 (GLMExamples.Rmd) 
Error: processing vignette 'GLMExamples.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
Execution halted
Running examples in ‘mcPAFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPAFit
> ### Title: estimates the Preferential Attachment function in a temporal
> ###   complex network without temporal information.
> ### Aliases: mcPAFit
> ### Keywords: package Preferential Attachment function Markov chain Monte
> ###   Carlo Gibbs sampling missing timeline
> 
> ### ** Examples
> 
> library(mcPAFit)
> N      <- 1000 #number of nodes in the network 
> M      <- 500  #number of needed sample
> lag   <-  1
> start <-  100
> 
> data   <- create_sim_data(N = N, alpha = 1)
> write.table(data$random[,1:2], row.names = FALSE,
+             col.names = FALSE, file = "input.txt")
> system.time(mcPAFit(file_name = "input.txt",burn_in = 0, s = 5, skip = 1, 
+             needed_sample = M, G = 20,only_active_node = 1, random = 0))
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 15) >= this->size() (which is 0)
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/medSTC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

arm (Version 1.9-3, built: 2016-11-21)

Working directory is /home/ripley/R/packages/tests32/merTools.Rcheck/vign_test/merTools/vignettes

Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:MASS':

    select

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: Rcpp
rstanarm (Version 2.13.1, packaged: 2016-11-20 16:59:31 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call(backend, constraints, matrices, parameters, algebras, expectations,     computes, data, intervalList, communication, options, defVars,     silent || !interactive(), PACKAGE = "OpenMx")
 2: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 3: mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...), error = function(e) e)
 8: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
 9: summary(meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE))))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MethyBayes.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-63 (compiled_models.Rmd) 
Error: processing vignette 'compiled_models.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Package which this enhances but not available for checking: ‘MonetDBLite’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.1Mb
Packages suggested but not available for checking: ‘geojsonio’ ‘rmapshaper’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.4Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Packages suggested but not available for checking: ‘graphite’ ‘NFPdata’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error in re-building vignettes:
  ...
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: graphite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'graphite'
Quitting from lines 198-206 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
could not find function "pathways"
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    include   3.2Mb
Running ‘test-all.R’ [17s/17s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  res1$solution not equal to `solution.opt`.
  2/2 mismatches (average diff: 0.00818)
  [1] 0.328 - 0.333 == -0.00572
  [2] 0.307 - 0.296 ==  0.01064
  
  
  Error: nlopt_add_inequality_mconstraint returned NLOPT_INVALID_ARGS.
  2. Failure: Test HS023. (@test-hs023.R#90) -------------------------------------
  res$solution not equal to `solution.opt`.
  1/2 mismatches
  [1] 3 - 1 == 2
  
  
  3. Failure: Test HS023. (@test-hs023.R#95) -------------------------------------
  all(eval_g_ineq(res$solution)$constr <= res$options$tol_constraints_ineq) isn't true.
  
  
  testthat results ================================================================
  OK: 40 SKIPPED: 0 FAILED: 3
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  2. Failure: Test HS023. (@test-hs023.R#90) 
  3. Failure: Test HS023. (@test-hs023.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/nopaco.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/nortestARMA.Rcheck/00install.out’ for details.
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    help   2.1Mb
Packages suggested but not available for checking: ‘RAppArmor’ ‘feather’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.0Mb
    libs     2.3Mb
    models   4.3Mb
Package unavailable to check Rd xrefs: ‘umx’
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxComputeGradientDescent
> ### Title: Optimize parameters using a gradient descent optimizer
> ### Aliases: MxComputeGradientDescent-class mxComputeGradientDescent
> 
> ### ** Examples
> 
> data(demoOneFactor)
> factorModel <- mxModel(name ="One Factor",
+   mxMatrix(type="Full", nrow=5, ncol=1, free=FALSE, values=0.2, name="A"),
+     mxMatrix(type="Symm", nrow=1, ncol=1, free=FALSE, values=1, name="L"),
+     mxMatrix(type="Diag", nrow=5, ncol=5, free=TRUE, values=1, name="U"),
+     mxAlgebra(expression=A %*% L %*% t(A) + U, name="R"),
+   mxExpectationNormal(covariance="R", dimnames=names(demoOneFactor)),
+   mxFitFunctionML(),
+     mxData(observed=cov(demoOneFactor), type="cov", numObs=500),
+      mxComputeSequence(steps=list(
+      mxComputeGradientDescent(),
+      mxComputeNumericDeriv(),
+      mxComputeStandardError(),
+      mxComputeHessianQuality()
+     )))
> factorModelFit <- mxRun(factorModel)
Running One Factor with 5 parameters

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call(backend, constraints, matrices, parameters, algebras, expectations,     computes, data, intervalList, communication, options, defVars,     silent || !interactive(), PACKAGE = "OpenMx")
 2: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 3: mxRun(factorModel)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    nifti   4.1Mb
Running examples in ‘P2C2M-Ex.R’ failed
The error most likely occurred in:

> ### Name: p2c2m.complete
> ### Title: Execute the complete P2C2M pipeline via a single command
> ### Aliases: p2c2m.complete
> 
> ### ** Examples
> 
> ## Example of the minimal data requirements to run P2C2M
> 
> # The absolute path to the input directory is set
> inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
> 
> # The name of the xml-file generated by BEAUTi and located in 
> # "inPath" is set
> inFile <- "sim.E.003.small.xml"
> 
> # Posterior predictive simulations with a setting of 2 simulation 
> # replicates are preformed
> sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
Error in python.exec(code, get.exception) : cannot import name izip
Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/pacotest.Rcheck/00install.out’ for details.
Running examples in ‘PAFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: calculate_error_fitness
> ### Title: Calculating fitness estimation error
> ### Aliases: calculate_error_fitness
> 
> ### ** Examples
> 
>   library("PAFit")
>   net        <- GenerateNet(N = 50 , m = 1 , mode = 1 , alpha =0.5 , shape = 100 , rate = 100)
>   net_stats  <- GetStatistics(net$graph)
>   result     <- PAFit(net_stats)
Error in PAFit(net_stats) : Warning: Log likelihood decreased.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  ‘remoter’ ‘pbdCS’
Package which this enhances but not available for checking: ‘remoter’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.6Mb
    examples   1.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   2.4Mb
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### Name: unifDAG
> ### Title: Uniform Sampling of Directed Acyclic Graphs (DAG)
> ### Aliases: unifDAG unifDAG.approx
> ### Keywords: graphs models
> 
> ### ** Examples
> 
> # require("Rgraphviz")
> set.seed(123)
> dag1 <- unifDAG(n=10)
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Packages suggested but not available for checking: ‘geoR’ ‘georob’
Packages unavailable to check Rd xrefs: ‘geoR’, ‘RandomFields’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Error: Package(s) needed for this function to work but notinstalled: georob geoR
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/pETM.Rcheck/00install.out’ for details.
File ‘PET/libs/PET.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘art.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘art.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Quitting from lines 755-769 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Package suggested but not available for checking: ‘OCplus’
Package unavailable to check Rd xrefs: ‘OCplus’
Package suggested but not available for checking: ‘ReportingTools’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/polmineR.Rcheck/00install.out’ for details.
Running examples in ‘poppr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bitwise.dist
> ### Title: Calculate a dissimilarity distance matrix for SNP data.
> ### Aliases: bitwise.dist
> 
> ### ** Examples
> 
> set.seed(999)
> x <- glSim(n.ind = 10, n.snp.nonstruc = 5e2, n.snp.struc = 5e2, ploidy = 2)

 *** caught segfault ***
address 7400000, cause 'memory not mapped'
Running ‘test-all.R’ [37s/46s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.0.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.3.0. To get started, type package?poppr
  OMP parallel support: available
  
   *** caught segfault ***
  address 7000000, cause 'memory not mapped'
Running ‘testthat.R’ [35s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(popprxl)
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.0.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.3.0. To get started, type package?poppr
  OMP parallel support: available
  
  popprxl is loaded. Use read.genalexcel() to read in your data.
  
  > 
  > test_check("popprxl")
  1. Error: Geographic data can be imported (@test-import.R#34) ------------------
  Number of samples (Row 1, Column B) is not numeric. 
    I found: NA 
  1: read.genalexcel(geox, sheet = 1, geo = TRUE, genclone = FALSE) at testthat/test-import.R:34
  2: stop(msg)
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: Geographic data can be imported (@test-import.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   5.6Mb
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘microbenchmark’
Installation failed.
See ‘/home/ripley/R/packages/tests32/preseqR.Rcheck/00install.out’ for details.
Package required but not available: ‘geoR’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/ProFit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 71-76 (ProliferativeIndexVignette.Rmd) 
Error: processing vignette 'ProliferativeIndexVignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    examples   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/pystr.Rcheck/00install.out’ for details.
Running examples in ‘qgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: centrality_auto
> ### Title: Automatic centrality statistics of graphs
> ### Aliases: centrality_auto
> ### Keywords: graphs centrality
> 
> ### ** Examples
> 
> set.seed(1)
> adj <- matrix(sample(0:1,10^2,TRUE,prob=c(0.8,0.2)),nrow=10,ncol=10)
> Q <- qgraph(adj)
> centrality_auto(Q) 

 *** caught segfault ***
address 85c00000, cause 'memory not mapped'

Traceback:
 1: base::.Call(.NAME, ...)
 2: .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode),     PACKAGE = "igraph")
 3: graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted,     diag = diag)
 4: graph.adjacency(adjmatrix = abs(1/x), mode = ifelse(directed.gr,     "directed", "undirected"), weighted = (if (weighted.gr) TRUE),     diag = FALSE)
 5: centrality_auto(Q)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       3.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-100 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.5Mb
Packages suggested but not available for checking: ‘RMySQL’ ‘its’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 141-142 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-31 (Performance.Rmd) 
Error: processing vignette 'Performance.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    app   6.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.6Mb
Running examples in ‘ramidst-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbn_generator
> ### Title: Generates a random dynamic Bayesian network
> ### Aliases: dbn_generator
> 
> ### ** Examples
> 
> d <- dbn_generator(3,2,2)
Error in .jfindClass(as.character(class)) : class not found
Calls: dbn_generator -> J -> jclassName -> .jfindClass
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RandomFields.Rcheck/00install.out’ for details.
Found the following significant warnings:
  "randomForestSRC.c", line 11363: warning: improper pointer/integer combination: arg #2
See ‘/home/ripley/R/packages/tests32/randomForestSRC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Package required but not available: ‘RandomFields’

Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘RArcInfo-Ex.R’ failed
The error most likely occurred in:

> ### Name: RArcInfo
> ### Title: RArcInfo
> ### Aliases: RArcInfo
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> #See example(plotpoly) for another example
> 
> library(RArcInfo)
> 
> datadir<-system.file("exampleData",package="RArcInfo")
> infodir<-system.file("exampleData","info",package="RArcInfo")
> coveragedir<-system.file("exampleData","wetlands",package="RArcInfo")
> 
> #get.bnddata needs the last slash...
> infodir<-paste(c(infodir,"/"), collapse="")
> 
> #List all the tables
> 
> covnames<-get.namesofcoverages(datadir)
> tablenames<-get.tablenames(infodir)
> 
> 
> #Display the name of the table and its fields
> for(i in 1:length(tablenames[[1]]))
+ {
+ 	print(c("Table: ",tablenames$TableName[i]))
+ 
+ 	fields<-get.tablefields(infodir,tablenames$TableName[i])
+ 	print("Fields")
+ 	for(j in 1:length(fields))
+ 		print(fields[[j]][1])
+ 
+ 	#Get the data
+ 	if(i==1)
+ 		tabledata<-get.tabledata(infodir,tablenames$TableName[i])
+ 	else
+ 		tabledata<-c(tabledata, get.tabledata(infodir,tablenames$TableName[i]) )
+ }
[1] "Table: "                          "WETLANDS.BND                    "
Error in get.tablefields(infodir, tablenames$TableName[i]) : 
  ERROR 3: Attempt to read past EOF in /home/ripley/R/Lib32/RArcInfo/exampleData/info/arc0000.nit.
Calls: get.tablefields -> .Call
Execution halted
Running ‘valencia.R’
  Running ‘wetlands.R’
Running the tests in ‘tests/wetlands.R’ failed.
Complete output:
  > library(RArcInfo)
  Loading required package: RColorBrewer
  > 
  > datadir<-system.file("exampleData",package="RArcInfo")
  > infodir<-system.file("exampleData","info",package="RArcInfo")
  > coveragedir<-system.file("exampleData","wetlands",package="RArcInfo")
  > 
  > #get.bnddata needs the last slash...
  > infodir<-paste(c(infodir,"/"), collapse="")
  > 
  > #List all the tables
  > 
  > covnames<-get.namesofcoverages(datadir)
  > tablenames<-get.tablenames(infodir)
  > 
  > 
  > #Display the name of the table and its filds
  > for(i in 1:length(tablenames[[1]]))
  + {
  + 	print(c("Table: ",tablenames$TableName[i]))
  + 
  + 	fields<-get.tablefields(infodir,tablenames$TableName[i])
  + 	print("Fields")
  + 	for(j in 1:length(fields))
  + 		print(fields[[j]][1])
  + 
  + 	#Get the data
  + 	if(i==1)
  + 		tabledata<-get.tabledata(infodir,tablenames$TableName[i])
  + 	else
  + 		tabledata<-c(tabledata, get.tabledata(infodir,tablenames$TableName[i]) )
  + }
  [1] "Table: "                          "WETLANDS.BND                    "
  Error in get.tablefields(infodir, tablenames$TableName[i]) : 
    ERROR 3: Attempt to read past EOF in /home/ripley/R/Lib32/RArcInfo/exampleData/info/arc0000.nit.
  Calls: get.tablefields -> .Call
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    etc    2.2Mb
    po     1.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rCBA.Rcheck/00install.out’ for details.
Running examples in ‘rcdk-Ex.R’ failed
The error most likely occurred in:

> ### Name: eval.desc
> ### Title: Evaluate a Molecular Descriptor
> ### Aliases: eval.desc
> ### Keywords: programming
> 
> ### ** Examples
> 
> smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
> mols <- sapply(smiles, parse.smiles)
> 
> dnames <- get.desc.names('constitutional')
Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;",  : 
  RcallMethod: cannot determine object class
Calls: get.desc.names -> .jcall -> .External
Execution halted
Error in re-building vignettes:
  ...
Loading required package: fingerprint

Error: processing vignette 'rcdk.Rnw' failed with diagnostics:
 chunk 11 
Error in .jcall("org/guha/rcdk/util/Misc", "S", "getSmiles", molecule,  : 
  RcallMethod: cannot determine object class
Execution halted
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons. Currently only supports Font Awesome icons.
> ### Aliases: icon
> 
> ### ** Examples
> 
> rmd <- '
+ ```{r}
+ library(rchallenge)
+ ```
+ <link rel="stylesheet" 
+  href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
+ `r icon("fa-user")`
+ `r icon("fa-user fa-lg")`
+ `r icon("fa-user fa-2x")`
+ `r icon("fa-user fa-3x")`
+ `r icon("fa-user fa-3x fa-border")`
+ '
> file <- tempfile()
> cat(rmd, file=file)
> writeLines(readLines(file))

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.4Mb
    po    2.2Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    include  25.2Mb
Running examples in ‘RcppCCTZ-Ex.R’ failed
The error most likely occurred in:

> ### Name: toTz
> ### Title: Shift datetime object from one timezone to another
> ### Aliases: toTz
> 
> ### ** Examples
> 
> toTz(Sys.time(), "America/New_York", "Europe/London")
Error in toTz(Sys.time(), "America/New_York", "Europe/London") : 
  Bad 'from' timezone
Calls: toTz -> .Call
Execution halted
Running ‘simpleTests.R’
Running the tests in ‘tests/simpleTests.R’ failed.
Complete output:
  > 
  > library(RcppCCTZ)
  > 
  > ord <- "America/Chicago"
  > lax <- "America/Los_Angeles"
  > lga <- "America/New_York"
  > htr <- "Europe/London"
  > utc <- "UTC"
  > 
  > now <- ISOdatetime(2016, 11, 29, 12, 00, 00, tz="UTC")
  > 
  > format(toTz(now, utc, lax), tz=lax)
  /usr/share/zoneinfo/America/Los_Angeles: No such file or directory
  Error in toTz(now, utc, lax) : Bad 'to' timezone
  Calls: format -> toTz -> .Call
  Execution halted
Running examples in ‘RcppGetconf-Ex.R’ failed
The error most likely occurred in:

> ### Name: getAll
> ### Title: Return all System Configuration Settings
> ### Aliases: getAll
> 
> ### ** Examples
> 
> head(getAll(), 30)
Error in getAll() : Memory allocation error
Calls: head -> getAll -> .Call
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppHoney.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rcpp.Rcheck/00install.out’ for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   3.7Mb
    lib       6.0Mb
    libs      1.6Mb
Package required but not available: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSelenium’
Error in re-building vignettes:
  ...
Quitting from lines 16-19 (rDVR-basics.Rmd) 
Error: processing vignette 'rDVR-basics.Rmd' failed with diagnostics:
there is no package called 'RSelenium'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot5d5317ec63e6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5d5317ec63e6.png': No such file or directory
Quitting from lines 21-25 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘V8’
Running ‘testthat.R’ [15s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readr)
  > 
  > test_check("readr")
  1. Failure: locale affects am/pm (@test-parsing-datetime.R#173) ----------------
  `a` not equal to `b`.
  Attributes: < Names: 1 string mismatch >
  Attributes: < Length mismatch: comparison on first 2 components >
  Attributes: < Component 2: Modes: character, list >
  Attributes: < Component 2: Lengths: 1, 4 >
  Attributes: < Component 2: names for current but not for target >
  Attributes: < Component 2: Attributes: < target is NULL, current is list > >
  Attributes: < Component 2: target is character, current is tbl_df >
  'is.NA' value mismatch: 1 in current 0 in target
  
  
  testthat results ================================================================
  OK: 406 SKIPPED: 2 FAILED: 1
  1. Failure: locale affects am/pm (@test-parsing-datetime.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘readxl-Ex.R’ failed
The error most likely occurred in:

> ### Name: excel_sheets
> ### Title: List all sheets in an excel spreadsheet.
> ### Aliases: excel_sheets
> 
> ### ** Examples
> 
> excel_sheets(system.file("extdata/datasets.xlsx", package = "readxl"))
[1] "iris"     "mtcars"   "chickwts" "quakes"  
> excel_sheets(system.file("extdata/datasets.xls", package = "readxl"))
[1] "iris"     "mtcars"   "chickwts" "quakes"  
> 
> # To load all sheets in a workbook, use lapply
> path <- system.file("extdata/datasets.xls", package = "readxl")
> lapply(excel_sheets(path), read_excel, path = path)

 *** caught segfault ***
address 307b460, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/redist.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Running examples in ‘reprex-Ex.R’ failed
The error most likely occurred in:

> ### Name: un-reprex
> ### Title: Un-render a reprex
> ### Aliases: un-reprex reprex_invert reprex_clean reprex_rescue
> 
> ### ** Examples
> 
> ## a rendered reprex can be inverted, at least approximately
> x <- reprex({
+   #' Some text
+   #+ chunk-label-and-options-cannot-be-recovered, message = TRUE
+   (x <- 1:4)
+   #' More text
+   y <- 2:5
+   x + y
+ }, show = FALSE)
Error in reprex_(r_file) : 
Cannot render this code.
Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Calls: reprex -> reprex_
Execution halted
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/ripley/R/packages/tests32/rexpokit.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/RGBM.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc     2.2Mb
    fonts   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 79-84 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘hyperdraw’ ‘hypergraph’ ‘rggobi’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help  10.6Mb
    libs   9.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘feather’
Running examples in ‘rio-Ex.R’ failed
The error most likely occurred in:

> ### Name: gather_attrs
> ### Title: Gather attributes from data.frame variables
> ### Aliases: gather_attrs
> 
> ### ** Examples
> 
> e <- import("http://www.stata-press.com/data/r13/auto.dta")
Error in df_parse_dta_file(spec, encoding) : 
  Failed to parse /tmp/RtmplHayrs/file248b14dd2378.dta: Invalid file, or file has unsupported features.
Calls: import ... convert_attributes -> read_dta -> df_parse_dta_file -> .Call
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    datasets   9.0Mb
installed size is 46.5Mb
  sub-directories of 1Mb or more:
    exe  46.5Mb
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: Alatasetal_A
> ### Title: Alatasetal_A KEEL Association Rules Algorithm
> ### Aliases: Alatasetal_A R6_Alatasetal_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/home/ripley/R/Lib32/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- Alatasetal_A(dat)
> 
> #Run algorithm
> algorithm$run()
Executing algorithm...
java -jar RunKeel.jar/tmp/RtmpdSayjs/experiment_2017-02-02_15-00-402656/results/KEELToPMML/TSTAlatasetal_A/result0s0file0.pmml
Error! Error in private$readOutputs(paste0(private$mainPath, "/results/KEELToPMML/TST", : Results were not stored. Execution error.
> 
> #Rules in format arules
> algorithm$rules
NULL
> 
> #Show a number of rules
> algorithm$showRules(2)
Error! Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘inspect’ for signature ‘"NULL"’
> 
> #Return a data.frame with all interest measures of set rules
> algorithm$getInterestMeasures()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘quality’ for signature ‘"NULL"’
Calls: <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    java   4.8Mb
File ‘RMC/libs/RMC.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rmetasim/libs/rmetasim.so’:
  Found ‘__1cDstdEcout_’, possibly from ‘std::cout’ (C++)
    Objects: ‘Democlass.o’, ‘Landscape.o’, ‘PackedIndividual.o’,
      ‘rmetasim.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RDRToolbox’
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R  10.1Mb
Package unavailable to check Rd xrefs: ‘StatDA’
Package suggested but not available for checking: ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rootWishart.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘geoR’ ‘RandomFields’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 44-45 (rplexos.Rmd) 
Error: processing vignette 'rplexos.Rmd' failed with diagnostics:
'folders' must be a vector of existing folders or the wildcard "*"
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Package required but not available: ‘wdman’

Package suggested but not available for checking: ‘Rcompression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.2Mb
Running examples in ‘rstanarm-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_model
> ### Title: Example model
> ### Aliases: example_model
> 
> ### ** Examples
> 
> example_model <- 
+   stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
+              data = lme4::cbpp, family = binomial,
+              # this next line is only to keep the example small in size!
+              chains = 2, cores = 1, seed = 12345, iter = 500)

SAMPLING FOR MODEL 'binomial' NOW (CHAIN 1).
Running ‘testthat.R’ [31s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Part of the rstanarm package for estimating model parameters
  > # Copyright (C) 2015 Trustees of Columbia University
  > # 
  > # This program is free software; you can redistribute it and/or
  > # modify it under the terms of the GNU General Public License
  > # as published by the Free Software Foundation; either version 3
  > # of the License, or (at your option) any later version.
  > # 
  > # This program is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > # 
  > # You should have received a copy of the GNU General Public License
  > # along with this program; if not, write to the Free Software
  > # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  > 
  > library(testthat)
  > library(rstanarm)
  Loading required package: Rcpp
  rstanarm (Version 2.14.1, packaged: 2017-01-16 18:47:11 UTC)
  - Do not expect the default priors to remain the same in future rstanarm versions.
  Thus, R scripts should specify priors explicitly, even if they are just the defaults.
  - For execution on a local, multicore CPU with excess RAM we recommend calling
  options(mc.cores = parallel::detectCores())
  > Sys.unsetenv("R_TESTS")
  > example(example_model)
  
  exmpl_> example_model <- 
  exmpl_+   stan_glmer(cbind(incidence, size - incidence) ~ size + period + (1|herd),
  exmpl_+              data = lme4::cbpp, family = binomial,
  exmpl_+              # this next line is only to keep the example small in size!
  exmpl_+              chains = 2, cores = 1, seed = 12345, iter = 500)
  
  SAMPLING FOR MODEL 'binomial' NOW (CHAIN 1).
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs        4.1Mb
    unitTests   1.0Mb
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (trie_usage.Rmd) 
Error: processing vignette 'trie_usage.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 116-126 (using_rucrdtw.Rmd) 
Error: processing vignette 'using_rucrdtw.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rwirelesscom.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running examples in ‘RxnSim-Ex.R’ failed
The error most likely occurred in:

> ### Name: RxnSim-package
> ### Title: Functions to compute chemical reaction and molecular similarity
> ### Aliases: RxnSim-package RxnSim rxnsim
> 
> ### ** Examples
> 
> ## Not run: Reaction similarity
> rs.compute('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C')
Error in .jcall("org/guha/rcdk/util/Misc", "Ljava/lang/Object;", "getProperty",  : 
  RcallMethod: cannot determine object class
Calls: rs.compute ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rzmq.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    sample_data   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Sabermetrics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 149-195 (schumaker.Rmd) 
Error: processing vignette 'schumaker.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Found the following executable files:
  vignettes/Indices_cache/html/Ceara-election_0d515408b54fd6997da9c38a8521d02a.rdb
  vignettes/SciencesPo_cache/html/Ceara-election_ecf5fc665d12287cb4f45d6dfb91d746.rdb
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Running examples in ‘SDraw-Ex.R’ failed
The error most likely occurred in:

> ### Name: grts.line
> ### Title: Draw a equi-probable GRTS sample from a linear (line) resource.
> ### Aliases: grts.line
> ### Keywords: design survey
> 
> ### ** Examples
> 
> 
> # Draw sample
> HI.sample <- grts.line(HI.coast,100,50)
Error in spsurvey::grts(design = Equaldsgn, DesignID = "Site", type.frame = sframe.type,  : 
  
A little-endian processor is required for the grts function.
Calls: grts.line -> grts.equi -> <Anonymous>
Execution halted
Running examples in ‘Segmentor3IsBack-Ex.R’ failed
The error most likely occurred in:

> ### Name: BestSegmentation
> ### Title: BestSegmentation
> ### Aliases: BestSegmentation
> ### Keywords: R-package PDPA Segmentation
> 
> ### ** Examples
> 
> require(Segmentor3IsBack);
> N=2000 
> x=rnbinom(3*N,size=1.3,prob=rep(c(0.7,0.2,0.01),each=N));
> res=Segmentor(data=x,model=3,Kmax=10, keep=TRUE);  
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: Segmentor -> Segmentor.default
Execution halted
Running examples in ‘semTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: auxiliary
> ### Title: Analyzing data with full-information maximum likelihood with
> ###   auxiliary variables
> ### Aliases: auxiliary cfa.auxiliary sem.auxiliary growth.auxiliary
> ###   lavaan.auxiliary
> 
> ### ** Examples
> 
> # Example of confirmatory factor analysis
> 
> HS.model <- ' visual  =~ x1 + x2 + x3
+               textual =~ x4 + x5 + x6
+               speed   =~ x7 + x8 + x9 '
> 			  
> dat <- data.frame(HolzingerSwineford1939, z=rnorm(nrow(HolzingerSwineford1939), 0, 1))
> 			  
> fit <- cfa(HS.model, data=dat, meanstructure=TRUE) 
> fitaux <- auxiliary(HS.model, aux="z", data=dat, fun="cfa") # Use lavaan script
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “lavModel” is not valid for slot ‘Model’ in an object of class “lavaanStar”; is(value, "Model") is not TRUE
Calls: auxiliary ... asMethod -> as<- -> asMethod -> slot<- -> checkSlotAssignment
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: tabix.read.table
> ### Title: Read tabix file, similar to running tabix in command line.
> ### Aliases: tabix.read.table
> 
> ### ** Examples
> 
> fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
> snp <- tabix.read.table(fileName, "1:196623337-196632470")
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
[ti_index_load] wrong magic number.
[ti_index_load] fail to load the index: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz.tbi
Cannot open specified tabix file: /home/ripley/R/Lib32/seqminer/vcf/all.anno.filtered.extract.vcf.gz
Error in strsplit(body, "\t") : non-character argument
Calls: tabix.read.table -> do.call -> strsplit
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    www   9.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    www   7.1Mb
Running examples in ‘sidier-Ex.R’ failed
The error most likely occurred in:

> ### Name: double.plot
> ### Title: Haplotype and population networks including mutations and
> ###   haplotype frequencies.
> ### Aliases: double.plot
> 
> ### ** Examples
> 
> cat(">Population1_sequence1",
+ "TTATAAAATCTA----TAGC",
+ ">Population1_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population1_sequence3",
+ "TTATAAAAATTA----TAGC",
+ ">Population1_sequence4",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence1",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population2_sequence2",
+ "TAAT----TCTA----TAAC",
+ ">Population2_sequence3",
+ "TTATAAAA--------TAGC",
+ ">Population2_sequence4",
+ "TTAT----TCGAGGGGTAGC",
+ ">Population3_sequence1",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence2",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence3",
+ "TTAT----TCGA----TAGC",
+ ">Population3_sequence4",
+ "TTAT----TCGA----TAGC",
+      file = "ex2.fas", sep = "\n")
> library(ape)
> double.plot(align=read.dna(file="ex2.fas",format="fasta"))
Warning in pie.network(align = align, indel.method = indel.method, substitution.model = substitution.model,  :
  Population names defined by algorithm between character 1 and the first symbol '_' in sequences name.
Error in rep(colnames(pop2)[which(pop2 != 0)], pop2[which(pop2 != 0)]) : 
  invalid 'times' argument
Calls: double.plot -> pie.network -> pop.dist
Execution halted
Running examples in ‘simba-Ex.R’ failed
The error most likely occurred in:

> ### Name: hexgrid
> ### Title: Produces the nodes of an equidistant grid.
> ### Aliases: hexgrid
> ### Keywords: methods datagen
> 
> ### ** Examples
> 
> ## produces a grid with r=400:    
> test.grd <- hexgrid(456000, 7356700, r=400)
> ## for plotting the following is recommended as it preserves 
> ## real positions:
> library(geoR)
Error in library(geoR) : there is no package called ‘geoR’
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Loading required package: fingerprint

Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
 chunk 2 
Error in .jcall("org/guha/rcdk/util/Misc", "[Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  RcallMethod: cannot determine object class
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <45> run based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running ‘testthat.R’ [112s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  1. Failure: dkbinom() sums to 1 (@test_dkbinom.R#61) ---------------------------
  `x1` not equal to 1.
  1/1 mismatches
  [1] 1 - 1 == 1.11e-15
  
  
  testthat results ================================================================
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: dkbinom() sums to 1 (@test_dkbinom.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/SnakeCharmR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 170-174 (pairwiseSNHT.Rnw) 
Error: processing vignette 'pairwiseSNHT.Rnw' failed with diagnostics:
invalid 'times' argument
Execution halted
Running examples in ‘soil.spec-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.opus-method
> ### Title: Reads binary OPUS files containing spectroscopy
> ### Aliases: read.opus read.opus,character-method read.opus,list-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## Original binary Opus files:
> pth = system.file(package = "soil.spec")
> lst <- as.list(list.files(path=pth, pattern="*.0$", full.names=TRUE))
> file.info(lst[[1]])
                                                 size isdir mode
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 167196 FALSE  644
                                                             mtime
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 03:49:58
                                                             ctime
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 03:51:26
                                                             atime uid gid
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 2016-12-25 23:46:24 501   1
                                                uname grname
/home/ripley/R/Lib32/soil.spec/icr_087266_B2.0 ripley  other
> xx <- read.opus(lst)
Error in seq.default(lxv, fxv, (fxv - lxv)/(NPT1 - 1)) : 
  wrong sign in 'by' argument
Calls: read.opus ... read.opus -> lapply -> FUN -> rev -> seq -> seq.default
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.0Mb
Package required but not available: ‘RandomFields’

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot33637396a8d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot33637396a8d.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘sparsesvd-Ex.R’ failed
The error most likely occurred in:

> ### Name: sparsesvd
> ### Title: Singular Value Decomposition of a Sparse Matrix.
> ### Aliases: sparsesvd
> 
> ### ** Examples
> 
> M <- rbind(
+   c(20, 10, 15,  0,  2),
+   c(10,  5,  8,  1,  0),
+   c( 0,  1,  2,  6,  3),
+   c( 1,  0,  0, 10,  5))
> M <- Matrix::Matrix(M, sparse=TRUE)
> print(M)
4 x 5 sparse Matrix of class "dgCMatrix"
                  
[1,] 20 10 15  . 2
[2,] 10  5  8  1 .
[3,]  .  1  2  6 3
[4,]  1  .  . 10 5
> 
> res <- sparsesvd(M, rank=2L) # compute first 2 singular components

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
 2: sparsesvd(M, rank = 2L)
An irrecoverable exception occurred. R is aborting now ...
Running ‘formats.R’ [15s/20s]
Running the tests in ‘tests/formats.R’ failed.
Complete output:
  > ## any sparse matrix format that inherits from dMatrix should work
  > library(sparsesvd)
  > library(Matrix)
  > 
  > M <- rbind(
  +   c(20, 10, 15,  0,  2),
  +   c(10,  5,  8,  1,  0),
  +   c( 0,  1,  2,  6,  3),
  +   c( 1,  0,  0, 10,  5))
  > 
  > res1 <- sparsesvd(as(M, "dgCMatrix")) # standard format (column-compressed)
  
   *** caught segfault ***
  address 4, cause 'memory not mapped'
  
  Traceback:
   1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
   2: sparsesvd(as(M, "dgCMatrix"))
  An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘SpatialPack-Ex.R’ failed
The error most likely occurred in:

> ### Name: codisp
> ### Title: Codispersion Coefficient
> ### Aliases: codisp
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> ## This example uses the camg data set, available in the geoR Package
> ## (Ribeiro and Diggle, 2001).
> 
> ## required to loading the camg data set from geoR package 
> library(geoR)
Error in library(geoR) : there is no package called ‘geoR’
Execution halted
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    data   3.5Mb
    doc    4.8Mb
    help   5.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.7Mb
    etc    2.0Mb
sh: -version:  not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: -version:  not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: -version:  not found
sh: -version:  not found
sh: -version:  not found
sh: -version:  not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/sppmix.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/sprint.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.


Error: processing vignette 'Area_Design.Rnw' failed with diagnostics:
 chunk 1 (label = processor) 
Error in eval(expr, envir, enclos) : 
A little-endian processor is required for this vignette.
Execution halted
Package which this enhances but not available for checking: ‘RMySQL’
Running examples in ‘StAMPP-Ex.R’ failed
The error most likely occurred in:

> ### Name: stamppFst
> ### Title: Fst Computation
> ### Aliases: stamppFst
> 
> ### ** Examples
> 
> # import genotype data and convert to allele frequecies 
> data(potato.mini, package="StAMPP")
> potato.freq <- stamppConvert(potato.mini, "r")
> 
> # Calculate pairwise Fst values between each population
> potato.fst <- stamppFst(potato.freq, 100, 95, 1)

 *** caught segfault ***
address 8, cause 'memory not mapped'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__f90_stop’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 480-491 (drivers.Rmd) 
Error: processing vignette 'drivers.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Packages suggested but not available for checking: ‘tmap’ ‘tmaptools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 108-113 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
there is no package called 'tmap'
Execution halted
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/subprocess.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
File ‘survrec/libs/survrec.so’:
  Found ‘rand_’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 4000, cause 'memory not mapped'

Traceback:
 1: .Call("ztrlan_eigen", X, neig, opts, lambda, U)
 2: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/TauStar.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 65-72 (tibble.Rmd) 
Error: processing vignette 'tibble.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 111-116 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
Package suggested but not available for checking: ‘rmapshaper’
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  75501764 is too close to the limit
Execution halted
Running ‘simple.R’
Running the tests in ‘tests/simple.R’ failed.
Complete output:
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Running examples in ‘TPmsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: image.TPCmsm
> ### Title: image method for a TPCmsm object
> ### Aliases: image.TPCmsm
> ### Keywords: hplot methods multivariate survival
> 
> ### ** Examples
> 
> # Set the number of threads
> nth <- setThreadsTP(2)
> 
> # Create survTP object
> data(heartTP)
> heartTP_obj <- with( heartTP, survTP(time1, event1, Stime, event, age=age) )
> 
> # Compute LIN conditional transition probabilities with confidence band
> TPCmsm_obj <- transLIN(heartTP_obj, s=57, t=310, x=0, conf=TRUE, n.boot=100,
+ method.boot="basic")

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call(Rf_BtoTPCmsm, lst, UT, UX, s, t, x, statenames, as.integer(nboot),     conflevel, methodboot, PACKAGE = "TPmsm")
 2: BtoTPCmsm(lst, UT, UX, s, t, xi, state.names, n.boot, conf.level,     method.boot)
 3: TransBoot.TPC(object, s, t, state.names, n.boot, conf.level,     method.boot, xi, ...)
 4: TransBoot(object, s, t, state.names, n.boot, conf.level, method.boot,     xi, ...)
 5: TransMethod.TPC(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     ...)
 6: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, xi = x, bw = bw, window = window, methodweights = method.weights,     ...)
 7: transLIN(heartTP_obj, s = 57, t = 310, x = 0, conf = TRUE, n.boot = 100,     method.boot = "basic")
An irrecoverable exception occurred. R is aborting now ...
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/treeHFM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
negative edges length changed to 0!
Quitting from lines 115-133 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘TSMySQL’
Package suggested but not available for checking: ‘gcmr’
Error in re-building vignettes:
  ...
Loading required package: splines
Loading required package: gamlss.data
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.0-1  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

GAMLSS-RS iteration 1: Global Deviance = 803.7 
GAMLSS-RS iteration 2: Global Deviance = 803.7 
GAMLSS-RS iteration 3: Global Deviance = 803.7 
GAMLSS-RS iteration 1: Global Deviance = 805.6 
GAMLSS-RS iteration 2: Global Deviance = 805.6 
GAMLSS-RS iteration 3: Global Deviance = 805.6 
Loading required package: stats4
Loading required package: tseries
Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: TTR

Attaching package: 'TTR'

The following object is masked from 'package:gamlss.dist':

    DPO

Version 0.4-0 included new data defaults. See ?getSymbols.
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  iterations terminated because half-step sizes are very small
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step

Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
 chunk 40 (label = gcmr-package) 
Error in library("gcmr") : there is no package called 'gcmr'
Execution halted
Packages suggested but not available for checking: ‘TSMySQL’ ‘RMySQL’
Packages unavailable to check Rd xrefs: ‘TSMySQL’, ‘RMySQL’
Package unavailable to check Rd xrefs: ‘TSMySQL’
Installation failed.
See ‘/home/ripley/R/packages/tests32/umx.Rcheck/00install.out’ for details.
Packages required but not available: ‘RandomFields’ ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
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installed size is 29.8Mb
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    data  29.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
  ‘microbenchmark’ ‘RMySQL’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'purrr'

The following objects are masked from 'package:dplyr':

    contains, order_by

Quitting from lines 280-302 (valr.Rmd) 
Error: processing vignette 'valr.Rmd' failed with diagnostics:
there is no package called 'microbenchmark'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.3Mb
    help   2.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc           3.8Mb
    htmlwidgets   3.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 112: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
Running examples in ‘walkr-Ex.R’ failed
The error most likely occurred in:

> ### Name: complete_solution
> ### Title: Complete Solution
> ### Aliases: complete_solution
> 
> ### ** Examples
> 
> A <- matrix(1, ncol = 3)
> b <- 0.5
> complete_solution(A, b)

 *** caught segfault ***
address 4c00000, cause 'memory not mapped'
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package required but not available: ‘subprocess’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘iptools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 96-98 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘webuse-Ex.R’ failed
The error most likely occurred in:

> ### Name: webuse
> ### Title: webuse
> ### Aliases: webuse webuselist webuse-package
> 
> ### ** Examples
> 
> webuse("auto")
Error in df_parse_dta_raw(spec, encoding) : 
  Failed to parse file: Invalid file, or file has unsupported features.
Calls: webuse -> read_dta -> df_parse_dta_raw -> .Call
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/Wmisc.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 597-620 (wrswoR.Rmd) 
Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:
package 'microbenchmark' not found
Execution halted
installed size is 17.6Mb
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    java  17.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   4.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Found the following significant warnings:
  "NodeGC.c", line 385: warning: improper pointer/integer combination: op "=="
See ‘/home/ripley/R/packages/tests32/XML.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found

Error in .Object$initialize(...) : 
  Unable to start Julia connection on port 1251: all connections are in use
Calls: juliaSend ... <Anonymous> -> new -> initialize -> initialize -> <Anonymous>
Execution halted
Running examples in ‘XRPython-Ex.R’ failed
The error most likely occurred in:

> ### Name: RPython
> ### Title: An Evaluator for the Python Interface.
> ### Aliases: RPython
> 
> ### ** Examples
> 
> ev <- RPython()
> xx <- ev$Eval("[1, %s, 5]", pi)
Error in python.exec(expr) : 'dict' object has no attribute 'has_key'
Calls: <Anonymous> -> ServerEval -> python.exec
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/xyz.Rcheck/00install.out’ for details.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 31-44 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
there is no package called 'kebabs'
Execution halted
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 117.6Mb
  sub-directories of 1Mb or more:
    include  117.6Mb
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), lambda = lambda, 
+                          numthreads = 1, memory_size = 512, seed = 1, 
+                          use_ram = TRUE)

 *** caught segfault ***
address ffffffff, cause 'memory not mapped'

Traceback:
 1: .Call("BigQuic_BigQuicHelper", PACKAGE = "BigQuic", argvPasser)
 2: BigQuicHelper(argvPasser = c("-l", lambda[i], "-n", numthreads,     "-t", maxit, "-e", epsilon, "-k", k, "-m", memory_size, "-q",     verbose, "-r", isnormalized, inputFileName, outputFileName))
 3: BigQuic(inputFileName = paste(path.package("BigQuic"), "/extdata/testInput",     sep = ""), lambda = lambda, numthreads = 1, memory_size = 512,     seed = 1, use_ram = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ClusterR)
  Loading required package: gtools
  > 
  > test_check("ClusterR")
  Error: C stack usage  202014964 is too close to the limit
  testthat results ================================================================
  OK: 92 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.4Mb
Error in re-building vignettes:
  ...
Observations with missing time information found - removing 1 rows
Discrete time points created:  4
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  84370.0240592561

 OpenMx status code 10 not in list of acceptable status codes, 0
 OpenMx status code 10 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  30870.6383143812

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 3 of at maximum 16 tries

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 4 of at maximum 16 tries

 Fit attempt worse than current best:  105471.397837712 vs 30870.6383143812

Begin fit attempt 5 of at maximum 16 tries

 Fit attempt generated errors

Begin fit attempt 6 of at maximum 16 tries

 Fit attempt worse than current best:  88529.0428589223 vs 30870.6383143812

Begin fit attempt 7 of at maximum 16 tries

 *** caught segfault ***
address 0, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot6a471d275b4e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6a471d275b4e.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot6b2f6e75544e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6b2f6e75544e.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Running ‘has-devel.R’
  Running ‘test-that.R’ [74s/104s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) -
  invalid 'times' argument
  1: expect_true(!is.null(find_topic("foofoo"))) at testthat/test-help.r:45
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: find_topic("foofoo")
  7: find_pkg_topic(path, topic)
  8: topic_index(pkg)
  9: build_topic_index(pkg)
  10: invert(lapply(rds, aliases))
  
  Updating collate directive in  /tmp/RtmpGCaOib/testCollateOrder/DESCRIPTION 
  
  testthat results ================================================================
  OK: 377 SKIPPED: 10 FAILED: 1
  1. Error: help and ? find files for devtools-loaded packages (@test-help.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__f90_esuw’, possibly from ‘write’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.1Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/RtmpIJaG10"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  1. Error: glmnet (@test-methods.r#23) ------------------------------------------
  dim(X) must have a positive length
  1: fit_glmnet(iris[-5], iris$Species) at testthat/test-methods.r:23
  2: glmnet::cv.glmnet(x, y, family = family, nfolds = nfolds, foldid = foldid, alpha = alpha, 
         lambda = lambda, ...)
  3: apply(nz, 1, median)
  4: stop("dim(X) must have a positive length")
  
  testthat results ================================================================
  OK: 182 SKIPPED: 0 FAILED: 1
  1. Error: glmnet (@test-methods.r#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynIRT
> ### Title: Dynamic IRT estimation via Variational Inference
> ### Aliases: dynIRT
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> ### Replication of Martin-Quinn Judicial Ideology Scores
> ### Based on July 23, 2014 (2014 Release 01) release of the Supreme Court Database
> ### Start values and priors based on replication code provided by Kevin Quinn
> 
> data(mq_data)
> 
> ## Estimate dynamic variational model using dynIRT()
> lout <- dynIRT(.data = mq_data$data.mq,
+                     .starts = mq_data$cur.mq,
+                     .priors = mq_data$priors.mq,
+                     .control = {list(
+                     threads = 1,
+                     verbose = TRUE,
+                     thresh = 1e-6,
+ 		    maxit=500
+                     )})

==================== 
dynIRT: Dynamic IRT via Variational Inference


error: Mat::init(): size is fixed and hence cannot be changed
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::init(): size is fixed and hence cannot be changed
Running examples in ‘fBasics-Ex.R’ failed
The error most likely occurred in:

> ### Name: akimaInterp
> ### Title: Bivariate Spline Interpolation
> ### Aliases: akimaInterp akimaInterpp
> ### Keywords: programming
> 
> ### ** Examples
>  
> ## akimaInterp -
>    # Akima Interpolation:    
>    if (require(akima)) {
+      set.seed(1953)
+      x = runif(999) - 0.5
+      y = runif(999) - 0.5
+      z = cos(2*pi*(x^2+y^2))
+      ans = akimaInterp(x, y, z, gridPoints = 41, extrap = FALSE)
+      persp(ans, theta = -40, phi = 30, col = "steelblue",
+         xlab = "x", ylab = "y", zlab = "z")
+      contour(ans)
+    }
Loading required package: akima
Warning in akima::interp.new(x, y, z, xo, yo, linear = FALSE, ncp = NULL,  :
  interp.new() is deprecated, use interp()
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in persp.default(ans, theta = -40, phi = 30, col = "steelblue",  : 
  invalid 'z' limits
Calls: persp -> persp.default
Execution halted
Running examples in ‘gamsel-Ex.R’ failed
The error most likely occurred in:

> ### Name: gamsel
> ### Title: Fit Regularization Path for Gaussian or Binomial Generalized
> ###   Additive Model
> ### Aliases: gamsel
> ### Keywords: regression smooth nonparametric
> 
> ### ** Examples
> 
> data=gendata(n=500,p=12,k.lin=3,k.nonlin=3,deg=8,sigma=0.5)
> attach(data)
> bases=pseudo.bases(X,degree=10,df=6)
> # Gaussian gam
> gamsel.out=gamsel(X,y,bases=bases)
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)
> gamsel.cv=cv.gamsel(X,y,bases=bases)
> par(mfrow=c(1,1))
> plot(gamsel.cv)
> par(mfrow=c(3,4))
> plot(gamsel.out,newx=X,index=20)
> # Binomial model
> gamsel.out=gamsel(X,yb,family="binomial")
> par(mfrow=c(1,2),mar=c(5,4,3,1))
> summary(gamsel.out)

 *** caught segfault ***
address 663c83f9, cause 'memory not mapped'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
    vign       1.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Warning: Ignoring unknown aesthetics: data_id, tooltip
Warning: Ignoring unknown aesthetics: data_id, tooltip
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot37304414aa3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot37304414aa3.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshota2824e6747b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota2824e6747b.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [24s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  1. Failure: inherits timezone from data (@test-scale-date.R#18) ----------------
  sc$timezone not equal to NULL.
  Types not compatible: character vs NULL
  
  
  testthat results ================================================================
  OK: 778 SKIPPED: 0 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [17s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gsrc)
  > 
  > test_check("gsrc")
  1. Failure: cnv returns correct output (@test_cnv.R#18) ------------------------
  dim(dat$cnv) not equal to c(12, 100).
  1/2 mismatches
  [1] 10 - 12 == -2
  
  
  2. Failure: segm returns correct output (@test_segm.R#17) ----------------------
  dim(dat$cna) not equal to c(104, 6).
  1/2 mismatches
  [1] 103 - 104 == -1
  
  
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: cnv returns correct output (@test_cnv.R#18) 
  2. Failure: segm returns correct output (@test_segm.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S2352340915000062/1-s2.0-S2352340915000062-mmc6.xlsx/311593/html/S2352340915000062/5528a88e468e01866744f28fc42139c6/mmc6.xlsx'
Quitting from lines 29-43 (synteny.Rmd) 
Error: processing vignette 'synteny.Rmd' failed with diagnostics:
cannot open URL 'http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S2352340915000062/1-s2.0-S2352340915000062-mmc6.xlsx/311593/html/S2352340915000062/5528a88e468e01866744f28fc42139c6/mmc6.xlsx'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /usr/local/share/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-4 
trying URL 'ftp://ftp.bafg.de/pub/REFERATE/GRDC/ltdata/europe.zip'
ftp data connection made, file length 4812722 bytes
==================================================
downloaded 4.6 MB

Station has monthly records
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Quitting from lines 252-254 (hddtools_vignette.Rmd) 
Error: processing vignette 'hddtools_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [38s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(healthcareai)
  Type ?healthcareai to read the docs.
  > 
  > test_check("healthcareai")
  [1] 0.9402367
  1. Failure: AUC_rf is the same each time the test is run (@test-develop-supervised-model.R#143) 
  as.numeric(rf$getAUROC()) - 0.9374753 < 1e-06 isn't true.
  
  
  testthat results ================================================================
  OK: 104 SKIPPED: 7 FAILED: 1
  1. Failure: AUC_rf is the same each time the test is run (@test-develop-supervised-model.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc          13.8Mb
    htmlwidgets   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> TDh(D,h)
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address a61a78f8, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # NOTE: This will not test an uninstalled package.
  > library(testthat)
  > test_check('ifaTools')
  Loading required package: ifaTools
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: reshape2
  Loading required package: rpf
  Loading required package: parallel
  Loading required package: OpenMx
  Loading required package: digest
  Loading required package: MASS
  Loading required package: Matrix
  Loading required package: Rcpp
  To take full advantage of multiple cores, use:
    mxOption(NULL, 'Number of Threads', parallel::detectCores())
  
  Attaching package: 'OpenMx'
  
  The following objects are masked from 'package:Matrix':
  
      %&%, expm
  
  1. Failure: univariatePrior (@test-prior.R#28) ---------------------------------
  m2$output$gradient not equal to m3$output$gradient.
  1/1 mismatches
  [1] 0.5 - 0.5 == -9.92e-05
  
  
  2. Failure: univariatePrior (@test-prior.R#28) ---------------------------------
  m2$output$hessian not equal to m3$output$hessian.
  1/1 mismatches
  [1] 2.1 - 4.08 == -1.98
  
  
  testthat results ================================================================
  OK: 7 SKIPPED: 0 FAILED: 2
  1. Failure: univariatePrior (@test-prior.R#28) 
  2. Failure: univariatePrior (@test-prior.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   7.1Mb
installed size is 209.2Mb
  sub-directories of 1Mb or more:
    extdata  208.5Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Running ‘testthat.R’ [21s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) ---------------
  invalid 'tz' value
  1: expect_equal(interval(t1, t2), new("Interval", 18316800, start = as.POSIXct("2007-01-01", 
         tz = "UTC"), tzone = "UTC")) at testthat/test-intervals.R:86
  2: compare(object, expected, ...)
  3: interval(t1, t2)
  4: as.POSIXct(start, tz = tzone)
  5: as.POSIXct.POSIXlt(start, tz = tzone)
  
  testthat results ================================================================
  OK: 2152 SKIPPED: 0 FAILED: 1
  1. Error: interval handles POSIXlt inputs (@test-intervals.R#86) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lav2lvnet
> ### Title: Convert lavaan model to lvnet model matrices
> ### Aliases: lav2lvnet
> 
> ### ** Examples
> 
> library("lavaan")
This is lavaan 0.5-23.1097
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

The following object is masked from ‘package:OpenMx’:

    vech

> 
> # Load dataset:
> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # lavaan model
> HS.model <- '
+ visual  =~ x1 + x2 + x3
+ textual =~ x4 + x5 + x6
+ speed   =~ x7 + x8 + x9 '
> 
> # fit via lavaan:
> lavFit <- cfa(HS.model, HolzingerSwineford1939[7:15],std.lv=TRUE)
> 
> # Fit via lvnet:
> mod <- lav2lvnet(HS.model, HolzingerSwineford1939[7:15])
> lvnetFit <- lvnet(Data, lambda = mod$lambda, psi = mod$psi)
Error: The job for model 'model' exited abnormally with the error message: Non-conformable matrices [(9 x 3) and (9 x 9)] in Matrix Multiply.
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot3c5e36605ae6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3c5e36605ae6.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot3add54f955b2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3add54f955b2.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'matching.tex' failed.
LaTeX errors:
! LaTeX Error: File `hvfloat.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.58 \usepackage
                {subcaption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Running examples in ‘mcPAFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPAFit
> ### Title: estimates the Preferential Attachment function in a temporal
> ###   complex network without temporal information.
> ### Aliases: mcPAFit
> ### Keywords: package Preferential Attachment function Markov chain Monte
> ###   Carlo Gibbs sampling missing timeline
> 
> ### ** Examples
> 
> library(mcPAFit)
> N      <- 1000 #number of nodes in the network 
> M      <- 500  #number of needed sample
> lag   <-  1
> start <-  100
> 
> data   <- create_sim_data(N = N, alpha = 1)
> write.table(data$random[,1:2], row.names = FALSE,
+             col.names = FALSE, file = "input.txt")
> system.time(mcPAFit(file_name = "input.txt",burn_in = 0, s = 5, skip = 1, 
+             needed_sample = M, G = 20,only_active_node = 1, random = 0))
terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 7) >= this->size() (which is 0)
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )

 *** caught segfault ***
address fc0ee170, cause 'memory not mapped'

Traceback:
 1: .Call(backend, constraints, matrices, parameters, algebras, expectations,     computes, data, intervalList, communication, options, defVars,     silent || !interactive(), PACKAGE = "OpenMx")
 2: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 3: mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...), error = function(e) e)
 8: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
 9: summary(meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE))))
An irrecoverable exception occurred. R is aborting now ...
installed size is 191.2Mb
  sub-directories of 1Mb or more:
    libs  190.9Mb
Error in re-building vignettes:
  ...
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 56-57 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
alpha adjustment required
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    include   3.2Mb
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  res1$solution not equal to `solution.opt`.
  2/2 mismatches (average diff: 0.00818)
  [1] 0.328 - 0.333 == -0.00572
  [2] 0.307 - 0.296 ==  0.01064
  
  
  testthat results ================================================================
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Failure: Test NLopt tutorial example with NLOPT_LN_COBYLA with gradient information. (@test-example.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘run-all.R’ [30s/33s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > #  Copyright 2013 Christian Sigg
  > #
  > #  This program is free software; you can redistribute it and/or modify
  > #  it under the terms of the GNU General Public License as published by
  > #  the Free Software Foundation; either version 2 of the License, or
  > #  (at your option) any later version.
  > #
  > #  This program is distributed in the hope that it will be useful,
  > #  but WITHOUT ANY WARRANTY; without even the implied warranty of
  > #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > #  GNU General Public License for more details.
  > #
  > #  A copy of the GNU General Public License is available at
  > #  http://www.r-project.org/Licenses/
  > 
  > library(testthat)
  > library(MASS)
  > library(glmnet)
  Loading required package: Matrix
  Loading required package: foreach
  Loaded glmnet 2.0-5
  
  > library(nscancor)
  > 
  > test_check("nscancor")
  1. Error: non-negative sparse CCA correlation equivalence (@test_acor.R#73) ----
  v collapsed to the zero vector, try relaxing the constraints
  1: equiv(10, 5) at testthat/test_acor.R:73
  2: nscancor(X, Y, xpredict = xpredict, ypredict = xpredict) at testthat/test_acor.R:70
  3: nscc_inner(X, Xp, Y, Yp, xpredict, ypredict, cc, iter_tol, iter_max, verbosity)
  4: stop("v collapsed to the zero vector, try relaxing the constraints")
  
  testthat results ================================================================
  OK: 83 SKIPPED: 0 FAILED: 1
  1. Error: non-negative sparse CCA correlation equivalence (@test_acor.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘oblique.tree-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.trim.sequence
> ### Title: Plot a Trim Sequence
> ### Aliases: plot.trim.sequence
> ### Keywords: tree
> 
> ### ** Examples
> 
> #grow an oblique tree
> data(Pima.tr, package="MASS")
> ob.tree <- oblique.tree(	type~.,
+ 				Pima.tr,
+ 				oblique.splits="only",
+ 				variable.selection="model.selection.aic")
> 
> #look at the tree
> plot(ob.tree);text(ob.tree)
> 
> #and its trim sequence
> plot(trim.oblique.tree(ob.tree))
Error in list.of.node.names.to.prune[[list.index]] : 
  subscript out of bounds
Calls: plot ... trim.once -> oblique.tree.prune.nodes -> %in% -> match
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data     1.0Mb
    libs     2.3Mb
    models   4.3Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxCI
> ### Title: Create mxCI Object
> ### Aliases: mxCI
> 
> ### ** Examples
> 
> 
> library(OpenMx)
> 
> # generate data
> covariance <- matrix(c(1.0, 0.5, 0.5, 1.0), 
+     nrow=2, 
+     dimnames=list(c("a", "b"), c("a", "b")))
>     
> data <- mxData(covariance, "cov", numObs=100)
> 
> # create an expected covariance matrix
> expect <- mxMatrix("Symm", 2, 2,
+     free=TRUE,
+     values=c(1, .5, 1),
+     labels=c("var1", "cov12", "var2"),
+     name="expectedCov")
> 
> # request 95 percent confidence intervals   
> ci <- mxCI(c("var1", "cov12", "var2"))
> 
> # specify the model
> model <- mxModel(model="Confidence Interval Example",
+     data, expect, ci,
+     mxExpectationNormal("expectedCov", dimnames=c("a", "b")),
+     mxFitFunctionML())
> 
> # run the model 
> results <- mxRun(model, intervals=TRUE)
Running Confidence Interval Example with 3 parameters

 *** caught segfault ***
address fc0ee170, cause 'memory not mapped'

Traceback:
 1: .Call(backend, constraints, matrices, parameters, algebras, expectations,     computes, data, intervalList, communication, options, defVars,     silent || !interactive(), PACKAGE = "OpenMx")
 2: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 3: mxRun(model, intervals = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [17s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) --------
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: all.equal.Workbook(wb_url, wb_file)
  7: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  8: lapply(X = X, FUN = FUN, ...)
  9: FUN(X[[i]], ...)
  10: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  11: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  12: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  13: attr.all.equal(target, current, ...)
  14: mode(current)
  
  testthat results ================================================================
  OK: 288 SKIPPED: 0 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Packages which this enhances but not available for checking:
  ‘org.Ag.eg.db’ ‘org.Pt.eg.db’ ‘org.Rn.eg.db’ ‘org.Ss.eg.db’
  ‘org.Bt.eg.db’ ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’
  ‘org.Dr.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mmu.eg.db’
  ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    include   4.1Mb
Running examples in ‘RcppBlaze-Ex.R’ failed
The error most likely occurred in:

> ### Name: fastLmPure
> ### Title: linear model fitting function based on RcppBlaze
> ### Aliases: fastLmPure
> 
> ### ** Examples
> 
> # according to fastLm example in RcppArmadillo
> data(trees, package="datasets")
> flm <- fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)

 *** caught segfault ***
address fcb4ca82, cause 'memory not mapped'

Traceback:
 1: .Call("RcppBlaze_fastLmPure", PACKAGE = "RcppBlaze", X, y, type)
 2: fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)
An irrecoverable exception occurred. R is aborting now ...
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    include   3.7Mb
    lib       5.1Mb
    libs      1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot3f52a9445a4.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3f52a9445a4.png': No such file or directory
Quitting from lines 21-25 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help  10.6Mb
    libs   7.8Mb
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: Alatasetal_A
> ### Title: Alatasetal_A KEEL Association Rules Algorithm
> ### Aliases: Alatasetal_A R6_Alatasetal_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/home/ripley/R/Lib32/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- Alatasetal_A(dat)
> 
> #Run algorithm
> algorithm$run()
Executing algorithm...
java -jar RunKeel.jar/tmp/RtmpMXaiMj/experiment_2017-02-25_17-40-582656/results/KEELToPMML/TSTAlatasetal_A/result0s0file0.pmml
Error! Error in private$readOutputs(paste0(private$mainPath, "/results/KEELToPMML/TST", : Results were not stored. Execution error.
> 
> #Rules in format arules
> algorithm$rules
NULL
> 
> #Show a number of rules
> algorithm$showRules(2)
Error! Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘inspect’ for signature ‘"NULL"’
> 
> #Return a data.frame with all interest measures of set rules
> algorithm$getInterestMeasures()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘quality’ for signature ‘"NULL"’
Calls: <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rsomoclu.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs        4.3Mb
    unitTests   1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
> 
> ### ** Examples
> 
> param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+               geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
> param <- makeAnnotationParameter(param)
> print(param)
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"

$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"

$geneFileFormat
[1] "refFlat"

$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"

$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

> annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
 2: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <32> run based on previous optim s ...
Running examples in ‘SMCP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SMCP
> ### Title: Smoothed minimax concave penalization (SMCP) method for
> ###   genome-wide association studies.
> ### Aliases: SMCP sp
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> x=matrix(rnorm(100*20),100,20)
> y=rnorm(100)
> fit=SMCP(x,y,0.3,0.3,3)
> #solution path for this data
> s.p=sp(x,y,0.3,10,0.05,3)
Error in SMCP(x, y, alpha, delta * i, gamma) : 
  NA/NaN/Inf in foreign function call (arg 6)
Calls: sp -> SMCP -> .C
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot63837a6a7b96.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot63837a6a7b96.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘formats.R’ [3s/11s]
Running the tests in ‘tests/formats.R’ failed.
Complete output:
  > ## any sparse matrix format that inherits from dMatrix should work
  > library(sparsesvd)
  > library(Matrix)
  > 
  > M <- rbind(
  +   c(20, 10, 15,  0,  2),
  +   c(10,  5,  8,  1,  0),
  +   c( 0,  1,  2,  6,  3),
  +   c( 1,  0,  0, 10,  5))
  > 
  > res1 <- sparsesvd(as(M, "dgCMatrix")) # standard format (column-compressed)
  
   *** caught segfault ***
  address 4, cause 'memory not mapped'
  
  Traceback:
   1: .Call(svdLAS2_, dim(M), M@i, M@p, M@x, as.integer(rank), as.double(tol *     c(-1, 1)), as.double(kappa))
   2: sparsesvd(as(M, "dgCMatrix"))
  An irrecoverable exception occurred. R is aborting now ...
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    data   3.5Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.0Mb
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call("ztrlan_eigen", X, neig, opts, lambda, U)
 2: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  184836240 is too close to the limit
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.7Mb
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: confint.MxModel
> ### Title: Get confidence intervals from an MxModel
> ### Aliases: confint.MxModel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> latents = c("G")
> manifests = names(demoOneFactor)
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
Running One Factor with 10 parameters
Warning: In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)
> m2 = confint(m1) # default: CIs added, but user prompted to set run = TRUE
Adding CIs for all free parameters
Some CIs have been requested, but have not yet been run. Add 'run = TRUE' to your confint() call to run them.
To store the model run capture it from confint like this:
m1 = confint(m1, run = TRUE)
> m2 = confint(m2, run = TRUE) # CIs run and reported
10 CIs found
Running One Factor with 10 parameters

 *** caught segfault ***
address fc0ee170, cause 'memory not mapped'

Traceback:
 1: .Call(backend, constraints, matrices, parameters, algebras, expectations,     computes, data, intervalList, communication, options, defVars,     silent || !interactive(), PACKAGE = "OpenMx")
 2: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 3: mxRun(object, intervals = TRUE)
 4: confint.MxModel(m2, run = TRUE)
 5: confint(m2, run = TRUE)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found

Error in .Object$initialize(...) : 
  Unable to start Julia connection on port 1912: all connections are in use
Calls: juliaSend ... <Anonymous> -> new -> initialize -> initialize -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 75-82 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("dataone")
  Loading required package: dataone
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  result[[1]]$abstract does not match "chlorophyll".
  Actual value: "Two YSI water quality sondes and loggers were installed onto a navigation light pole in Kentucky Lake KY, one at a depth of one meter below the lake surface, the other at one meter above the lake bottom in February 2005.  Water Temperature, pH, dissolved oxygen, conductivity, oxidation reduction potential, and turbidity data are collected from each sonde every 15 minutes.  Chlorophyll a data are collected from the one meter depth.  Lake elevations are estimated from depth data collected from the sonde anchored near the lake bottom."
  
  
  testthat results ================================================================
  OK: 197 SKIPPED: 31 FAILED: 1
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  No models could be fitted.
  1: expect_equal(summary(ds(egdata, 4, key = "hn", order = 5))$ddf$name.message, "half-normal key function with cosine(2,3,4,5) adjustments") at testthat/test_ds.R:171
  2: compare(object, expected, ...)
  3: summary(ds(egdata, 4, key = "hn", order = 5))
  4: ds(egdata, 4, key = "hn", order = 5)
  5: stop("No models could be fitted.")
  
  testthat results ================================================================
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Error: adjustments expand correctly (@test_ds.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DNAprofiles.Rcheck/00install.out’ for details.
Running examples in ‘EcoHydRology-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Cross validating the tbats model
  Fitting the auto.arima model
  Fitting the nnetar model
  Fitting the stlm model
  Fitting the tbats model
  Fitting the ets model
  Fitting the thetam model
  testthat results ================================================================
  OK: 110 SKIPPED: 0 FAILED: 1
  1. Failure: Testing is.hybridModel(), fitted.hybridModel(), residuals.hybridModel(), and accuracy.hybridModel() (@test-hybridModel.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
calcDistances.Splines: no visible global function definition for
  ‘smooth.spline’
calcDistances.Splines: no visible global function definition for
  ‘predict’
eQTL: no visible global function definition for ‘as’
eqtlLM: no visible global function definition for ‘lm’
genotypePlot: no visible global function definition for ‘boxplot’
genotypePlot: no visible global function definition for ‘axis’
plot.eqtl: no visible global function definition for ‘par’
plot.mdr: no visible global function definition for ‘density’
plotGeneLocation: no visible global function definition for ‘rect’
plotGeneLocation: no visible global function definition for ‘text’
plotGeneLocation: no visible global function definition for ‘axis’
plotGeneLocation: no visible global function definition for ‘lines’
plotIt: no visible global function definition for ‘axis’
plotIt: no visible global function definition for ‘lines’
plotIt: no visible global function definition for ‘par’
plotIt: no visible global function definition for ‘points’
plotSingle.eqtl: no visible global function definition for ‘pdf’
plotSingle.eqtl: no visible global function definition for ‘dev.off’
visTrans: no visible global function definition for ‘rainbow’
visTrans: no visible global function definition for ‘layout’
visTrans: no visible global function definition for ‘par’
Undefined global functions or variables:
  as axis boxplot density dev.off layout lines lm par pdf points
  predict rainbow rect smooth.spline text
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "axis", "boxplot", "layout", "lines", "par",
             "points", "rect", "text")
  importFrom("methods", "as")
  importFrom("stats", "density", "lm", "predict", "smooth.spline")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
* installing *source* package ‘brassicaData’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (brassicaData)
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
pandoc: unable to decommit memory: Invalid argument
trying URL ‘http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S2352340915000062/1-s2.0-S2352340915000062-mmc6.xlsx/311593/html/S2352340915000062/5528a88e468e01866744f28fc42139c6/mmc6.xlsx’
Quitting from lines 29-43 (synteny.Rmd) 
Error: processing vignette ‘synteny.Rmd’ failed with diagnostics:
cannot open URL ‘http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S2352340915000062/1-s2.0-S2352340915000062-mmc6.xlsx/311593/html/S2352340915000062/5528a88e468e01866744f28fc42139c6/mmc6.xlsx’
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 50 SKIPPED: 0 FAILED: 8
  1. Error: gutenberg_get_mirror works (@test-download.R#13) 
  2. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#22) 
  3. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#23) 
  4. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#31) 
  5. Failure: Can download Charles Dickens' Christmas Carol and Jane Austen's Persuasion (@test-download.R#32) 
  6. Failure: Can download books from a data frame with gutenberg_id column (@test-download.R#43) 
  7. Failure: We can download a file that only has a -8 version (@test-download.R#50) 
  8. Failure: read_zip_url can download and read a zip file (@test-utils.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
   # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 63-86 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
Timeout was reached
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/largeVis.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: message(sprintf("Page %s of %s Returned. Response contains %s of %s %s. ", x$meta$current_page, 
         x$meta$total_pages, x$meta$per_page, x$meta$total_entries, ngettext(x$meta$total_entries, 
             "notice", "notices")))
  3: sprintf("Page %s of %s Returned. Response contains %s of %s %s. ", x$meta$current_page, 
         x$meta$total_pages, x$meta$per_page, x$meta$total_entries, ngettext(x$meta$total_entries, 
             "notice", "notices"))
  
  testthat results ================================================================
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: Search Works (@tests.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
pandoc: unable to decommit memory: Invalid argument
Warning: Ignoring unknown aesthetics: height
simpleWarning in download.file(url, tf, mode = "wb", quiet = TRUE): downloaded length 0 != reported length 2153760


Quitting from lines 111-115 (RFinfer-examples.Rmd) 
Error: processing vignette ‘RFinfer-examples.Rmd’ failed with diagnostics:
cannot take a sample larger than the population when ‘replace = FALSE’
Execution halted
Codoc mismatches from documentation object 'c,Medline-method':
\S4method{c}{Medline}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library(testthat)
  > library(rplexos)
  > 
  > test_check("rplexos")
  Error: 'folders' must be a vector of existing folders or the wildcard "*"
  testthat results ================================================================
  OK: 0 SKIPPED: 6 FAILED: 0
  Execution halted
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Loading required package: rsdmx
  1. Error: DSD is properly fetched by readSDMX when there is no dsdRef (using flowRef) (@test_Data.R#36) 
  HTTP request failed with status: 403 The number of requests for /api/1.0/sdmx/GetData/ exceeds 50.
  1: readSDMX(providerId = "KNOEMA", resource = "data", flowRef = "SADG2015", dsd = TRUE) at testthat/test_Data.R:36
  2: stop("HTTP request failed with status: ", h$value()["status"], " ", h$value()["statusMessage"])
  
  <simpleError in regexpr("<!DOCTYPE html>", content): object 'content' not found>
  testthat results ================================================================
  OK: 216 SKIPPED: 53 FAILED: 1
  1. Error: DSD is properly fetched by readSDMX when there is no dsdRef (using flowRef) (@test_Data.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘RXKCD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getXKCD
> ### Title: Display your favorite XKCD comic in R
> ### Aliases: getXKCD
> 
> ### ** Examples
> 
> 
> library("RXKCD")
> significant <- getXKCD(882, display=FALSE)
Error in file(con, "r") : cannot open the connection
Calls: getXKCD -> fromJSON -> fromJSON -> I -> structure -> unique
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Sabermetrics.Rcheck/00install.out’ for details.
Running examples in ‘sequoia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sequoia
> ### Title: Pedigree Reconstruction
> ### Aliases: sequoia
> 
> ### ** Examples
> 
> data(SimGeno_example, LH_HSg5, package="sequoia")
> 
> SeqOUT <- sequoia(GenoM = SimGeno_example,
+                   LifeHistData = LH_HSg5, MaxSibIter = 0)
At line 127 of file Sequoia.f90
Fortran runtime error: Actual string length is shorter than the declared one for dummy argument 'genofilefr' (-915622145/255)
Running examples in ‘sisus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> 
> 
> # set working directory for many output files with setwd()
> 
> 
> # see http://statacumen.com/sisus for workbook
> 
> 
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> 
> 
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... get.data -> as.matrix -> <Anonymous> -> file.exists
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 6
  1. Failure: basic (@test-strip.R#13) 
  2. Failure: big (@test-strip.R#20) 
  3. Failure: libre (@test-strip.R#29) 
  4. Failure: abiword (@test-strip.R#39) 
  5. Failure: Japanese (cp932) (@test-strip.R#49) 
  6. Failure: Chinese and Korean (@test-strip.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘vegalite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached
  testthat results ================================================================
  OK: 66 SKIPPED: 0 FAILED: 2
  1. Failure: normal usage (@test_caching_gathering.R#27) 
  2. Failure: setting cache file (@test_caching_gathering.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/abcdeFBA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y"
  y[1]: "aeiouAEIOUy"
  
  
  testthat results ================================================================
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) 
  2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) 
  3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) 
  4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    2.9Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'acceptance_sampling_manual.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          K^^[]^^W>o<fc>h^^Zj<93>^(E<94><98><e1>B<a1><85>`^^GfW<b0>q<91><b5><bb>v<e5><da>MW]<b9><95><ae>tӮ<eb><bf><e0><aa>Y<94>B<b2>H^^P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...߾<bd>s<e7>N6<9b><c5>O)<a5><94>rmm<cd>0<8c>B<a1> <a5>dX<ee><ed><ed><e1><95>eY<8f>^^^=<da><dd>ݽ}
                                                  <fb><f6><f2><f2><b2>R^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.20 ...ZYYY[[^^C2<9f>?^^?<8e>-<87><9f><d9>l<d6>4<cd>l6<fb><e2><c5><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ACSN-vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AER.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bc>Aι<ee>M<ea>^^X<84>^^PA^^P<e8><ba>.<84>H$^^R<ba><ae>æ^^GA<d0><ed>v<87>t\<a8>
                                                  <ff><f9><f3><e7>l6[<af><d7>e'D<f4><ea>ի<d5><d5>UT^^[<c3>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...ޯP<af><d7><d5>`|H@<f8><93>V<bf>^^Q<c8><c9>9<97>S^^[<86><a1><a6>i(<f7>}^^_<fb>/9<cd>x<f6>}
                                                  <9f><88>@`<c6>؟^^?<be><fb><e3><8f>^^?9N<c3>0d<c3>0<9f>g...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.24 ...^^?<d7>2^^L^^F۷<d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘AFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: evaluateVariogramModels
> ### Title: evaluateVariogramModels method to evaluate the basic variogram
> ###   models
> ### Aliases: evaluateVariogramModels
> ###   evaluateVariogramModels,AFMImageVariogramAnalysis-method
> 
> ### ** Examples
> 
> library(AFM)
> 
> data("AFMImageOfRegularPeaks")
> # take an extract of the image to fasten the calculation      
> AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
[1] "40 40 31 40 71 40 71"
> # e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
> AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
>  
> AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
Warning in data.table(lib = c("AFM", "gstat", "fractaldim", "fftwtools"),  :
  Item 1 is of size 4 but maximum size is 5 (recycled leaving remainder of 1 items)
>  
>  # Variogram analysis 
> sampleFitPercentage<-3.43/100
> variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
> variogramAnalysis@omnidirectionalVariogram<- 
+               AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
+                                                      AFMImageVariogramAnalysis=variogramAnalysis)
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."
Error in CRS("+init") : no colon in init= string
Calls: <Anonymous> -> CRS
Execution halted
Package required and available but unsuitable version: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/alphashape3d.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'amei.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...߾<8d><c6>L&<c3>9<ff><ee><bb><ef>^^Xc_~<f9><e5><f5><eb><d7>s<b9>^^\<ba>q<ce><ef>޽<fb><c5>^^W_\<bc>
                                                  xq~~~aa!<9b><cd><ce><ce><ce>b<e4>\.W<af><d7><c7><c7><c7>^^Y...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<9b>^^L<c7>0<8f>Z<ad><86><bb><b2><85><88>8<e7>^^@<92><aa><aa><a6>i<a2><b1>X,<fa><be><8f>G<d0><e2><fb>~4|Å\D
                                                  Ƙ<bc><85><b7><d4>j<b5>v<e6><dc>^^Y8;<c5>ի<8d>ȨSp^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <c3>0<96><97><97><af>\<b9>
             <e2><ba>.F+^^T^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.24
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/anacor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/animalTrack.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

The following object is masked from 'package:qdap':

    %>%

The following object is masked from 'package:qdapTools':

    id

The following objects are masked from 'package:qdapRegex':

    escape, explain

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 56-58 (ANLP_Documentation.Rmd) 
Error: processing vignette 'ANLP_Documentation.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/tokenizers/NGramTokenizer : Unsupported major.minor version 51.0
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyannot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Anthropometry.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: Conversion from REAL(8) to default-kind COMPLEX(4) at (1) might loose precision, consider using the KIND argument
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/appell.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keykristen.colors: no visible global function definition for
  ‘colorRampPalette’
kristen.colors: no visible global function definition for ‘grey’
plot3d.points: no visible global function definition for ‘heat.colors’
plot3d.points: no visible global function definition for ‘plot’
ragged.image: no visible global function definition for ‘heat.colors’
ragged.image: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘grey’
scatterplot.density: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘abline’
scatterplot.density: no visible global function definition for ‘lm’
scatterplot.density: no visible global function definition for ‘legend’
vertical.image.legend: no visible global function definition for ‘par’
vertical.image.legend: no visible global function definition for
  ‘image’
vertical.image.legend: no visible global function definition for ‘axis’
vertical.image.legend: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
sh: rst2pdf: command not found
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
conversion by rst2pdf failed!
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the ‘lazyeval’ namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the ‘lazyeval’ namespace
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/arulesViz.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'llama'
  
  The following object is masked from 'package:BBmisc':
  
      normalize
  
  > test_check("aslib")
  Loading required package: aslib
  Error in .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Instances : Unsupported major.minor version 51.0
  Calls: test_check ... eval -> parseASScenario -> read.arff -> .jnew -> .External
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AtelieR.Rcheck/00install.out’ for details.
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.4Mb
Error in re-building vignettes:
  ...
  input string 487 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bartMachine.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o^^[<d5>^^V?uh<92>yJ=<b9><b4>/qG8q<86>V<a4>-JSy<c3>C<aa>^^\!<8b>%^^[^^T<84><c4>^^V<f5>^^O`<c3>6<cb>v^^A6^^H...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...T*e<9a><a6>eY<f1>u<92>R<fe><f0><c3>^^O<b6>m^^O^^O^^O<a3><f4><e7><9f>^^?<fe>裏<ae>\<b9>
                                                  <92>L&<e3><f1>x<c0><b8><ab><cf>^^Gݸq<a3>X,nV:55<b5><b3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...ȣG<8f><c0><86>eY<9f>}<f6>^^Y$MU <a2>^^O?<fc>0<9d>N^^O^^O^^O<ef>r
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Package unavailable to check Rd xrefs: ‘mritc’
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
File ‘BayesSAE/libs/BayesSAE.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘HBsae.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘R2jags’
Running examples in ‘BCEs0-Ex.R’ failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Package suggested but not available for checking: ‘beadarrayExampleData’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'beanplot.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S<dd>^^Z^^?<9a><be><a1>w@frn<ef><d5><da>2<a6>^^\<f0><f6><95>+i<a1><f0>.^^DM<c1><e8>Fp<d7>U<f7><ae><dd>	<ae><dc><f6>/<90>׽<a2><88>.<b2>m^^V
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<cd>qb-s<fd>H<ee><e2>w<f3>0o?<92><c6>&jj~<8b>rr<be><e6><s~<e7><f9>8<e7>L^^G<ea><f5>:<9d>\D
                                                  ~<f4>^^@<ba><8b><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d3>D<ce><ce><ce>N"<91><d0>ZW<ab>U<d3>4<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
Running examples in ‘benchmarkme-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_ram
> ### Title: Get the amount of RAM
> ### Aliases: get_ram
> 
> ### ** Examples
> 
> ## Return (and pretty print) the amount of RAM
> get_ram()
sh: system_profiler: command not found
Error in if (power < 1) { : missing value where TRUE/FALSE needed
Calls: <Anonymous> -> print.bytes
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keybeqi2: no visible global function definition for ‘na.omit’
beqi2: no visible global function definition for ‘browseURL’
readAMBI: no visible global function definition for ‘read.csv’
readBEQI: no visible global function definition for ‘read.csv’
readERF: no visible global function definition for ‘read.csv’
readTWN: no visible global function definition for ‘read.csv’
read_ITI_FIBI: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'betareg-ext.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...x(^^T<f2>}?^^R<89>^^L,<e7><d3><e2><ff>۴<^^Q<f0>Ȝs<d7>uM<d3>ܩZ<cb>[<fc><f4>}
                                                  ?^^T^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<9a>f<ad>V<b3>,<eb><db>o<bf>=z<f4><e8><c4>ĄeYB^^HM<d3>^^P3p<ce>QF<83><9d>D^^Q]<8c>^
                                                  6<9b><cd>d2B^^H<c7>q^^P<be><98><a6>iY^^V^^Q#...
! Extra }, or forgotten $.
l.18 ...t<ee>ܹF<a3><c1>^^X[XX0M3<91>H^^P<d1><db>o<bf>m<9a><e6><f0><f0>0^^Q<f9><be><af>$A<d9><f7>}
                                                  <df><f7>5<ad>#<ce
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 123.2Mb
  sub-directories of 1Mb or more:
    include  123.2Mb
File ‘bifactorial/libs/bifactorial.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘misc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘krit.o’, ‘pv.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.9Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RODBC’
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Biocomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bios2mds.Rcheck/00install.out’ for details.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/birdring.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘GOSemSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because profiling.Rmd appears to be an R Markdown v2 document.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘fPortfolio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blockmodeling.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.
Found the following significant warnings:
  Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Dummy argument 'ch_mymsg' at (1) was declared INTENT(OUT) but was not set
  Warning: Dummy argument 'da_gpvals' at (1) was declared INTENT(OUT) but was not set
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Blossom.Rcheck/00install.out’ for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
File ‘BMN/libs/BMN.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 280.4Mb
  sub-directories of 1Mb or more:
    include    2.6Mb
    lib      277.7Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bootsPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bpca.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 449 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BradleyTerry.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...^Ha<db><f6><f0><f0>0<d8>~<fd><f5><d7>^^[7nܹs'^^\^^Ns<ce>^^_?~<fc>駟޾}
                                                  <fb><fc><f9><f3><c9>d<f2>H^^T{dګ^^Xƥx<fc><91>i^^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^@+<c6>X<^^^^^WB<cc><ce><ce>~<f1><c5>^^W<e9>t<fa><f9><f3><e7><c1>`^^P<e8>D<ef>څfff^
                                                  <bc>x188X<af><d7>?<fb><ec><b3>t:=>><be><b2><b2><92>J<a5>^^N...
! Extra }, or forgotten $.
l.16 ...^^Hڜs۶^^S<89>D<f7><e3><ec>Hg<be>w<92>锋<d7>!<b4>d<b3><d9><e3><99><c7>ah^^O<ec>z<ca>}
              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/brainR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyscene4d: no visible global function definition for ‘rainbow’
write4D.file : <anonymous>: no visible global function definition for
  ‘col2rgb’
writeWebGL_split : split_triangles: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  col2rgb rainbow rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
to your NAMESPACE file.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    libs  49.2Mb
Running examples in ‘c3net-Ex.R’ failed
The error most likely occurred in:

> ### Name: c3net
> ### Title: All in one function to infer network with C3NET
> ### Aliases: c3net
> ### Keywords: misc
> 
> ### ** Examples
> 
> data(expdata)
> data(truenet)
> 
> net <- c3net(expdata, network=TRUE)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: c3net ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘camel/libs/camel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘SFGen.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘SFGen.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CampaR1.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /usr/local/share/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-3 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cape.Rcheck/00install.out’ for details.
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'CaRpools.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because CaRpools.Rmd appears to be an R Markdown v2 document.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Package required but not available: ‘OpenCL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cati.Rcheck/00install.out’ for details.
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some ‘make’ programs ignore lines not ending in LF.
The following files look like leftovers/mistakes:
  ‘Causata-vignette.log’
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cdcsis.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cems.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 505 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChainLadder.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS
                 ;<e8><d0>7\x<83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 w<ab><b4><b4><90><c1>TQ	\nS;<e8><d0>7\x
                       <83><df>/<ef><f1><fa>K<df><f5>|<86>p^^H7<c9><f9><90>s^^?<95>&<d0><ef><f7><e1>^^[^^P<fc><ec>^^D&^^Dz<ca>^^Ez<ca>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...e3^^X<d8>?<e5>b^^Du[.<97>s<b9><9c>mۙLFUU۶<a7><a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ChaosGame.Rcheck/00install.out’ for details.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=Auckland&zoom=8&size=640x640&scale=2&maptype=hybrid&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Auckland&sensor=false
Quitting from lines 136-154 (cfStation.Rmd) 
Error: processing vignette 'cfStation.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clpAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clues.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:tools’:

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/comato.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyHopkins.index: no visible global function definition for ‘runif’
MBM.em: no visible global function definition for ‘runif’
PAM.cluster: no visible global function definition for ‘dist’
calculate.layout: no visible global function definition for ‘optim’
min.distance: no visible global function definition for ‘dist’
plot.conceptmap: no visible global function definition for ‘par’
plot.conceptmap: no visible global function definition for ‘plot’
plot.conceptmaps: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mogene10sttranscriptcluster.db’
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyconf: no visible global function definition for ‘read.csv’
conf: no visible global function definition for ‘write.csv’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘sd’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘qt’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘pt’
plot.mya: no visible global function definition for ‘dt’
plot.mya: no visible global function definition for ‘rgb’
write_html.conf_input: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  browseURL dt pt qt read.csv rgb sd write.csv
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "dt", "pt", "qt", "sd")
  importFrom("utils", "browseURL", "read.csv", "write.csv")
to your NAMESPACE file.
Package required but not available: ‘RcppTOML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/conjoint.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyConjoint: no visible global function definition for ‘dev.new’
Conjoint: no visible global function definition for ‘barplot’
caFactorialDesign: no visible global function definition for ‘cor’
caModel: no visible global function definition for ‘as.formula’
caModel: no visible global function definition for ‘lm’
caModel: no visible global function definition for ‘summary.lm’
caSegmentation: no visible global function definition for ‘kmeans’
caUtilities: no visible global function definition for ‘as.formula’
caUtilities: no visible global function definition for ‘lm’
caUtilities: no visible global function definition for ‘summary.lm’
partutilities: no visible global function definition for ‘as.formula’
partutilities: no visible global function definition for ‘lm’
partutils: no visible global function definition for ‘as.formula’
partutils: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘as.formula’
profsimcode: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘model.matrix’
totalutilities: no visible global function definition for ‘as.formula’
totalutilities: no visible global function definition for ‘lm’
totalutilities: no visible global function definition for
  ‘model.matrix’
utlsplot: no visible global function definition for ‘dev.new’
utlsplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ConsRank.Rcheck/00install.out’ for details.
Running examples in ‘ConvergenceConcepts-Ex.R’ failed
The error most likely occurred in:

> ### Name: investigate
> ### Title: Investigate examples and exercises from the paper
> ### Aliases: investigate
> ### Keywords: dplot iplot distribution htest
> 
> ### ** Examples
> 
> investigate()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: investigate ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corehunter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corregp.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘cpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: cpa-package
> ### Title: Confirmatory Path Analysis through the d-sep tests
> ### Aliases: cpa-package
> ### Keywords: package
> 
> ### ** Examples
> 
> x <- cpa()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: cpa ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cb>^^L<8e><99><98>y<8b>#<8e><a6><98><d8>^^Fl^^By><b2><ac><f1>̹^^_g~<f7>|<dc>s<8f><db>\<d7>
                                                  <85><97><97><da>_<f4>^^D<9a>K-<f1><8e>3<b5><c4>;<ce><d4>^^R<ef>8<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...}<f6><d9>g<a3><a3><a3>B<88><c5><c5>ť<a5><a5>|>^^?<f9><f2>e|<a4>i^^Zʃ<bd><fd><f0><c3>^^O^^_}
                                                  <f4><91><a6>i׮]<db><c3>tݽS.<97><ab><f2><f4><c1><83>^^G<fb><e8><b3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ in
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
  input string 416 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 422 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'crch.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cc><db><c0>H<bb>^^^<b7><d8>]<f1>^^\^^Y;-E<f9>)c<c9>O<8a><94><8b>9p<ca>^^A<e5><c2>-g<94>\<f3>
                                                  ^^W<e4><9a>?a9gOsC9^^RiFV^^T<81>4bl...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^X-&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><fd>^^]J)<a5>^^T.N?<d5>Z<f3>}
                                                  <a5><94><d6><fa><ac><96><a7><db><f3><f5><fa><fa><fa><e9>.<b8><93>l?^^L<fe>5|<d3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.15 .
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crimCV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crs.Rcheck/00install.out’ for details.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Invalid MIT-MAGIC-COOKIE-1 keygen.xnorm: no visible global function definition for ‘extendrange’
plot.clsd: no visible global function definition for ‘plot’
plot.crs: no visible global function definition for ‘par’
plot.crs: no visible global function definition for ‘plot’
plot.crs: no visible global function definition for ‘topo.colors’
plot.npglpreg: no visible global function definition for ‘par’
plot.npglpreg: no visible global function definition for ‘plot’
plot.npglpreg: no visible global function definition for ‘topo.colors’
printClear: no visible global function definition for ‘flush.console’
printPop: no visible global function definition for ‘flush.console’
printPush: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  extendrange flush.console par plot topo.colors
Consider adding
  importFrom("grDevices", "extendrange", "topo.colors")
  importFrom("graphics", "par", "plot")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘predict’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘predict’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM: no visible global function definition for ‘predict’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
predict.kpbb: no visible global function definition for ‘predict’
uni.fpca: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm predict qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "predict", "qnorm", "rnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ctsem.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d1><f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>
                                                  ^<b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.19 ...<f3>Sw<e0>^^D,<b9><ed>E^^N0<e3>m!`6^^A<e0><eb>ׯ^^[<86>^^Q<8d>Fs<b9>\<bd>^
                                                  <b7>,krrR<d7><f5>H$<82><8e>^^X<8d><88>^^J
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 <ec>B<bc>\.g
  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cudaBayesreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/curvHDR.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component "links": Component 4: Component 3: Modes: character, numeric
  Component "links": Component 4: Component 3: target is character, current is numeric
  Component "links": Component 5: Component 3: Modes: character, numeric
  Component "links": Component 5: Component 3: target is character, current is numeric
  
  
  testthat results ================================================================
  OK: 7 SKIPPED: 2 FAILED: 2
  1. Error: d3_dep-* src href is a valid url (@test_deps.R#18) 
  2. Failure: d3_igraph works (@test_igraph.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DAKS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<8e><ad>^^_<b6><9c>X<ae><de>A<8c>fgf<e7><cd><fb><cc>{o޼<fd><c4><f7>}<ba><be>^^T<fa><d8>^^S<b8>\^^Z
                                                  <b3>7<ca>4fo<94>i<cc><de>(Ә<bd>Q<a6>1{<a3>L<ff>l<f6>LӔ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...|~gg端<be><c2><d0><f9>|<de>4<cd>l6<ab>:d^^X<c6>ӧO<f1><ee><cf>><fb>lgg<e7><e1>Ç<b9>\N
                                                  ^^H^^A<96>VVV<a4><94>h<a0><94>^^RB,//<f3>PD<f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...?<fe><f9><e7><f9><f9><f9>p8<bc><b2><b2><f2><dd>w<df>^^Y<86><a1><eb>z.<97><db><dc><dc><fc><fe><fb><ef>s<b9>^^\^^F\F
                                                  /DCDB^^W^^J
The control sequence at the end of the top 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot16c4d558b2e19.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c4d558b2e19.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotd0b5ddd2219.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd0b5ddd2219.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DBKGrad.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Invalid MIT-MAGIC-COOKIE-1 keyThere are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Running examples in ‘DecorateR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DECORATE
> ### Title: Binary classification with DECORATE (Melville and Mooney, 2005)
> ### Aliases: DECORATE
> 
> ### ** Examples
> 
> 
> data(iris)
> y <- as.factor(ifelse(iris$Species[1:100]=="setosa",0,1))
> x <- iris[1:100,-5]
> dec <- DECORATE(x = x, y = y)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: DECORATE ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Delaporte.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:seriation':

    bluered, greenred

The following object is masked from 'package:stats':

    lowess

Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 925-927 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.1Mb
Package suggested but not available for checking: ‘dclone’
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Running examples in ‘detrendeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: detrendeR-package
> ### Title: detrendeR - A Graphical User Interface to process and visualize
> ###   tree-ring data using R
> ### Aliases: detrendeR-package detrendeR
> ### Keywords: package
> 
> ### ** Examples
> 
> detrender()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: detrender ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
Package required but not available: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dgmbGui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DiceView.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DirichletReg.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DiversityOccupancy.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘DivMelt-Ex.R’ failed
The error most likely occurred in:

> ### Name: DivMelt_gui
> ### Title: User Interface for the Diversity Assay Analysis Tool
> ### Aliases: DivMelt_gui
> ### Keywords: interface
> 
> ### ** Examples
> 
> ##
> library (DivMelt)
> DivMelt_gui()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DivMelt_gui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    include  19.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
Zibs.pairwise.pr.locus: no visible global function definition for
  ‘combn’
dist.pair.cdf : r.scalar: no visible global function definition for
  ‘uniroot’
dist.pair.cdf: no visible global function definition for ‘head’
dist.pair.cdf: no visible global function definition for ‘tail’
est.freqs: no visible global function definition for ‘setNames’
write.genepop: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  combn head setNames tail uniroot write.table
Consider adding
  importFrom("stats", "setNames", "uniroot")
  importFrom("utils", "combn", "head", "tail", "write.table")
to your NAMESPACE file.
.ccd.1.41: no visible global function definition for ‘rnorm’
.ccd.1.41: no visible global function definition for ‘formula’
.ccd.1.41: no visible global function definition for ‘coef’
.ccd.1.41: no visible global function definition for ‘runif’
.ccd.1.41 : <anonymous>: no visible global function definition for
  ‘as.formula’
.gen.des.old.way: no visible global function definition for ‘runif’
Dopt.augment: no visible global function definition for ‘rnorm’
Dopt.augment: no visible global function definition for ‘as.formula’
Dopt.augment: no visible global function definition for ‘model.matrix’
Dopt.design: no visible global function definition for ‘as.formula’
Dopt.design: no visible global function definition for ‘model.matrix’
Scalc: no visible global function definition for ‘dist’
bbd.design: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘as.formula’
ccd.augment: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘model.frame’
ccd.augment: no visible binding for global variable ‘na.pass’
generators.from.design: no visible global function definition for
  ‘formula’
generators.from.design : <anonymous>: no visible global function
  definition for ‘as.formula’
lhs.design: no visible global function definition for ‘cor’
rsm.design: no visible global function definition for ‘as.formula’
rsmformula: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula coef cor dist formula model.frame model.matrix na.pass
  rnorm runif
Consider adding
  importFrom("stats", "as.formula", "coef", "cor", "dist", "formula",
             "model.frame", "model.matrix", "na.pass", "rnorm", "runif")
to your NAMESPACE file.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
Running examples in ‘dpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: dpa-package
> ### Title: Dynamic Path Approach for Analyzing time-dependent simulation
> ###   data
> ### Aliases: dpa-package dpa
> 
> ### ** Examples
> 
> #Start the GUI with:
> dpa.start()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dpa.start ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package suggested but not available for checking: ‘dtplyr’
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Missing or unexported object: ‘RSQLite::rsqliteVersion’
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dprep.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 352 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DSL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<ce><fc><fc><bc><e3>8X^^W<c6>X<bb><dd>^^F<fd><9a><a6><e1>E<ac>:^^O8<e7><e3><e9><de>><a1>^^_\^^G
                                                  <8e><ee>^^?<dc>q^^F<c7>1<c8>3^^L^^C<cc><c1>O<a9>3<fb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <fa><e8><de>e)<e9><8d><c6>_[<f7><86>^^]<97><e4><9d>^^@0<ad><bd><d7>}7<f2><fe><8c>p<b6>e\<d3>
                                        4<d3><e9><b4>i<9a>H<c0>^^A8<92><f9><f9>y<d3>4www<9f>>}<fa><f9>矟<d1>^^D.-<e7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
\GenericError  ...                                
                                                    #4  \errhelp \@err@     ...
l.25 ...^^X^^R^^@<c6>&<9b>ͦ<d3><e9>l<d6>L<a7><e3><a6>Yo6<9f><ee><ec><<e7>|<ab>Ri
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because DT.Rmd appears to be an R Markdown v2 document.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 371 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 387 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dtw.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...4?<fa><e8><a3>w<de>y<87><88>T^^?)<e5><ec><ec>,<98><8f><c7><e3>[[[<bf><fc><f2>˗_~)<84>x>^^C<ed>^
                                                  <e8><c1><83>^^G<fb>Z<ee>޽[<af><d7>{<9a>$<<e4><d9>	{<dd><c9><e1>^...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.15 ...<bf><93>^^?<a1><f6><b1> z><93>^^O<b4><fb><c1><88><cb>KW<9c><bd><93><8a><96><a3>^^P<84><87>^^P²<ac>\.<f7>
                                                  <e8>ѣ^^O><f8> <97>˽<fa>꫻<bb><bb><b3><b3><b3>g<b7><f4><bb>...
! You can't use `\spacefactor' in math mode.
\add@accen
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘dynamicGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: DynamicGraph
> ### Title: DEPRECATED: Simple interface to dynamicGraph
> ### Aliases: DynamicGraph
> ### Keywords: dplot hplot iplot dynamic graphs methods multivariate
> 
> ### ** Examples
> 
> require(tcltk); require(dynamicGraph)
> 
> # Example 1:
> 
> W <- dg(as(new("dg.simple.graph", vertex.names = 1:5), "dg.graph"),
+         control = dg.control(title = "Very simple"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.9Mb
    libs   7.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs     2.4Mb
    models   4.3Mb
File ‘EBS/libs/EBS.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/edrGraphicalTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eegkit.Rcheck/00install.out’ for details.
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: get_epqs(locations, ...)
  3: httr::GET(url)
  4: request_perform(req, hu$handle$handle)
  5: request_fetch(req$output, req$url, handle)
  6: request_fetch.write_memory(req$output, req$url, handle)
  7: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: get_elev_point returns correctly (@test-get_elev_point.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 137-145 (introduction_to_elevatr.Rmd) 
Error: processing vignette 'introduction_to_elevatr.Rmd' failed with diagnostics:
Timeout was reached
Execution halted
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'elrm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.20 ...V^^AZ^^[<e1>dF^^L{^^C<94>ұ<b1><b1>`0<88><a4>^^[<86>Q<ab>հj<92><c9>d<ae>\<b9>
                                                  ^^B^^@mm<da>^^^<bb>r<a2>f樺ǈ;<cd>4<a7>s...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.25 <c1><8e>N<92>$<d4>:<8c>^^A<d8>^^X<8e><e3>J<a5>R<8b>^^[ ^^G><bd>c,^^Y<9d>B<f5><a9>}
                                             !<d0>^^Y<f8><ec>	<97>𥪪<f5>z<9d><b5><cb>^^Y<d1>X>d<87><8f>u{t!...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.45 x<9c><ed>\<cf>
          k^^[<d7>^^V>Q쪢<89
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hgu133plus2.db’
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: +RTS: command not found
Quitting from lines 315-317 (creating-EML.Rmd) 
Error: processing vignette 'creating-EML.Rmd' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/emma.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 129-154 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...<e5><81>h	ԂXqI<a9><c9><c0>H^^H<b5>N<93>K<c6>C<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7>9<dc><e7>/}
                                                  <c4>v,Gg!<c6>wν<ba><e7><9e><df>=<f7>|\ydkk<8b>N.<8d>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.15 ...<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 390 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 391 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 405 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 406 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Execution halted
Running examples in ‘erpR-Ex.R’ failed
The error most likely occurred in:

> ### Name: erp.infl
> ### Title: inspect the influence of a subject on the average (single
> ###   electrode).
> ### Aliases: erp.infl
> 
> ### ** Examples
> 
> 
> data(ERPsets)
> 
> erp.infl(base="Exp1_word_subj", numbers=1:20, electrode="OZ", 
+ startmsec=-200, endmsec=1500, erplist=ERPsets)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: erp.infl ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package unavailable to check Rd xrefs: ‘RODBC’
Package required but not available: ‘forensim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Evomorph.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'evtree.tex' failed.
LaTeX errors:
! TeX capacity exceeded, sorry [text input levels=15].
\@filef@und ->evtree.tpt 
                         
l.16 ...BO=<b5><e4><d0><de>r<88><ce>m)<88>B<f1><a1><a5>X^^Em^^E)^^NYX-&<c4>M<bd>x-<8c><9e>\[
                                                  <d3><dd>纛<84>H<ef><f0><a9><e7><ed>S^^\<fd><b0>c'<ca><d3><f7> vg...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'exams.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^^^{<ec><bd><e7>Rȭ<f4>蛡<85>P^^]bL^^L6^^L<ac>^^W<e1><d6>-^^Y<b4>Y\U
                                                  <e2><8f>ǻU<ed><8d><f3>K<fa>^^O_<f5><fe><ad>^^Sےc'<91><ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>RQJY<96>5`'A^^P<ec><ef><ef><97><cb><e5>z<bd>n<9a>&<fa>!<a2><ad><ad><ad><d9><d9>Y4^^[<b0><b7><b8>\q
                                                  <e6>|Ypb<8e>a<ba>D"<81><89>'<a2>z<bd><de><ed>v<cf>1<df>^^W+...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Please use \mathaccent for accents in math mode.
\add@accent ...@sp
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    exiftool  10.2Mb
Package suggested but not available for checking: ‘golubEsets’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: kernlab
Quitting from lines 23-26 (advanced-vignette.Rmd) 
Error: processing vignette 'advanced-vignette.Rmd' failed with diagnostics:
there is no package called 'golubEsets'
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FAiR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘OpenML’
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  Loading required package: farff
  1. Error: quick test with small arffs (@test_quick.R#6) ------------------------
  java.lang.UnsupportedClassVersionweka/core/Instances : Unsupported major.minor version 51.0
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff(path2) at /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/farff.Rcheck/tests/testthat/helper.R:17
  3: .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader"))
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fastcox.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘akima’ ‘spatial’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Running examples in ‘FCMapper-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph.fcm
> ### Title: Fuzzy cognitive map graph
> ### Aliases: graph.fcm
> 
> ### ** Examples
> 
> 
> matrix = matrix(nrow=7,ncol=7)
> matrix[1,] = c(0,-0.5,0,0,1,0,1)
> matrix[2,] = c(1,0,1,0.2,0,0,0.6)
> matrix[3,] = c(0,1,0,0,0,0,0)
> matrix[4,] = c(0.6,0,0,1,0,0,0.1)
> matrix[5,] = c(0,0.5,0,0,1,0,-0.6) 
> matrix[6,] = c(0,0,-1,0,0,0,0)
> matrix[7,] = c(0,0,0,-0.5,0,0,1)
> concept.names = c("A","B","C","D","E","F","G")
> 
> results = nochanges.scenario(matrix,iter=25,concept.names)
> 
> graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graph.fcm ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fds.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyread.hmd: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/feature.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keyparseHelp: no visible global function definition for ‘help’
parseHelp: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  help unzip
Consider adding
  importFrom("utils", "help", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FieldSim.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyfieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-87 (fiftystater.Rmd) 
Error: processing vignette 'fiftystater.Rmd' failed with diagnostics:
ScaleColorPlane was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘fisheyeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: POIcoords<-
> ### Title: Update POI slots
> ### Aliases: POIcoords<-
> 
> ### ** Examples
> 
>    ## IRIS Example
>    data(iris)
>    
>    # distance of each element to each dimension max and min
>    matrizSim = cbind(
+                1 - (max(iris[,1]) - iris[,1]) / (max(max(iris[,1]) - iris[,1])),
+                1 - (max(iris[,2]) - iris[,2]) / (max(max(iris[,2]) - iris[,2])),
+                1 - (max(iris[,3]) - iris[,3]) / (max(max(iris[,3]) - iris[,3])),
+                1 - (max(iris[,4]) - iris[,4]) / (max(max(iris[,4]) - iris[,4])),
+ 
+                1 - (min(iris[,1]) - iris[,1]) / (min(min(iris[,1]) - iris[,1])),
+                1 - (min(iris[,2]) - iris[,2]) / (min(min(iris[,2]) - iris[,2])),
+                1 - (min(iris[,3]) - iris[,3]) / (min(min(iris[,3]) - iris[,3])),
+                1 - (min(iris[,4]) - iris[,4]) / (min(min(iris[,4]) - iris[,4])))
> 
>    # exaggerate diffs
>    matrizSim  = matrizSim^3 
>    
>    # Create POI plot
>    irisPOI = POICreate('POI')
>    irisPOI@matrizSim <- matrizSim
>    irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
+                              'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')
>    POIcoords(irisPOI) <- POICalc(irisPOI ,length(irisPOI@wordsInQuery))
>    irisPOI@docs <- cbind(matrix(seq(1:nrow(irisPOI@objeto))),matrix(seq(1:nrow(irisPOI@objeto))))
>    irisPOI@colores <- c(rep(2,50),rep(3,50),rep(4,50))
>    try(rm('POI.env'), silent = T)
Warning in rm("POI.env") : object 'POI.env' not found
>    plotPOI(irisPOI)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: plotPOI ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fit4NM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because fitbitScraper-examples.Rmd appears to be an R Markdown v2 document.
Quitting from lines 29-40 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
Value for option cookie (10022) must be length-1 string
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
  DONE!
  bird likely dod not move, exiting without result
  testthat results ================================================================
  OK: 27 SKIPPED: 0 FAILED: 2
  1. Error: map_flightr_ggmap_works (@test_data_result_summary_and_plotting.R#36) 
  2. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: ‘data.table’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/foodweb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error: only replacement of elements is allowed
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/forestFloor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ForImp.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because formattable-data-frame.Rmd appears to be an R Markdown v2 document.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 346 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Formula.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 p<81>'<f6>^^\<f3>`<cc><e9><e7><c0>^^Sa<ee>yB<b0><81><c4>q<9c><fe>7<f2><e7><8a>9/<db><de><fc><b4>\<f1>
                                           <fd>ޫ<9d><c6>E<80><82><f4>^^V<e7>^^\<b8>^^G^^Y0<c6>hG^^W<87><cc>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.23 ...G<9e>3<97><cb><cd><cc><cc><d4>j5<ac><93>B<a1><b0><b0><b0>P(^^T^^R<89><84>a^^X<aa><aa>nmm)<8a><e2>y^
                                                  <a5>Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>...
! Undefined control sequence.
l.23 ...Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>ѣG<b3><b3><b3>B<88>X,<96><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rsymphony’

Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frailtypack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frontiles.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
Running examples in ‘FSelector-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.simple.formula
> ### Title: Converting to formulas
> ### Aliases: as.simple.formula
> 
> ### ** Examples
> 
>   data(iris)
>   result <- cfs(Species ~ ., iris)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: cfs ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ftsa.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Package required but not available: ‘breastCancerVDX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘cffdrs’
Error in re-building vignettes:
  ...
  input string 191 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 192 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 200 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.31 ...<f9><f3><a7>\.;q*<e0><88><ed><ed><ed><d0> <ac>~<d0><e6>+W<88><ca><e5>2J<fb>Μ^^@σ<83><83>0<89><f1>x\T
                                                  <c3>^^Q^^Y<e2>~^^H<ed><de>^^U`<8c><f5><f7><f7><e3><93>s<ce>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.34 ΘeY<b9>\N
            <84>x<a2>B^^DX^^@E?T<ed>^^P<91>E<a3>ю<8e><8e>|>/<8a>GD<94><cb>尙<c3><dd>z^^E<f6>^^P+x<^^^I<92>$I<d2>4M<92>$UU^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.36 <8c>C@^^OP^^D\<b2>
                 <c0><fd>\<a6>A<bb>X<ee><a0><cd>7x<8d><a1><f2><d9>ù<87>	<99><9e><9e>~<f4><e8>^^QB<8d><ab>W<af>^^B^^Tt^<f2><a2>]^^Nq<d2>^^@<d4>#O<ab>^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you h
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘gamlss.demo-Ex.R’ failed
The error most likely occurred in:

> ### Name: demoDist
> ### Title: Interface for demonstrating the gamlss.family distributions
> ### Aliases: demoDist
> ### Keywords: distribution regression
> 
> ### ** Examples
> 
> ## do not run 
> demoDist()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: demoDist ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.7Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.18 <92><a1>><df><ef><af>NJ^^C^^C~<d2><e7>^^[^^Zhl|<fb><f6><ed><e6><a3>ٶ}
                                       <f3><e6>M۶gffZ<b6>ll<86><bd><f6><80>^^V<dc>;^^W<f2><e9>k<f5>X<ea>w<9f><fc><e5><ef>֦...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.18 ...`<8c>QJ3<99>L^^?^^?<ff><e0><e0> ^^@PJ^^S<89>D:<9d>ƨ<ea><ec>ٳ<8b><8b><8b>W<ae>\<99>
                                                  <9e><9e><be>r<e5><ca><de>'<b7><b7>@<e3><87>a<cb>^^^b<96><e6>]fff^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
        
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.0Mb
    libs   8.7Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     42.9Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.2Mb
Package suggested but not available for checking: ‘paleofire’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gdimap.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because tutorial.Rmd appears to be an R Markdown v2 document.
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gensphere.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/geoelectrics.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyimage.glm.krige.bayes: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors
Consider adding
  importFrom("grDevices", "heat.colors")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GeoXp.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘stable’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-115 (examples-from-paper.Rmd) 
Error: processing vignette 'examples-from-paper.Rmd' failed with diagnostics:
StatEdges was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GGEBiplotGUI.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘ggiraphExtra-Ex.R’ failed
The error most likely occurred in:

> ### Name: ggAncova
> ### Title: Make an interactive plot for an ANCOVA model
> ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm
> 
> ### ** Examples
> 
> require(moonBook)
Loading required package: moonBook
> require(ggplot2)
Loading required package: ggplot2
> require(ggiraph)
Loading required package: ggiraph
> ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE)
Error: GeomInteractivePoint was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  > library(testthat)
  > library(ggiraphExtra)
  > 
  > test_check("ggiraphExtra")
  Loading required package: ggplot2
  Loading required package: ggiraph
  Loading required package: plyr
  Error: GeomInteractivePoint was built with an incompatible version of ggproto.
  Please reinstall the package that provides this extension.
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
GeomInteractivePoint was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because an_introduction.Rmd appears to be an R Markdown v2 document.
Loading required package: ggplot2
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
Fontconfig warning: line 146: blank doesn't take any effect anymore. please remove it from your fonts.conf
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotfc0629dcd35c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotfc0629dcd35c.png': No such file or directory
Quitting from lines 13-27 (an_introduction.Rmd) 
Error: processing vignette 'an_introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because using_ggmcmc.Rmd appears to be an R Markdown v2 document.
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Registering fonts with R
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + 
  + kentucky = mergeBugsData(kentucky, kSummary)
  + 
  + if(require('sp', quietly=TRUE)) {
  +   pdf("spplotBym.pdf",height=4,width=8)
  +   print(spplot(kentucky, "FittedRateCounty.mean"))
  +   dev.off()
  + }
  + 
  + }
  Error in R2OpenBUGS::bugs(forBugs$ragged, inits = int2, model.file = "bym.txt",  : 
    Cannot find the OpenBUGS program
  Execution halted
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    libs  36.7Mb
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  52.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gmatrix.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library('testthat')
  > 
  > test_check('Gmisc')
  Loading required package: Gmisc
  Loading required package: Rcpp
  Loading required package: htmlTable
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  testthat results ================================================================
  OK: 116 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 205 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 206 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 214 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'googleVis.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <ed><c1>E<98>e҃<a7>z<ea>ѣ<82>x^^V<(xt^^?<80><88><ee>\E
                                  <8a>B^^[<88>^^Y<e2><L'a"A:'^^AM<b2><c9>V<fb><98>&Vs<b0><f9>^^\^^^^^\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<97><cb>=x<f0>`vv<f6>ڵk<87>^^O^^_<be>x<f1><a2>i<9a><8f>^^_?<f6>}<ff>ʕ+^^W.\<98>
                                                  <9d><9d><d5>4mmmM<92><a4><b9><b9><b9>;w<ee>D^^^<d5>n<b6>[<d3>4...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ^^@^^X<86>^^A^^@<c5>b<b1><eb> {<ba><9f><84><90>r<b9>L<bb>\<b3>
                                  <d9>$<84><8c><8f><8f>˲L^^Hy<f9><f2><a5><e7>y<93><93><93><8d>F^^C^^@<c2>0ܖ<a4>q^^O
The control sequence at the end of the top line
of your error message was nev
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPC.Rcheck/00install.out’ for details.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: gpuMatrix Integer Matrix multiplication (@test_gpuMatrix_algebra.R#318) 
  2. Error: gpuMatrix Single Precision Matrix Cholesky Decomposition (@test_gpuMatrix_chol.R#25) 
  3. Error: vclMatrix permute (@test_order.R#21) 
  4. Error: Switching GPU vclMatrix Single Precision Column Sums (@test_switch_gpu_vclMatrix_row_col.R#36) 
  5. Error: Switching GPU vclMatrix Single Precision Row Sums (@test_switch_gpu_vclMatrix_row_col.R#82) 
  6. Error: Switching GPU vclMatrix Single Precision Column Means (@test_switch_gpu_vclMatrix_row_col.R#127) 
  7. Error: Switching GPU vclMatrix Single Precision Row Means (@test_switch_gpu_vclMatrix_row_col.R#173) 
  8. Error: Switching GPU vclMatrix Single Precision Block Column Sums (@test_switch_gpu_vclMatrix_row_col.R#376) 
  9. Error: Switching GPU vclMatrix Single Precision Block Row Sums (@test_switch_gpu_vclMatrix_row_col.R#424) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gputools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GrammR.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running the tests in ‘tests/demo-graphics.R’ failed.
Last 13 lines of output:
  +           at = mean(par("usr")[1:2]), cex=0.7, font=3)
  + }
  > 
  > demo11 <- function() {
  +     par(bg="cornsilk")
  +     coplot(lat ~ long | depth, data = quakes, pch = 21, bg = "green3")
  + }
  > 
  > plotdiff(expression(demo1()), "demo-1")
  Error in system2("compare", c("-metric AE", paste0(label, c("-graphics.png",  : 
    error in running command
  Calls: plotdiff -> plotcompare -> system2
  Execution halted
Error in re-building vignettes:
  ...

Loading required package: lme4

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

The following object is masked from 'package:stats':

    step

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Quitting from lines 293-301 (introduction_to_groupdata2.Rmd) 
Error: processing vignette 'introduction_to_groupdata2.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/grt.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gdalUtils’
Errors in running code in vignettes:
when running code in ‘gWidgets.Rnw’
  ...

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


  When sourcing ‘gWidgets.R’:
Error: [tcl] invalid command name "toplevel".
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gWidgetstcltk
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Loading required package: digest
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


Error: processing vignette 'gWidgets.Rnw' failed with diagnostics:
 chunk 3 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetsRGtk2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetstcltk.Rcheck/00install.out’ for details.
Running examples in ‘h2o-Ex.R’ failed
The error most likely occurred in:

> ### Name: aaa
> ### Title: Starting H2O For examples
> ### Aliases: aaa
> 
> ### ** Examples
> 
> h2o.init()

H2O is not running yet, starting it now...

Note:  In case of errors look at the following log files:
    /tmp/RtmpbYCRf7/h2o_urbanek_started_from_r.out
    /tmp/RtmpbYCRf7/h2o_urbanek_started_from_r.err

java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)

Starting H2O JVM and connecting: ............................................................ 
[1] "localhost"
[1] 54321
[1] TRUE
[1] -1
[1] "Failed connect to localhost:54321; Connection refused"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed connect to localhost:54321; Connection refused
[1] 7
Error in h2o.init() : H2O failed to start, stopping execution.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/h5.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 107.4Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  trying URL 'ftp://ftp.bafg.de/pub/REFERATE/GRDC/ltdata/africa.zip'
  ftp data connection made, file length 2730333 bytes
  ==================================================
  downloaded 2.6 MB
  
  testthat results ================================================================
  OK: 57 SKIPPED: 0 FAILED: 2
  1. Error: Test HadDAILY function (@test-HadDAILY.R#6) 
  2. Error: Test TRMM function (@test-TRMM.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-4 
trying URL 'ftp://ftp.bafg.de/pub/REFERATE/GRDC/ltdata/europe.zip'
ftp data connection made, file length 4812722 bytes
==================================================
downloaded 4.6 MB

Station has monthly records
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Retrieving data from data provider.
Quitting from lines 252-254 (hddtools_vignette.Rmd) 
Error: processing vignette 'hddtools_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: viridis

---------------------
Welcome to heatmaply version 0.7.0
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(heatmaply))
---------------------

Quitting from lines 83-85 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hgam.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HierO.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/highriskzone.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiPLARM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hiPOD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hoardeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/homals.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HomoPolymer.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/humarray.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HUM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyCalculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hypervolume.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iBUGS.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   7.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iClick.Rcheck/00install.out’ for details.
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> #data("returnsDaily24")
> #y=returnsDaily24[,c(1,5)]
> 
> ## Simulation data
> dat=rnorm(100,5,1)
> y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ICS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1><bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1>
                                                  <bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^S<a7><8d>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <c3>^^PB\<be>
            |<f9>Ǐ^^_<86>a<80>H!D&<93>A7|^^Z<86>a<9a>&c<8c>1<b6><b9><b9>9::jYV&<93>i<e3>z^^O<e0>իWM-+++{{{<bd>X<eb>d^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 cB<88><ef><9e>^^W<c4><e3>Q<c6>^^L<c7><f9>O2^^Yk^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because US-Engineering-Weather-Map.Rmd appears to be an R Markdown v2 document.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ifa.Rcheck/00install.out’ for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  14.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ilc.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs     13.2Mb
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Missing link or links in documentation object 'ask.user.yn.question.Rd':
  ‘winDialog’

Missing link or links in documentation object 'check.for.updates.R.Rd':
  ‘winDialog’

Missing link or links in documentation object 'installr.Rd':
  ‘winDialog’

Missing link or links in documentation object 'os.manage.Rd':
  ‘winDialog’

Missing link or links in documentation object 'updateR.Rd':
  ‘winDialog’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred QSPRpred-class
> 
> ### ** Examples
> 
> data(qspr.data)
> smis <- paste(qspr.data[,1])
> ty <- qspr.data[,c(2,5)]
> trainidx <- sample(1:nrow(qspr.data), 5000)
> testidx <- (1:nrow(qspr.data))[-trainidx][1:100]
> 
> data(qsprpred_EG_5k) 
> ## same as run => qsprpred_EG_5k <- 
> 
> #-----arguments
> #smis: SMILES string set (character vector) for training
> #y: property sets (matrix) for training  
> #v_ymin: minimum value of target properties
> #v_ymax: maximum value of target properties
> #v_descriptor: function transforming SMILES strings to feature matrix 
> #v_fpnames: character vectors indicating finger print used in the descriptor
> #w0: matrix representing prior mean of coeffients in linear regression model
> #V0_inv: matrix representing the prior variance of coeffients in linear regression model
> #a0: numeric value representing the location parameter in gamma prior 
> #b0: numeric value representing the shape parameter in gamma prior 
> #------
> 
> predictions <- qsprpred_EG_5k$qspr_predx(smis[testidx])  

get fingerprint graph from SMILES strings          
Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;",  : 
  RcallMethod: cannot determine object class
Calls: <Anonymous> ... get.smiles.parser -> .get.chem.object.builder -> .jcall -> .External
Execution halted
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
  input string 443 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 451 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 452 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 460 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<b6>m<cb><f6><81>^^?<c9>?<e5><cc>B^^H<<c4><ef><f0>؞p<b9><cb>~<a6>i~<f3><cd>7<bf><fc><f2><8b>i<9a><86>a\<bf>
                                                  ~]<d7>u<<b7>m<bb>P(<88>^^V<b2>٬a^^X<d8><df><f4><f4><f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<fd><f6><db><fe><9b>xud^^Lݼy<b3>'a<d6>u]Q^^T<f9><a7>a^^X?<fd><f4><93><a2>(<f1>x\^^H
                                                  <f1><e5><97>_^<bb>vm~~~gg<e7><d7>_^^?<9d><9d><9d>5^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<e6>y<fe><fc>y2<99><f4></<99>L<86><a3>^^E^^L,<95>J<9f>^^?<fe><b9><e3>8<99>L<e6>,<c8><eb>^^W\p
                                                  <dd>^^[<90><d7><cf>8<96><e5>4MS<d7>u<c6><d8><c2><c2><c2><d8><d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
l.19 ...	]<d7>^^AJ^^R<89>D<b3>ٔ<f3><ef><ef><ef>g<b3><d9>J<a5><92><cd>f^^AP8<e7><e5><b2>_(d\^^W
                                                  <97>})<f6>^^@<ca>)D<84>^^_<be><bf><f3><d3>O<8d>7ޘ<e6><fc>2...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.24 <9e>^^P<91>g}}
             ^^]<d8>^^_^^A<8d><88>^^TEY^^<ae><d5>j<e8>^^Z<db><dc><dc>l6<9b>2<b7>B
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 424 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 442 is invalid in this locale
Execution halted
Error in re-building vignettes:
  ...
 1: .Call(rmd_b64encode_data, readBin(inFile, "raw", n = fileSize))
 2: paste("data:", mime::guess_type(inFile), ";base64,", .Call(rmd_b64encode_data,     readBin(inFile, "raw", n = fileSize)), sep = "")
 3: .b64EncodeFile(inFile)
 4: sub(src, .b64EncodeFile(inFile), imgSrc, fixed = TRUE)
 5: FUN(X[[i]], ...)
 6: lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc)
 7: unlist(lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc))
 8: .b64EncodeImages(ret)
 9: eval(expr, envir, enclos)
10: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
11: eval(expr, envir, enclos)
12: eval(expr, p)
13: eval.parent(substitute(eval(quote(expr), envir)))
14: local({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)})
15: markdown::markdownToHTML(out, output, encoding = encoding, ...)
16: knit2html(..., force_v1 = TRUE)
17: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet,     envir = globalenv())
18: vweave(...)
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: buildVignettes(dir = "/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Jdmbs.Rcheck/vign_test/Jdmbs")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
File ‘jointDiag/libs/jointDiag.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘jedi.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Invalid MIT-MAGIC-COOKIE-1 keyStartKappa: no visible global function definition for ‘read.csv’
StartKappa: no visible global function definition for ‘na.omit’
StartKappa: no visible global function definition for ‘write.csv2’
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Kernelheaping.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?<ec>dc'U<a5>^^N-.u<ba><b2><bb>E<b8><88>e<a3>V^^P<b0>!<dd>^^F<ab><84>^ғo=<e4><a4><d0>C^^O=<e5>VBo<f9>^^C^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...<f7>}^^Lb<9a>f<9c>5<9f><b8>~<fd>zL<f2><d6><d6><d6>^^XcCCC+++^^_|<f0><c1><fa><fa>z6<9b>}
                                                  <f0><e0><c1><e8><e8><a8><e7>yO<9e><<f1><<8f><88><d2><e9><f4><da><da><da>ŋ^^W...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.17 ...O<9e><<f1><<8f><88><d2><e9><f4><da><da
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KernSmoothIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmlShape.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 100 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 b<84><bd><a5>?^^T<9a>[<c1><bf><a0>^^?Ls^<85><e2>^^_Ћ^^E<a5>$<87>6v<91>\B
                                               <a6><ea><90>[q<d9>M<e8>E^^R<bf><87>^^O>&<ab><8d>k<a2>&<b5><fb>9<88>;...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 ^^YIN<ac><a5>^^[\<8a>
                 sY<cc>Q<d7>'<db>a^^P^^Dggg<c9>d^^R<8a>M$^^R<f9>|<9e>u^^N<e3>D<8e><87><8d><9c>ե+_)U,^^Vi<94>^^VB5<98>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.22 ...<88>H<b7>L<a5>^^T<8b>^^A/m<8d><d0><ed>v<85>^^P<be><ef><f3>O^^W<8b>E6㩘<99>',<9a><ca>\<de>
     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc            1.0Mb
    libs          10.3Mb
    testdata       1.9Mb
    vignettedata   2.0Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.7Mb
    libs      4.0Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'an_introduction_to_lifecontingencies_package.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           [E^^Z<ff><b0><9b><8d>_q<de><f3><90>n0i^^S<9b><d1>^^VXj^^RKO<da>C^^Q<b8>R}^^B<a9> V9<ad><c4>	<e5>Ω7đ^^^<b8>p<b4>8TB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.15 ...<93><b6><f1><f8><bd><ba><c9>k<da><d8>{<f8>mF&<ff><9c><b4>	M<b2><fe>)zz^^?f<e6><cd><f7><e6><9b><ef><fb>}ߌ<f3>\<ab>
                                                  բ<a3>߳<ee><c0><fe><a2>+<de>aFW<bc>Ì<ae>x<87>^^Y]<f1>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...+<de>aFW<bc>Ì<ae>x<87>^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Package which this enhances but not available for checking: ‘reactR’
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs      18.6Mb
    testdata   1.5Mb
Error in re-building vignettes:
  ...
  input string 785 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmer.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Mh
           ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...F<a0><ba>v<ed>Zggg<ad>V{<fd><fa>5^^Q9<8e>388866<a6><94><8a><e3>^^X<fd>^^]<c7><c1><83><ae>^
                                                  <bd><9a>J<a5>l<db>v^^\^^G<9f>J<a9><87>^^O^^_<c6>q|...
! Extra }, or forgotten $.
l.17 Ԓ<da>[}
          <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
I've deleted a group-closing 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error: has.localsolver(ls.path) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'localsolver.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because localsolver.Rmd appears to be an R Markdown v2 document.
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.mode.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 442 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'logcondens.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...[<f8><f8>㏻~8<9d>NC^^\<cb>d2<ba><ae>^^SB><fd><f4>ӑ<91>^^Q!D&<93><f9>ꫯ<de>}
                                                  <f7><dd>vڙ<9d><9d><b5>,˲,<ce><f9><d7>_^^?=11^^Aa...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.23 ...<aa>mۚ<a6>I<bb>b<8c><fd><fa><eb><af><c8>e<99><aa><aa><c2>-If<c6>X4^^Z-<97>ˊ<a2>p<ce>UU<a5><94>z<bd>^
                                                  7<c9>^^O<91><a3><92><f3><f0><95><c1><be><bb><a7><bf><8c><e8>^^@^<a1>PP^...
! You can't use `\spacefactor' in math mode.
\@ ->\spacefactor 
                  \@m 
l.24 ...<aa><aa>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/longitudinalData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LOST.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyTOS2D: no visible global function definition for ‘medpolish’
countTextures: no visible global function definition for ‘medpolish’
plot.imageQT: no visible global function definition for ‘segments’
simTexture: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Maeswrap.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  15.0Mb
objc[22618]: Class GNotificationCenterDelegate is implemented in both /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/magick.Rcheck/magick/libs/magick.so and /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rsvg/libs/rsvg.so. One of the two will be used. Which one is undefined.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotcc924daff2c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotcc924daff2c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot2004ddf08f6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2004ddf08f6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Missing or unexported object: ‘leaflet::addScaleBar’
Unexported object imported by a ':::' call: ‘leaflet:::getMapData’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   4.3Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
File ‘medSTC/libs/medSTC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘medstc/medstc.o’, ‘medstc/corpus.o’,
      ‘svmlight/svm_common.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘medstc/corpus.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mefa.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 <f0>F<b6>9<dc> <9d>N˗<b9>\N
                  <b6>?<<af><9c><a5>)^^EZ<f4>^^X<d2><e9>t*<95><9a><99><99><91>k<d2>u]<ae><fb><97>_~<f9><f0><c3>^^O
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 Ðmt]<c7><ca>._<be>\<ab>
                 <d5>^^Xc<8c><b1><a9><a9><a9>t:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...^^L^^Yc<ba><ae><e3>^^Fs^^R<b3>w-g'S^^SӒN<a7>Og^^]OBG\^^O
                                                  <ba><ca><d9><c9>t^^Z<b8>^^G<82><a7>w<e9>ҥH$R<a9>T<e2><f1><f8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.27 ...]<e6>^^D<cf><d9>lvhh<c8>u]<c8><c4>u<dd>۷o<ef><ec><ec><c4>b<b1>L&S<af><d7>^^]<c7><e9><ef><ef><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyworkspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MergeGUI.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
Package required and available but unsuitable version: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetSizeR.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MFHD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MicroStrategyR.Rcheck/00install.out’ for details.
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘miniGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeWidgetCmd
> ### Title: R functions to build a GUI window
> ### Aliases: makeWidgetCmd
> ### Keywords: utilities misc
> 
> ### ** Examples
> 
>   require(tcltk)
>   ##
>   ##  a simple example
>   ## 
>   g <- function(a=1,b=rnorm) {cat("--g--");paste("g(a,b)=",a+b(a))}
>   h <- function(a=1,b=3,c=3) {cat("--h--");paste("h(a,b,c)=",a+b+c)}
>   ## create functions
>   gg <- makeWidgetCmd("Hay it is g !!",g,GRAB=FALSE)
>   hh <- makeWidgetCmd("Hay h here !!",h,GRAB=FALSE)
>   ## calling them
>   gg()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: gg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required package: tkrplot
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Invalid MIT-MAGIC-COOKIE-1 keyWarning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘BRugs’

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlDNA.Rcheck/00install.out’ for details.
Running examples in ‘mlr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotFilterValues
> ### Title: Plot filter values using ggplot2.
> ### Aliases: plotFilterValues
> 
> ### ** Examples
> 
> fv = generateFilterValuesData(iris.task, method = "chi.squared")
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: generateFilterValuesData ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  17: .jnew("weka/core/Attribute", attname[i])
  
  testthat results ================================================================
  OK: 2388 SKIPPED: 2 FAILED: 6
  1. Error: clustering performance (@test_base_clustering.R#16) 
  2. Error: clustering performance with missing clusters (@test_base_clustering.R#28) 
  3. Error: clustering resample (@test_base_clustering.R#42) 
  4. Error: clustering benchmark (@test_base_clustering.R#55) 
  5. Error: clustering tune (@test_base_clustering.R#72) 
  6. Error: check measure calculations (@test_base_measures.R#187) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:mlt':

    coef<-

This is mgcv 1.8-16. For overview type 'help("mgcv-package")'.

Attaching package: 'mgcv'

The following object is masked from 'package:nnet':

    multinom


Re-fitting to get Hessian


Re-fitting to get Hessian


Re-fitting to get Hessian

Quitting from lines 2519-2527 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
NAs are not allowed in subscripted assignments
Execution halted
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...2^^F<e2><f5>2^^F<e2><f5>2<9e>m񤔏<bd>TJ<f1><cd>t:<dd>V<ad><c3><e3><96>eI)q<ff><e0>S<b9>\<ce>
                                                  ^^?<93><ab>^^U<8b>E^^?5<a5>^^T^^Z<f1>w<e3><b1>x...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>¯l^^S<d2><ff><e0><c1>^^V<b8>p<f0><92><db><d9><da>ڪxxR<b3><a8>ӹ<e7><dd><c9>	~^^RQ<b9>\<fe>
                                                  <ec><b3><cf><c0>7"<92>R~<f7><dd>w<df>|<f3><cd>G^^_}t<fd><fa>u<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 <84>L<a7>Ӧi<82><a5>^^_~<f8><e1><b5>k<d7>r<b9><9c>a^^XB^^H"<ca>f<b3>^^W.\^^X
                                             ^^Y^^Y<d1>4
The control sequence at the end of the top line
of your error message w
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monogeneaGM.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 872 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o<db>F^^V^^?<96>[<cb>,^^RSD<82><ae><e2>]F^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 ...<cd><cd>o<be><f9><a6><c7><d4><fd>s<a6><d5><d5><d5>Z<ad>vD<83>^^G^^O^^^<9c><df><e8>c<fe>(<de>^^[\^^Z
                                                  r<f1><c6><ef>ܹs<ac>^^N<b7>o߾|<f9>r.<97>^^[^^_...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ..._<8f>F<a3><cb><cb>ˏ^^^=<92>eY^^P<84><c3><da>3Ʈ_<bf><9e><cd>f<af>_<bf><8e>[۶u]WUu}
                                                  }<bd>\.<a7>R)4VUUQ<94>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘mph/libs/mph.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mph.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mph.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mra.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
  4. check_translations() works (@test.R#73) - running msgfmt on file1277c49983631 failed
  
  5. check_translations() works (@test.R#73) - running msgfmt on file1277c280df0b6 failed
  
  Failed -------------------------------------------------------------------------
  1. Failure: check_for_gettext() works (@test.R#4) ------------------------------
  check_for_gettext() isn't true.
  
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msir.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MSQC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mtk.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyDesigner.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyNote: found 2 marked UTF-8 strings
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pgirmess’
Error in re-building vignettes:
  ...
  input string 414 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multgee.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 "M\<cd>
         U[<a1>Ffa<89>^^]<ea><86>^^?!<a8>ˮ<ba>E<dd><f1>^^WT<ed><be>^^R<92>%<a4>f<c1><a2>^^Y<a9>1^^QT<89>^^Xն<d2>^^T<df><ca>Gc<dc>`L<89>O<...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^D^^B<cd>fSI|<f2>H^^?<<97>J<a5>X,<86>i<eb><f5><ba><ea>LD<b9>\n
                                      ||<9c>1<96><cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}<e7>3wO<ff><df><e0><84>lx<cb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...<cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   1.8Mb
    libs       2.7Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 218-223 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
unused argument (prsep = "")
Execution halted
Error in re-building vignettes:
  ...
  input string 305 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 306 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 307 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch-Errata.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyconceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyplot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.nblast.Rcheck/00install.out’ for details.
Running examples in ‘nat.nblast-Ex.R’ failed
The error most likely occurred in:

> ### Name: nblast
> ### Title: Calculate similarity score for neuron morphologies
> ### Aliases: nblast
> 
> ### ** Examples
> 
> # load sample Kenyon cell data from nat package
> data(kcs20, package='nat')
> # search one neuron against all neurons
> scores=nblast(kcs20[['GadMARCM-F000142_seg002']], kcs20)
> # scores from best to worst, top hit is of course same neuron
> sort(scores, decreasing = TRUE)
GadMARCM-F000142_seg002 ChaMARCM-F000586_seg002 GadMARCM-F000423_seg001 
              4043.1766               1914.8224               1772.8506 
GadMARCM-F000442_seg002 FruMARCM-M000115_seg001 FruMARCM-F000085_seg001 
              1007.4565                853.8108                713.2106 
FruMARCM-F001929_seg001 FruMARCM-F001494_seg002 GadMARCM-F000050_seg001 
               604.4071                481.4737                480.4146 
GadMARCM-F000071_seg001 FruMARCM-M001339_seg001 FruMARCM-F000188_seg001 
               448.1516                433.9340                404.0470 
GadMARCM-F000476_seg001 FruMARCM-F000270_seg001 FruMARCM-F000706_seg001 
               313.2021                254.7516                204.2116 
FruMARCM-M000842_seg002 FruMARCM-M001051_seg002 FruMARCM-M001205_seg002 
               196.4543                140.8164               -251.4999 
GadMARCM-F000122_seg001 FruMARCM-F001115_seg002 
              -262.2352               -520.2581 
> hist(scores, breaks=25, col='grey')
> abline(v=1500, col='red')
> 
> # plot query neuron
> open3d()
null 
   1 
> # plot top 3 hits (including self match with thicker lines)
> plot3d(kcs20[which(sort(scores, decreasing = TRUE)>1500)], lwd=c(3,1,1))
Error in xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  : 
  'x' is a list, but does not have components 'x', 'y'  and 'z'
Calls: plot3d -> plot3d.default -> xyz.coords
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because NBLAST-Clustering.Rmd appears to be an R Markdown v2 document.
Invalid MIT-MAGIC-COOKIE-1 keyQuitting from lines 56-59 (NBLAST-Clustering.Rmd) 
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x', 'y'  and 'z'
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.templatebrains.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NeatMap.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keydata.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘KEGG.db’
Running examples in ‘netClass-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv.aep
> ### Title: Cross validation for aepSVM (aepSVM)
> ### Aliases: cv.aep
> ### Keywords: aep
> 
> ### ** Examples
> 
> library(netClass)
> data(expr)
> data(ad.matrix)
> x <- expr$genes
> y <- expr$y
> 
>  library(KEGG.db)
Error in library(KEGG.db) : there is no package called ‘KEGG.db’
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘network-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.paj
> ### Title: Read a Pajek Project or Network File and Convert to an R
> ###   'Network' Object
> ### Aliases: read.paj read.paj.simplify switchArcDirection
> ###   readAndVectorizeLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> require(network)
> 
> par(mfrow=c(2,2))
> 
> test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
Warning in file(file, "rt") :
  cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net': HTTP status was '0 (null)'
Error in file(file, "rt") : cannot open the connection
Calls: read.paj -> file
Execution halted
Running the tests in ‘tests/read.paj_tests.R’ failed.
Last 13 lines of output:
  > 
  > 
  > 
  > # this file has character encoding issues
  > scotland<-tempfile('scotland',fileext='.zip')
  > download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',scotland)
  trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  Error in download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  : 
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  In addition: Warning message:
  In download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  :
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip': HTTP status was '0 (null)'
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neuroim.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              2.4Mb
    classic-bugs   1.5Mb
    include        3.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because trees_with_root_edge.Rmd appears to be an R Markdown v2 document.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) It seems you should call rmarkdown::render() instead of knitr::knit2html() because vignette_get_nltt_values.Rmd appears to be an R Markdown v2 document.
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nmcdr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Running examples in ‘NoiseFiltersR-Ex.R’ failed
The error most likely occurred in:

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: EF ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 190-198 (NoiseFiltersR.Rnw) 
Error: processing vignette 'NoiseFiltersR.Rnw' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nonlinearTseries.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/norm2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NPCirc.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OceanView.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/oc.Rcheck/00install.out’ for details.
installed size is 74.2Mb
  sub-directories of 1Mb or more:
    libs  73.9Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 359 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^^G0X<b9>To<98><e5>R<bd>a<96>K<f5><86>Y.<d5>^^[f<b9>To<98><e5>o<af><9e>^^PB^^H<d1><fd>^
                                                  J)<84><98><9b><9b><8b>~<ed>.|૪<db>]<a5><bb><97>R<a9>$:^^R...
! Undefined control sequence.
l.16 ...A<a0><9e><89>h@^^Z<9e>^^]s<c2>J^^C<b5>U<b7>\:<86>a<96>><cc>Y*<95><ce>f^^\/"<b9>\<ee>
                                                  y<80><bf><e0><e0>^^\<b8><df>SR*<95><a4><94>o<be><f9><e6><f8><f8>x<b3><d9>L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...a<9a><e6><d6>֖<aa><8e>q^^_Ѝs<ce>^^XS<9b><84> ^^H0^^W<f8><9a><c9>d<80>|h"<a5>\YY
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ontologySimilarity-GO-example.Rmd appears to be an R Markdown v2 document.
Quitting from lines 46-49 (ontologySimilarity-GO-example.Rmd) 
Error: processing vignette 'ontologySimilarity-GO-example.Rmd' failed with diagnostics:
could not find function "intersection_with_descendants"
Execution halted
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Missing or unexported object: ‘mlr::makePrediction’
Running examples in ‘OOBCurve-Ex.R’ failed
The error most likely occurred in:

> ### Name: OOBCurve
> ### Title: Out of Bag Learning curve
> ### Aliases: OOBCurve
> 
> ### ** Examples
> 
> library(ranger)
> library(randomForest)
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

The following object is masked from ‘package:ranger’:

    importance

The following object is masked from ‘package:ggplot2’:

    margin

> 
> # Classification
> data = getTaskData(sonar.task)
> mod = ranger(Class ~., data = data, num.trees = 100, keep.inbag = TRUE)
> 
> # Alternatively use randomForest
> # mod = randomForest(Class ~., data = data, ntree = 100, keep.inbag = TRUE)
> # Alternatively use train of mlr
> # mod = train(makeLearner("classif.ranger", keep.inbag = TRUE), sonar.task)
> 
> # Application of the main function
> results = OOBCurve(mod, measures = list(mmce, auc, brier), task = sonar.task, data = data)
Error: 'makePrediction' is not an exported object from 'namespace:mlr'
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: setHyperPars2.Learner(learner, insert(par.vals, args))
  7: stop(msg)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 5
  1. Error: classification ranger (@test_base.R#12) 
  2. Error: regression ranger (@test_base.R#25) 
  3. Error: classification randomForest (@test_base.R#40) 
  4. Error: regression randomForest (@test_base.R#53) 
  5. Error: trained model with mlr (@test_base.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenCL.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘mlr’

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 121.1Mb
  sub-directories of 1Mb or more:
    libs    113.3Mb
    models    4.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/optBiomarker.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyavg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘org.At.tair.db’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      2.8Mb
Error in re-building vignettes:
  ...
sh: rst2pdf: command not found
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
conversion by rst2pdf failed!
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IsoGene’
Invalid MIT-MAGIC-COOKIE-1 keygenRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 411 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dicom.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Al
           ^^SG^^W~<b1><89><cc>V<c2><de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9r<ab>P%<84>^^O<95>"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9
                                                  r<ab>P%<84>^^O<95>".(>`YTj<a4>^^U<b6><eb>?-<b4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<83>/<be><f8>b^^O<8b>^^\<f0><d8><eb>61l^^W@y.<97>K<a5>R<d9>l<f6>ȑ#sss<b9>\nzz
                                                  :^^H<d9>B<88>d2^^Y<bc>Q<e5>+<df><f7><a3>Ѩi<9a>B^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nifti.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^FD^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\<cd>k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^F
                                           D^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...!^^Dc^^L<f7>s<b9><dc><ce><ce>N<a5>Ry<fb><f6>-c^^L<8f>8<e7><9c><f3><e1><e1>aιl"[	!\<d7>
                                                  
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 !<96><96><96><aa><d5><ea><eb>ׯ?|<f8>^^@<af>ptW<b9>\<ae>
   
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running the tests in ‘tests/regtest-party.R’ failed.
Last 13 lines of output:
  > fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
  > pfit <- as.party(fit)
  > all(predict(pfit, newdata = kyphosis, type = "node") == fit$where)
  [1] TRUE
  > 
  > ## J48: iris data
  > library("RWeka")
  > data("iris", package = "datasets")
  > itree <- J48(Species ~ ., data = iris)
  Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
  Calls: J48 ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
  Execution halted
Errors in running code in vignettes:
when running code in ‘constparty.Rnw’
  ...
       8 0.5408163 0.4591837
       9 0.0729927 0.9270073

> library("RWeka")

> (j48 <- J48(Survived ~ ., data = ttnc))

  When sourcing ‘constparty.R’:
Error: java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid

Error: processing vignette 'constparty.Rnw' failed with diagnostics:
 chunk 10 (label = J48) 
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 419 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'party.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 !8<e7>hV*<95>p]<ad>V?<ff><fc><f3><f9><f9><f9>R<a9><84>^^A<a5>^^X<ed>v<fb><f2><e5><cb>B^^H!D<b9>\<fe>
                                                <f2><cb>/?<f9><e4><93>J<a5>r<e3><c6>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...^Uc,^^H^^B<c3>0<a0><<e7><e6><e6>*<95><ca><f8><f8><f8>G^^_}<d4>^^Oϧ|<ef><8d>}<f6><d9>g}
                                                  6<c5><fb>^^SB<f8><be><df>n<b7><a1>֛<cd>f*<95><8a><e3>xcc<a3><db>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

Depends: includes the non-default packages:
  ‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Errors in running code in vignettes:
when running code in ‘pathClass.rnw’
  ...

    union

Loading required package: lpSolve

> library(golubEsets)

  When sourcing ‘pathClass.R’:
Error: there is no package called ‘golubEsets’
Execution halted
Error in re-building vignettes:
  ...

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:BiocGenerics’:

    normalize, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘kinship2’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘rootSolve’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
   .C("powerR", as.integer(numOffspring), as.integer(numParents), 
       as.integer(numFamilies), as.integer(additionalOffspringPhenos), 
       as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest), 
       as.double(afreqMarker), as.double(penAA), as.double(penAB), 
       as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower), 
       as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele), 
       as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset), 
       as.integer(numSim), as.integer(ITERATION_KILLER), result, 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

Package which this enhances but not available for checking: ‘pmclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdPROF.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘pbdMPI’ ‘pbdCS’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdRPC’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
Running examples in ‘PBSmodelling-Ex.R’ failed
The error most likely occurred in:

> ### Name: PBSoptions-class
> ### Title: S4: Project Options Class
> ### Aliases: PBSoptions-class print,PBSoptions-method
> ###   show,PBSoptions-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> local(envir=.PBSmodEnv,expr={
+   #initialize an option manager with a single logical option
+   .mypkg <- new( "PBSoptions", filename="my_pkg.txt", 
+     initial.options=list( sillyhatday=FALSE ) )
+ 
+   #retrieving an option
+   silly <- getOptions( .mypkg, "sillyhatday" )
+   cat( "today is", ifelse( silly, "silly hat day!", "monday" ), "\n" )
+ 
+   #set an option
+   setOptions( .mypkg, sillyhatday = TRUE, photos = "/shares/silly_hat_photos" )
+ 
+   #create a GUI which works with options
+   createWin( c( 
+     "check name=optionsillyhatday text=\"silly hat day\"",
+     "entry name=optionphotos width=22 mode=character label=\"photos directory\"",
+     "button func=doAction text=save action=saveOptionsGUI(.mypkg)" ), astext = TRUE )
+ 
+   #update GUI values based on values stored in .mypkg's options
+   loadOptionsGUI( .mypkg )
+   print(getOptions( .mypkg ))
+ })
today is monday 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "tk_setPalette".
Calls: local ... eval -> eval -> createWin -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   6.1Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pcse.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<cb>^^RB^^X<86><c1>^^X#<a2><a5><a5><a5><8f>^^_?r<ce>s<b9>^^\<e7>|ee<e5><fa><f5><eb><8c>1\<cd>
                                                  f<b3><85>BA<8e><8a>1v<ef>޽^^NC?<e8>E<96><97><97><8f>o0?...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<ba><ae>^^GA^^@<ad><a8><e5>gu<af>^^^O<e0><d4>4<ad>M7EQ<a4>n^^X^^AΣ<a5>\ZXW
                                                  <9a><a6><95><cb>eιi<9a><ae><eb>b<b8><8e><e3>^^DA<c0>9<c7>^^B^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...b<b8><8e><e3>^^DA<c0>9<c7>^^B^^VB^^@<ae><ae><eb>B7<c3>0<e2><f1>8<b6>^^G<d7>uGFF\<d7>
                                                  E?݌<f9><ac><c0><f9><8d>0j^^O<e0>^^D~<a8>5u<98>^^\...
The control sequence at the end of
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘pedantics/libs/pedantics.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘pedantics.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘georob’ ‘spsurvey’
Packages unavailable to check Rd xrefs: ‘spsurvey’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

infoImage: no visible global function definition for ‘quantile’
markPoisson: no visible global function definition for ‘runif’
markPoisson: no visible global function definition for ‘flush.console’
phantom : model: missing arguments not allowed in calls to ‘c’
readData: no visible global function definition for ‘read.table’
readData: no visible global function definition for ‘read.image’
readSifData: no visible global function definition for ‘flush.console’
viewData: no visible global function definition for ‘gray’
viewData: no visible global function definition for ‘dev.cur’
viewData: no visible global function definition for ‘dev.set’
viewData: no visible global function definition for ‘X11’
viewData: no visible global function definition for ‘par’
viewData: no visible global function definition for ‘image’
viewData: no visible global function definition for ‘title’
writeData: no visible global function definition for ‘write.table’
writeData: no visible global function definition for ‘make.image’
writeData: no visible global function definition for ‘write.image’
Undefined global functions or variables:
  X11 dev.cur dev.set flush.console gray image make.image par quantile
  read.image read.table runif title write.image write.table
Consider adding
  importFrom("grDevices", "X11", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "image", "par", "title")
  importFrom("stats", "quantile", "runif")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
File ‘PET/libs/PET.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘misc.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘art.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘art.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pgam/libs/pgam.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘pgam.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pi0.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
Package required and available but unsuitable version: ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/playwith.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plot3Drgl.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘GSIF’ ‘gdalUtils’
Errors in running code in vignettes:
when running code in ‘jss1079.Rnw’
  ...
+ }
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

  When sourcing ‘jss1079.R’:
Error: trying to use CRAN without setting a mirror
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gstat
Loading required package: raster
Loading required package: sp
Loading required package: plotKML
plotKML version 0.5-6 (2016-05-02)
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 1 
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plsRcox.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         return(val)
     }, finally = options(warn = oldWarn))
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: private$errorHandler(req, res, e)
  
  testthat results ================================================================
  OK: 220 SKIPPED: 0 FAILED: 1
  1. Error: Includes work (@test-include.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in treedata(phy, dat) :
  The following tips were not found in 'data' and were dropped from 'phy':
	olivacea
Warning in treedata(phy, dat) :
  The following tips were not found in 'data' and were dropped from 'phy':
	olivacea

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pmg.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘polmineR.sampleCorpus’ ‘rcqp’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘sw.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'd_jss_paper.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...R,<89><ad>qI^J<a6>^^NT^^B<81>^^U6^^P<ac><f8><a5>^^O<c5>}n!<d4>^^O}
                                                  (<ec>e~h<fb>TJMa/3dx<b0>U^^O<83>b<b5>H^^Q...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<ec><e8>ڎ<e4>V<8a>~^^Xsu<ee>9<e7><9e><ef>~<df><f9><fe><9d><ef>v^^Y<86>^^A<ed><cb><f7><bd><80><e6><a2>C^
                                                  +<a3>C^+<a3>C^+<a3><cd>ɳ5d^^VJ)<e7><bc>!S^^...
! Extra }, or forgotten $.
l.15 ...<93>MXp<c3>`B<9e>^^?[<eb>1v<ff><f8><e7><a5>^^?W6^^?q<f9>'<d7>T<d7>i<d8><d4>7<bf>]<88><ad>}
                  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyfnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’ ‘org.Pt.eg.db’
  ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mm.eg.db’
  ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rosm’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/prim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because PRISMA.Rmd appears to be an R Markdown v2 document.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PropClust.Rcheck/00install.out’ for details.
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'countreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <c4><eb>g^^Z<88><d7><cf>4^^P<af><9f>i <de>^^Q^^RB^^H!<8e>ޗR<aa><eb>B<a1><80>1RJ\<e0>
                                                o<b5>Z
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 \K
       ?<d3><f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^<ad>V766^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^
         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Error in re-building vignettes:
  ...
  input string 401 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 409 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 410 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 418 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'raschmix.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 <82>`ss3<97>˹<ae><9b>L&^^Q<85>^^PQ<b9>\<9e>
                            <99><99><b1>,+<9d>N<c3><ee><a3>?^^H<82><bd><bd>=vhRJ<c4>.<9e><e7><e5>r<b9>C<93><f3><f8>X,<86><c9>^^]ǉ^^N;rN...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...<b3><a8>nC!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6>
                                                  <d4>\<9e><9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>///<c7><e3>qM<d3>\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...C!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6><d4>\<9e>
                                                  <9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>//
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qpcR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyMHbi2: no visible global function definition for ‘runif’
QRLMM: no visible binding for global variable ‘D’
QRLMM: no visible global function definition for ‘par’
QRLMM: no visible global function definition for ‘plot.ts’
QRLMM: no visible global function definition for ‘abline’
QRLMM: no visible global function definition for ‘qnorm’
QRLMM: no visible global function definition for ‘plot’
QRLMM: no visible global function definition for ‘axis’
QRLMM: no visible global function definition for ‘polygon’
QRLMM: no visible global function definition for ‘lines’
QRLMM: no visible global function definition for ‘smooth.spline’
QRLMM: no visible global function definition for ‘title’
QSAEM_COM_7: no visible global function definition for ‘pnorm’
grid_example: no visible global function definition for ‘par’
grid_example: no visible global function definition for ‘smooth.spline’
grid_example: no visible global function definition for ‘plot’
grid_example: no visible global function definition for ‘axis’
grid_example: no visible global function definition for ‘polygon’
grid_example: no visible global function definition for ‘lines’
grid_example: no visible global function definition for ‘abline’
grid_example: no visible global function definition for ‘title’
rALD: no visible global function definition for ‘runif’
Undefined global functions or variables:
  D abline axis lines par plot plot.ts pnorm polygon qnorm runif
  smooth.spline title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "polygon", "title")
  importFrom("stats", "D", "plot.ts", "pnorm", "qnorm", "runif",
             "smooth.spline")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qrmtools.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtlc.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/QuantifQuantile.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 430 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quantspec.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.21 ...[L=^^X^^L^^F<83>A<8e>Pض],^^V5M<b3>,<8b>]X0#<a5><c4>Z^^PQ<b9>\<b6>
                                                  ,+^^R<89>X<96><c5>^^A<8e>6<e9>E?{^^\e<e9>N^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...A<8e>6<e9>E?{^^\e<e9>N^^Nu^^V<8c><b0>,<8b><88>fff<d2><e9><b4>^^[c<a8>`<db>v<b9>\<8e>
                                                  D"<8c>Ir!VUU<80>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 <a7>ޭ^^@<89>^^H<be>ҹ<b0>^^G<ca><e5>rSSS<b9>\<8e>
                               <88><e0>^^VY<96>utt4<<^^\^^L^^F<a5><94>^<af>^^W^^F4/^^G<e4>!<f7><80>r0<ef>>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 ...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.5Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Release.Rmd appears to be an R Markdown v2 document.
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Use_case.Rmd appears to be an R Markdown v2 document.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 141-142 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2GUESS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\AL
           ^^[W^^S^^^^^L^^FL<8c><97><a7>^^R0N^^V̪nCq<8d><cb>V<88> ^^Q~UT<ad><9a>*<f4><92>S<a2><f6>ƥ<97><f6><94>^^^<a3>ޫ^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ...Tf<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}
                                                  }<bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.18 ...f<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}}
                                                  <bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^^...
I've deleted a 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2STATS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 ...^L^^L<e8><ba>N^^Hq8^^\8<ad><c7><e3>Y\\,^^V<8b><9d><9d><9d>o<bf><fd><b6>In^^O\<cb>
                                                  <b3>^^H<e3>o<^^^<a7><ba>gf^^H<f6>G,f<fe>]^^S...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<da>ڪiZOO<8f><a6>i<cb><cb><cb>^^V<8b>^^E^^@*<95>Jgg<a7><a2>(<8f>^^^=r:<9d><b9>\<ae>
                                                  V<ab><f5><f5><f5><cd><ce><ce><f6><f7><f7><ff><f6><db>o<ad><ad><ad>^^W/^^^D...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 <9d>?^^?^^^<eb>\N
                <a7>szz^^Z7^^A<ed>jqq<91><e7>yUU<91><b3>|><8f>\<86><c3>a<97>˅@^^\[^^X<86>!<84><9c>9s&<95>J<c5>b1Q^^T^^A<e0>...
The control sequence at the end of the top line
of your error message was neve
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R330.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rainbow.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAppArmor.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   9.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rase.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rggobi’ ‘RODBC’
Invalid MIT-MAGIC-COOKIE-1 key
(R:2730): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keydatgen: no visible global function definition for ‘rnorm’
optimization.IC: no visible global function definition for ‘optim’
outlier.replace: no visible global function definition for ‘qnorm’
pargen: no visible global function definition for ‘runif’
rav: no visible global function definition for ‘optim’
rav2file: no visible global function definition for ‘write.table’
standardized: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  optim qnorm rnorm runif sd write.table
Consider adding
  importFrom("stats", "optim", "qnorm", "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RBerkeley.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.2Mb
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcdk.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because RClone_qmsevpops.Rmd appears to be an R Markdown v2 document.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyenterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keycomputeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
Invalid MIT-MAGIC-COOKIE-1 keyBOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Invalid MIT-MAGIC-COOKIE-1 keyfncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keySampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
    po    2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppAPT.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.1Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs     22.5Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppEigen-Introduction.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^?^^_Q<bd>^^Y<ec>^^^<c1><d2><d2><d2><ce><ce>N<af><b0>u<88><b3>킞<b1><87><b0><b1><b1><b1><b1><b1><81>ǹ\<8e>
                                                  ^^^۶<fd><f0><e1><c3>gϞ<9d><b4><b8>ue^^O<e1><9a><dd><d3>tv...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<8e><8d><8d>!1<84>^^P<96>e<db><d2>܅<ee><e1><83>^^EAh-^^U<82>@<a5>HQ^^TT^^L\<83>
                                                  <be><9b>.C<b6>eY<c6>^^E<84>^^PUUQ<a9><e8><ab><d1>4<ad>V<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...^^W^^@Lӌ<c7><e3><8f>^^^=<9a><9a><9a><a2><95>_|4jc<ab><c4><f6><80><bd>^^N_<c1>yl`<b9>\<ee>
                                                  <c4><dc>w^^N]^^De<f9>|<de><e7><f3>i<9a>^^V<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.4Mb
    libs     11.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppOctave.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.2Mb
    libs      3.1Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 379 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...^E}۽c<86>HgI^^[]x<bb><f7>ώ<d6>a<8b>Mӄ<87><89><ac><e3><c2><c2>^^Bclnn^^N}
                                                  p<dc><c3>^^X<83><92>@g<ce>9<ec>><bc>-<c3>0|>_<ab><d5>""<c6>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.22 ...<ba><ae><b7>Z-8=<ed>v۲,8^^@^^Hm,<cb>"<a2><95><95>^^U<9f><cf><d7>n<b7><8b><c5>b8^^\^
                                                  XX "EQЧR<a9><e8><ba>.<cb>2F&<a2>b<b1>^^X^^H...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 88.2Mb
  sub-directories of 1Mb or more:
    include   4.1Mb
    lib      52.5Mb
    libs     31.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppTOML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcrypt.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot130762117424f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot130762117424f.png': No such file or directory
Quitting from lines 21-25 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing link or links in documentation object 'ClassGroups.Rd':
  ‘[rebus.unicode]{UnicodeProperty}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: ‘RODBC’ ‘RODBCext’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  11.4Mb
Invalid MIT-MAGIC-COOKIE-1 keycook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 84 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 85 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 93 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[Ok^^S<dd>^^W>o<fa><ab><b5>Pf<bc> <b1>(i<ea>l*^^H5<a5> <a5>P<c6>EvBw<ee>\<fb>
                                                 1<c4>m<bf><82>[wfe<b1><b8><b0><9b><f8>'Be ^^]<82>]^^H^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a2>J<a5>2??<af><94><9a><9e><9e><f6>}?<97><cb><d5>j5۶]<d7><c5>x!^^D^^C^^X^^Qv<b9>\<ce>
                                                  <e5>r<f8>Y<ad>V-<cb><c2><e4><fc>^^W7<c3>0<b4>,<ab><95>+0^^@...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<c7>h<b1>2O<8c><ba>u<eb>X[)^^E<ac>Ǌ<b8>ID<bb><bb><bb><90>^^V<88>ª<b0><b1>@,<cb><d0>h4\<d7>
                                                  <85>E
The control sequence at the end of the top line
of your error message was
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reshapeGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/restlos.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyGUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/retistruct.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs      100.2Mb
    pictures    1.3Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rggobi.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rgnuplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key
(R:76308): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> ### Name: gtkDfEdit
> ### Title: gtkDfEdit
> ### Aliases: gtkDfEdit [.gtkDfEdit [<-.gtkDfEdit RGtk2DfEdit
> 
> ### ** Examples
> 
>   win <- gtkWindowNew()

(R:2383): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:2383): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:2383): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 3: gtkWidgetShowAll(w)
 4: gtkWindowNew()
An irrecoverable exception occurred. R is aborting now ...
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.9Mb
    libs  14.7Mb
Invalid MIT-MAGIC-COOKIE-1 key.install_system_dependencies : <anonymous>: no visible global function
  definition for ‘unzip’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘menu’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘download.file’
as.GParamSpec: no visible global function definition for ‘new’
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because intro_rhandsontable.Rmd appears to be an R Markdown v2 document.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rhpc.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyrite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required and available but unsuitable version: ‘plumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmgarch.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmpi.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RnavGraph.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RnavGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: ng_get_color
> ### Title: Extract point coloring from an active navGraph session for a
> ###   particular data set.
> ### Aliases: ng_get_color
> 
> ### ** Examples
> 
> ## Define a NG_data object
> ng.iris <- ng_data(name = "IrisData", data = iris[,1:4])
> 
> ## start a navGraph session
> nav <- navGraph(ng.iris)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: navGraph ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Errors in running code in vignettes:
when running code in ‘RnavGraph.Rnw’
  ...
> sel <- sample(x = 1:11000, size = 600)

> p.digits <- digits[, sel]

> ng.i.digits <- ng_image_array_gray("USPS Handwritten Digits", 
+     p.digits, 16, 16, invert = TRUE, img_in_row = FALSE)

  When sourcing ‘RnavGraph.R’:
Error: [tcl] invalid command name "image".
Execution halted
Error in re-building vignettes:
  ...
    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Invalid MIT-MAGIC-COOKIE-1 keyWarning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

RnavGraph Version 0.1.8
Please read the package vignette. Use vignette("RnavGraph").


Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Img") : Tcl package 'Img' not found
Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function. Read the package vignette on how to set up tcl/tk.
Loading required package: grid

Error: processing vignette 'RnavGraph.Rnw' failed with diagnostics:
 chunk 57 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "image".

Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 82.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     79.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Error in re-building vignettes:
  ...
  input string 547 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 548 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 556 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?,<bf><ae><ba>`K^^Y^^B<89>P<ea>j<bb>PhIP<9d><ee>%<84>^^V<e5><a0>R<e8>!<b7><fc>^^C<a5><e4>_p<8f>9<94>B.=<b6>Đ<d2>^^F...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...^z^^ZrՒ^^@N8<c1><ff>r<b2>m{'<88><8e><c0>9Ȕ֥<de>?<c1><8d>~<f3><cd>7s<b9>\^^T
                                                  EP<98><87>=萃<b3><bf><dd>CD<83>B<ab>՚<9e><9e><c6>'^^QE...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 <e3><d6>n<b7><d1>^^E^^?<a5>-^^C^^U^^D<c1><cc>̌<ef><fb><b9>\^^N
                                      <f5><ad>V<cd>,˂<89>c<9e>(<97><cb>e!^^D<8f>hY<96>뺨L<9c>p^^_g<cf><f7>}^^...
The control sequence at the end of the top line
of your error message was never \def'ed. I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
File ‘robust/libs/robust.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘rb.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in S2(c(0.906882501852091, -2.27769597461744, -1.05320504986729,  : 
  could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RockFab.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RODBC.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package suggested but not available for checking: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rcanvec’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rotations.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rothermel.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpanel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpdb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycell.density.default: no visible binding for global variable
  ‘universalConstants’
conect.pdb: no visible binding for global variable ‘elements’
masses.default: no visible binding for global variable ‘elements’
toSymbols.character: no visible binding for global variable ‘elements’
toSymbols.integer: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘rgb’
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpoppler.Rcheck/00install.out’ for details.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RProtoBuf-paper.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.23 ...<a2>i^^ZVn3*<80><b0>^^X<89>^^H8<e5>ryqq<b1>^^W<d3><d2>_PV<af><d7>MӔۃ\<c9>
                                                  [<bd>^<cf>f<b3><9f>}<f6><99>i<9a><b0><ae><a0>,<93><c9>lmm<c9>w<a4>iZ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.24 ...<af><d7>q^^T^^Yc<d3><d3><d3>D<e4><fb>>^^Q<c1>^^?<f4><de><e5>^^[<a4>r<b6><a9><d6>Q<9a><f6>"<8b>e}
                                                  X<ce>|><8f><bc><f8><d0>V^^Nc^^L6
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.25 ^^AW&<93>	^^G<96>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RQuantLib.Rcheck/00install.out’ for details.
File ‘RSAgeo/libs/RSAgeo.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘RSAc.o’, ‘lib.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RSAc.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSAP.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsgcc.Rcheck/00install.out’ for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  19.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsml.Rcheck/00install.out’ for details.
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  55.5Mb
installed size is 237.6Mb
  sub-directories of 1Mb or more:
    libs  235.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘cvodes.o’, ‘sundials_cvodes.o’, ‘sundials_ida.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rsymphony.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rugarch.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RunuranGUI.Rcheck/00install.out’ for details.
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Missing or unexported object: ‘xml2::xml_find_first’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyrvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVPedigree.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RWeka.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘vcd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keycalc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sandwich-OOP.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bb>[<cf>^^VZ^^X!=<cf><cb>d2<f8><8e>TND<b5>Z<ed><83>^^O><c0> @u<ea><b2>@<ce>y<96><d7>\<bd>
                                                  ^^Q<d0>^^BT<f8><97>K<a1>P^^@q^^?Q^<f3>ػ<88>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.19 ...<ee>`0 "<c4>^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^
                                                  <bf><fe><ae>a\<95>RJ)<85><82><94>Ҷ<ed>b<b1>H<a1>^^N<8a>a^...
! Undefined control sequence.
l.19 ...^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^<bf><fe><ae>a\<95>
                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 5):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 6):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following object is masked from package:SciencesPo:

    turnout

.data was converted to a dataframe
Warning: New theme missing the following elements: axis.line.x, axis.line.y, panel.grid.major, panel.grid.minor
Quitting from lines 1090-1091 (SciencesPo.Rmd) 
Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics:
invalid 'times' argument
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SDD.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/semiArtificial.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 439 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 447 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 448 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 456 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<f4><af>i<9a>^^X<a2><94>m<db>['<8c>^^N<e9><85><de><eb><fd>ư<b0><b0><c0>^^X<b3>,<eb><e4>ɓW<ae>\1
                                                  M<f3><fe><fd><fb>W<af>^^^UB<98><a6><f9><f8><f1><e3><c9><c9>I<a5>T<bd>^<bf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^E^^\^^R<c2>^^[<fe>.,,<80>^^Y<a5><d4><e5>˗<a5><94>+++<b6>m^^S\<95>
                                           RB<88><f9><f9><f9>~<ad><a7><cf>ҋK<c4><d2>><cd><ff><8e><d9><db>o^^ZڽA<a6>=<a9>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 <82>?s<b9><94>m<bb><8d><c6><fb><9c>^^_<e5><fc>^^?^^WS<c3>0<94>R<8e><e3><cc><ce>΢^^Ec<b1>\<f2>
                                             E<a4><94><89>Db}}}bb<a2><d9>l&^^R<89>f<b3>)<84><a8>T
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 128.5Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  122.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sgPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shinyRGL.Rcheck/00install.out’ for details.
randomDAG: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smacof.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.22 ...<97><d7><de>׽<9d><f4><82><b1>~<c5><d3>u^^]R<f9><fd>~EQ8<e7>D<f4><f8><f1><e3><d5><d5>Uo3UU!9^^Q}
                                                  <f1><c5>^^W^^X<d3><c6><c6><c6><ec><ec><ec><f2><f2><f2>^^O?<fc><b0><ba><ba>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.22 ...<f5><d5>W<90>jii	<ed>!<c0><e3>Ǐ^^[<8d><c6><ed>۷!6^^Q<ed><ef><ef>omm<a9><aa><ba><b4><b4><d4><fb>h}
                                                  o0 <ca>d2<9a><a6>a<82>^^F<84>7)<de>^^E`D-Ì<be>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smint.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smoothtail.Rcheck/00install.out’ for details.
Running examples in ‘soilphysics-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitsoilwater
> ### Title: Interactive Estimation of van Genuchten's (1980) Model
> ###   Parameters
> ### Aliases: fitsoilwater
> 
> ### ** Examples
> 
> # Liu et al. (2011)
> h <- c(0.001, 50.65, 293.77, 790.14, 992.74, 5065, 10130, 15195)
> w <- c(0.5650, 0.4013, 0.2502, 0.2324, 0.2307, 0.1926, 0.1812, 0.1730)
> fitsoilwater(w, h)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: fitsoilwater ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘SPACECAP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPACECAP
> ### Title: Fits spatially-explicit capture recapture models
> ### Aliases: SPACECAP
> 
> ### ** Examples
> 
> SPACECAP()
Invalid MIT-MAGIC-COOKIE-1 keyError in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SPACECAP ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...

    RFoptions

The following object is masked from 'package:raster':

    atan2

The following objects are masked from 'package:base':

    abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
    expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
    round, sin, sinh, sqrt, tan, tanh, trunc

Loading required package: grid

Attaching package: 'grid'

The following object is masked from 'package:SpaDES':

    gpar

Quitting from lines 352-356 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc2412bdcf402.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2412bdcf402.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparr.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spatgraphs.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: 'lgamma' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SPECIES.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rgdal’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sphereplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
  input string 415 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<c1>
          k^^[W^^S<9f>H5<89><88>><ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D<fd>z<ed><b5><87><9e>K}O...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D
                                                  <fd>z<ed><b5><87><9e>K}O/<ba><f9><d0>@<bd>^^D;<82><86><84>,]<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^D^^V<ad>^^WU<95><a9><fd><bc>k<c5>]<b7>X<fa>^^N?4<ec><e7>ږ<94>ڎ<e5>j^^Nb<f5><f6
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sprint.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgreSQL’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SRRS ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   8.4Mb
    lib       1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/StatDA.Rcheck/00install.out’ for details.
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxchi
> ### Title: Stepwise detection of recombination breakpoints using MaxChi
> ### Aliases: maxchi
> ### Keywords: htest
> 
> ### ** Examples
>  demo(maxchi) 


	demo(maxchi)
	---- ~~~~~~

> inputFile<- system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(531,616,810)

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyDetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.7Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("SubspaceClustererBuilder", returnSig = "Lmoa/clusterers/hddstream/HDDStream;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous> -> .External
Execution halted
Package required but not available: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.2Mb
Package suggested but not available for checking: ‘RTCGA.clinical’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
there is no package called 'RTCGA.clinical'
Execution halted
File ‘survrec/libs/survrec.so’:
  Found ‘__gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keydlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyprocessSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: 'erfc' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1)
  apply.f:86:0: warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  burnop.f:29:0: warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:166:0: warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:195:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvgrainop.f:168:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvkillop.f:175:0: warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  plantop.f:87:0: warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:171:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1)
  sweep.f:56:0: warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:172:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 426 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'symmoments.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           ^^S<cb>^^Y<ff>b;^^?^^\<c0><bb>+^^^<90><86>8<b1><b6><e5>E<b4><c1><a1><b2>z^^H^^R5<95>,UBꡕ,<bd>'<ae>O^^QG<de>^^A<e5>^^]...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <e9>j^^Op<b9>\<82>
               <94><ac><aa><a2><de><d7>^^?<fc>à<89>f<b3><db><d0>y<88><eb><d2>-f=<99><d1>M]<dd>9<bd><b3><a7><fb><f0><f6><f7><f1>o<be><f2>5A<e0><86><a1><8a>zg<b7><95>.=<f7><e7><bf><fe><fb>?<e9><cd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<9e><be>x<f1><a2>,<cb>^^V<8b><85><e7><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package suggested but not available for checking: ‘GISTools’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TDMR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyaniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/termstrc.Rcheck/00install.out’ for details.
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs       6.7Mb
    tessdata  31.0Mb
Error in re-building vignettes:
  ...
  input string 398 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'texreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[<d7>^^V?<95><f2><d1>!A<d2>}-AQQ,.^^D<c3>Kp^^D^^C<85>^^Z<8a>C0Y4P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 RJ<a5><94>^^P^^BS<e7><f3>y)<a5><e3>8B^^H<c3>0<94>R/^
                                 <bc>8s<e6><cc>ݻw<85><82>^^P<c2>4M)<e5><ec>쬮<eb><85>B<81><88><a4><94>RJ<d3>4<85>^^PJ<a9><d5><d5><d5>...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 ...<8b>MMM^^]dÃa<ce>a<db>VG<86><c3>1<a7><94>ҶmP	<e4><c2>/3-^^X<8c>y<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Tigger-Vignette.Rmd appears to be an R Markdown v2 document.
Loading required package: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 111-116 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
drawGraph: no visible global function definition for ‘eqmcc’
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off eqmcc lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running the tests in ‘tests/simple.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tkrgl.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/var/folders/8q/c881c7rn7_x34vj58f4ywhvm0000h3/T//Rtmpb0djBE/DSL-20160505-034420-gjoxfxyrqb/chunk-15dc814df4a7b': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Package suggested but not available for checking: ‘OpenStreetMap’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 xí\Ï
          k^^[×^^V>^^]÷áêEñÅ}&ÏA28´`#»^^Hº(¸rÀÝtÿnJ¡Yµ.^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 ...l4^^ZDBJùÝwßÝ¿^^?_^^H.¼-eMNNîXVrr2pÝ×^
                                                  O$îæa^^Táú©óo³{ë^^RÑ^^[B...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.23 ^^G^^G^^GRÊ7oÎÌÌ^^XqæÌz½n^^X^^F|ù\.w
                                      
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSclust.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Packages suggested but not available for checking: ‘TSodbc’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/datastructure/ESTAT/DSD_ei_nama_q/1.0
Feb 26, 2017 10:17:31 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT
Feb 26, 2017 10:17:31 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSdist.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.3Mb
Running examples in ‘uplift-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkBalance
> ### Title: Standardized Differences for Stratified Comparisons
> ### Aliases: checkBalance
> ### Keywords: uplift xBalance
> 
> ### ** Examples
> 
> library(uplift)
> 
> set.seed(12345)
> dd <- sim_pte(n = 1000, p = 20, rho = 0, sigma =  sqrt(2), beta.den = 4)
> dd$treat <- ifelse(dd$treat == 1, 1, 0) 
> 
> checkBalance(treat ~ X1 + X2 + X3 + X4 + X5 + X6 , data = dd)
     strata  unstrat                                                              
     stat    treat=0  treat=1 adj.diff adj.diff.null.sd std.diff     z            
vars                                                                              
X1          0.01152  -0.00596 -0.01748         0.06006  -0.01840 -0.29103         
X2          0.03160  -0.02812 -0.05972         0.06236  -0.06057 -0.95778         
X3          0.01145  -0.02242 -0.03387         0.06355  -0.03370 -0.53303         
X4          0.01533  -0.03551 -0.05083         0.06370  -0.05046 -0.79801         
X5          -0.06440 0.02370  0.08810          0.06153  0.09060  1.43175          
X6          0.02237  -0.02177 -0.04414         0.06308  -0.04425 -0.69980         
---Overall Test---
        chisquare df p.value
unstrat      4.54  6   0.604
---
Signif. codes:  0 ‘***’ 0.001 ‘** ’ 0.01 ‘*  ’ 0.05 ‘.  ’ 0.1 ‘   ’ 1 
Error in ncol(DT) : object 'DT' not found
Calls: <Anonymous> ... withOptions -> tryCatch -> do.call -> <Anonymous> -> ncol
Execution halted
Package unavailable to check Rd xrefs: ‘rgdal’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         list(call = mc, handlers = handlers, levels = levels(mf[[1L]]), terms = attr(mf, 
             "terms"))), class = classes)
  5: RWeka_build_classifier(mf, control, name, handlers, options, init)
  6: read_model_frame_into_Weka(mf)
  7: read_data_into_Weka(mf, 1L)
  8: .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List"))
  
  testthat results ================================================================
  OK: 1068 SKIPPED: 20 FAILED: 1
  1. Error: test train/prediction base learner methods (@test_base_learner.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vars.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ?<f1><8b><96><eb><96>;<d9>l6^^V<8b>uM<<c3>0n޼<99>N<a7>1\Y
                                 <96><f1><a6><96><fb><9a><a6><a5>R)<88>^^Z<8f><c7><f9>D^^D<83><c1>D"<a1><eb><ba>,˲,뺎6<f8><9a>J<a5>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <bd>MMM<e1><9a>c^^?^^?<ff><ee>ݻ^^O^^_><9c><9b><9b><8b><c7>㌱<d9><d9>Y<bc><e8>$^^L\<cc>
                                                <84>H<d7><f5><d3><c7><dd>!<ba>,<9e><ae><eb>D<f4><e1><87>^^_z<9e>G<c7><fa><a1>cB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 0<c6>X<b5>ZE\<e6>
             <a7>.<98>L<c7>[H~n<c7><e3>q<90><b6><a5>^^_<f4><cf>?<fd>!<de>)<8c><b8><88><a6><a5><8b>^^\n<e3>^^X^^Xc<b0>^^G|<c7>^^X^^[<94><f3><f3><f3>t<ec>	^...
The control sequence at the end o
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VDA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VecStatGraphs3D.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyDrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vegan3d.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Error in re-building vignettes:
  ...
  input string 373 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'categoricalVGAM.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.24 ...<d5>j<95><9f>e<db>v<a9>T^^Z^^]^^]<c5><ef><b9>^^P<81>=ʳ]H<e9><a2>^^^<d2>_<a6><89>`L^
                                                  <8e>B<d4>b^^X^^@^^NII^^Fv2<f2>"3r...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca><fb>J9<a0>C<98><ae>ŧ`<c8><e3>"<91>^^H<ca>\t<e2>
                                                  <e7><bc>;<e8><dd>z<bd>>??<8f>^^O^^B<89>^^H^^Xv<fc>...
! Missing { inserted.
<to be read again> 
                   \edef 
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘VisuClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: FuzzyPlot
> ### Title: Displays a Fuzzy Plot
> ### Aliases: FuzzyPlot
> 
> ### ** Examples
> 
> 
> library(cluster)
> library(MASS)
> 
> # The example data
> data("MilchSmall")
> 
> M <- scale(MilchSmall[3:6])
> D <- dist(M)
> S <- sammon(D)
Initial stress        : 0.00738
stress after  10 iters: 0.00227, magic = 0.500
stress after  20 iters: 0.00204, magic = 0.500
stress after  30 iters: 0.00203, magic = 0.500
> F <- fanny(D, 6)
> 
> FuzzyPlot(S$points, F$membership, labels=MilchSmall[,2], 
+ 	clusterColors=c("red", "green", "magenta", "yellow", "blue", "black"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: FuzzyPlot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wand.Rcheck/00install.out’ for details.
Running examples in ‘wbsts-Ex.R’ failed
The error most likely occurred in:

> ### Name: tau.fun
> ### Title: Universal thresholds
> ### Aliases: tau.fun
> ### Keywords: threshold
> 
> ### ** Examples
>  
> 
> cps=c(400,470)
> set.seed(101)
> y=sim.pw.ar(N =2000,sd_u = 1,b.slope=c(0.4,-0.6,0.5),br.loc=cps)[[2]]
> #tau.fun(y) is the default value for C_i
> #Binary segmentation
> wbs.lsw(y,M=1)$cp.aft
NULL
> #Wild binary segmentation
> wbs.lsw(y,M=3500)$cp.aft
Error in while (ind.max < 0 | ind.max > e) { : 
  missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WMCapacity.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wnominate.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because wordcloud.Rmd appears to be an R Markdown v2 document.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...VB<e0>+W^^L<ce>O?<fd>^^T^^X[^^&"<ec>^^G"<82>p<e5>rYJ	<81><98>x&<b9>\<ce>
                                                  <f3><bc>d2	A<85>^^PA^^P<94>J%<f4><80>^^[<ef>g<a5>T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <95>l<f1><81><93>T*<85>ꥮ<eb>^^T<b9>^^]<88>sv<df><f7><85>^^P<cb><cb>˨^^Qan<9c><d7>an\2
                                                <8b><a6>s<b6>m+<a5><82>  "]<d7><f9><e4><bd><d1>h^^Pѩ<ca><ea>)<fa><b0>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.29 èV<ab><8b><8b><8b>tb<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/x12GUI.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java        4.6Mb
    unitTests   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YplantQMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YuGene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/Rtmp0oTpBw/R.INSTALL27c418fc62b1/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/ACEt.Rcheck/00install.out' for details.
prepare_Rd: ACEt-package.Rd:1: All text must be in a section
Running examples in 'ActuDistns-Ex.R' failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse -> dgumbel
Execution halted
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/audio.Rcheck/00install.out' for details.
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    java  64.3Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/BACA.Rcheck/00install.out' for details.
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at D:/temp/RtmpO6NQCP/RLIBS_28a0aba5a95/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
installed size is 125.9Mb
  sub-directories of 1Mb or more:
    include  125.0Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/BiSEp.Rcheck/00install.out' for details.
installed size is 73.1Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    lib      70.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BRugs.Rcheck/00install.out' for details.
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Running examples in 'chipPCR-Ex.R' failed
The error most likely occurred in:

> ### Name: amptest
> ### Title: Class '"amptest"'
> ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
> ###   show.amptest show,amptest-method plot.amptest plot,amptest-method
> ###   plot,amptest,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Compare a positive and a negative amplification reaction.
> # First simulate positive reaction (fluo.pos) and than the 
> # negative reaction (fluo.neg).
> # Simulation of an amplifiaction curve with some noise and a high signal.
> 
> fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
> ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
+ 		      noiselevel = 0.15)
Error in validObject(.Object) : 
  invalid class "amptest" object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: amptester -> new -> initialize -> initialize -> validObject
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Error in re-building vignettes:
  ...

Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:tools':

    toHTML

Loading required package: GO.db
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DAISIE.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1.  Failure: D1Client d1SolrQuery works (@test.D1Client.R#334) 
  2.  Error: D1Client d1SolrQuery works (@test.D1Client.R#335) 
  3.  Failure: D1Client d1IdentifierSearch works (@test.D1Client.R#365) 
  4.  Failure: D1Client d1IdentifierSearch works (@test.D1Client.R#366) 
  5.  Failure: CNode object index query works with query list param (@test.D1Node.R#25) 
  6.  Error: CNode object index query works with query list param (@test.D1Node.R#26) 
  7.  Failure: listQueryEngines, getQueryEngineDescription works for CNode, MNode (@test.D1Node.R#107) 
  8.  Error: listQueryEngines, getQueryEngineDescription works for CNode, MNode (@test.D1Node.R#108) 
  9.  Failure: CNode object index query works with query string param (@test.D1Node.R#138) 
  10. Error: CNode object index query works with query string param (@test.D1Node.R#139) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.5Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/DGCA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DNAprofiles.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/DNLC.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.3/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.9Mb
    libs   2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
NB: this package is only installed for sub-architecture 'x64'
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: smart_download
> ### Title: Download only those files that don't already exist
> ### Aliases: smart_download
> 
> ### ** Examples
> 
> cars <- etl("mtcars")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\RtmpQVerko\file4fb4349b1eda.sqlite3
> urls <- c("http://www.google.com", "http://www.nytimes.com")
> smart_download(cars, src = urls)
trying URL 'http://www.google.com'
Content type 'text/html; charset=ISO-8859-1' length unknown
.......... 
downloaded 10 KB

trying URL 'http://www.nytimes.com'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'http://www.nytimes.com'
Calls: smart_download -> mapply -> <Anonymous>
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             download.file(url, ...)
         }
     })(dots[[1L]][[2L]], dots[[2L]][[2L]])
  9: suppressWarnings(download.file(url, method = method, ...))
  10: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  11: download.file(url, method = method, ...)
  
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: smart_download works (@test-etl.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Running examples in 'fheatmap-Ex.R' failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Cross validating the tbats model
  Fitting the auto.arima model
  Fitting the nnetar model
  Fitting the stlm model
  Fitting the tbats model
  Fitting the ets model
  Fitting the thetam model
  testthat results ================================================================
  OK: 110 SKIPPED: 0 FAILED: 1
  1. Failure: Testing is.hybridModel(), fitted.hybridModel(), residuals.hybridModel(), and accuracy.hybridModel() (@test-hybridModel.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'fractal-Ex.R' failed
The error most likely occurred in:

> ### Name: findNeighbors
> ### Title: Nearest neighbor search in a multidimensional space
> ### Aliases: findNeighbors
> ### Keywords: distribution
> 
> ### ** Examples
> 
> ## Calculate the 10 nearest neighbors for each 
> ## point of 3-dimensional delayed coordinate 
> ## embedding of the beamchaos data. Exclude 
> ## self-neighbors from the output. 
> embedding <- embedSeries( beamchaos, dim = 3, tlag = 10 )
> nn <- findNeighbors( embedding, n.neighbor=10, olag=1 )
Error in z[[1]] + 1 : non-numeric argument to binary operator
Calls: findNeighbors
Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/fuzzyforest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gamsel.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/GOGANPA.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gputools.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2. Failure: segm returns correct output (@test_segm.R#17) ----------------------
  dim(dat$cna) not equal to c(104, 6).
  1/2 mismatches
  [1] 103 - 104 == -1
  
  
  testthat results ================================================================
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: cnv returns correct output (@test_cnv.R#18) 
  2. Failure: segm returns correct output (@test_segm.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
2/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/hBayesDM.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.2Mb
    libs   1.1Mb
NB: this package is only installed for sub-architecture 'x64'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  13.4Mb
Running examples in 'inarmix-Ex.R' failed
The error most likely occurred in:

> ### Name: diagnose
> ### Title: Diagnostics for the model fit.
> ### Aliases: diagnose
> ### Keywords: print
> 
> ### ** Examples
> 
> XX <- cbind(rep(1,9),c(0:8)/4)
> colnames(XX) <- c("const","time")
> coefs <- rbind(c(-.2,0),c(1.2,.3))
> alpha <- c(.2,.2)
> scale <- c(2,2)
> mix.prop <- c(.8,.2)
> 
> testdat <- GenerateMixData(200,coefs,alpha,scale,mix.prop,XX)
> testfit <- inarmix(y~time,nclasses=2,id=subject,data=testdat,maxiter=3)
Iteration:  1 
Iteration:  2 
Iteration:  3 
[1] 8.093961e-225
[1] 8.093961e-225
Error in solve.default(hh$dermat, hh$sqmat) : 
  system is computationally singular: reciprocal condition number = 8.09396e-225
Calls: inarmix -> tcrossprod -> solve -> solve -> solve.default
Execution halted
Missing or unexported object: 'metacom::IdentifyStructure'
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/LANDD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/largeVis.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    geojson  12.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: message(sprintf("Page %s of %s Returned. Response contains %s of %s %s. ", x$meta$current_page, 
         x$meta$total_pages, x$meta$per_page, x$meta$total_entries, ngettext(x$meta$total_entries, 
             "notice", "notices")))
  3: sprintf("Page %s of %s Returned. Response contains %s of %s %s. ", x$meta$current_page, 
         x$meta$total_pages, x$meta$per_page, x$meta$total_entries, ngettext(x$meta$total_entries, 
             "notice", "notices"))
  
  testthat results ================================================================
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: Search Works (@tests.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/maGUI.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.3/maps/libs/i386/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/maps/libs/x64/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
    misc   1.1Mb
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/mmap.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/nettools.Rcheck/00install.out' for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    CppCode   1.8Mb
    R         2.4Mb
    include   3.6Mb
    libs      1.5Mb
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  
  
  2. Failure: Test HS023. (@test-hs023.R#95) -------------------------------------
  all(eval_g_ineq(res$solution)$constr <= res$options$tol_constraints_ineq) isn't true.
  
  
  testthat results ================================================================
  OK: 41 SKIPPED: 0 FAILED: 2
  1. Failure: Test HS023. (@test-hs023.R#90) 
  2. Failure: Test HS023. (@test-hs023.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs     5.2Mb
    models   4.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: FUN(X[[i]], ...)
  10: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  11: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  12: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  13: attr.all.equal(target, current, ...)
  14: mode(current)
  
  testthat results ================================================================
  OK: 288 SKIPPED: 0 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/PANDA.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/ppiPre.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: initialize(value, ...)
  10: initialize(value, ...)
  11: callNextMethod()
  12: .nextMethod(.Object = .Object, ... = ...)
  13: validObject(.Object)
  14: stop(msg, ": ", errors, domain = NA)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: Small example works (@test_factorial_preprocessing.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Rblpapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    include   4.3Mb
    lib      20.4Mb
    libs      3.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: open(con, "rb")
  10: open.connection(con, "rb")
  
  testthat results ================================================================
  OK: 21 SKIPPED: 0 FAILED: 5
  1. Error: get_institutions() returns a tibble (@test_institutions.R#6) 
  2. Error: Function returns sensible data frames for sensible queries (@test_search_case_studies.R#6) 
  3. Error: get_tag_types() returns a tibble (@test_tag_types.R#6) 
  4. Error: get_tag_value() returns a tibble (@test_tag_values.R#6) 
  5. Error: get_units_of_assessment() returns a tibble (@test_units_of_assessment.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
        k =   34 ; sb/Sb = 0 ; sb = 0
        k =  414 ; sb/Sb = 0.60237132329825 ; sb = 387.816744112795
        Creating new point: f = 0.830052794117553
  Triangulating...
  Internal error in finddirection():  Unable to find a
    triangle leading from (-195.467775468, 4725.74636175) to  (192.266112266, 4832.37318087).
    Please report this bug to jrs@cs.berkeley.edu
    Include the message above, your input data set, and the exact
      command line you used to run Triangle.
  Error in RTriangle::triangulate(RTriangle::pslg(P = out$P, S = out$S[out$SB ==  : 
    Triangle exit, code $i
  Calls: retistruct.reconstruct ... ReconstructedOutline -> TriangulatedOutline -> <Anonymous> -> .Call
  Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  4: stop("500 - Server error", call. = FALSE)
  
  testthat results ================================================================
  OK: 44 SKIPPED: 0 FAILED: 6
  1. Error: Formating via 'source' works (@test_format_gq.R#18) 
  2. Error: Formating via 'config' works (@test_format_gq.R#39) 
  3. Error: Formating via 'config' needs all parameters (@test_format_gq.R#50) 
  4. Error: Formating via named parameters works (@test_format_gq.R#60) 
  5. Error: add_flags works properly guessing names for rvertnet dataset (@test_multiple_records.R#30) 
  6. Error: add_flags plays well with rgbif (@test_synergies.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 34-43 (rgbif-synergy.Rmd) 
Error: processing vignette 'rgbif-synergy.Rmd' failed with diagnostics:
500 - Server error
Execution halted
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-33~1.2/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  Loading required package: rsdmx
  1. Error: DSD is properly fetched by readSDMX when there is no dsdRef (using flowRef) (@test_Data.R#36) 
  HTTP request failed with status: 403 The number of requests for /api/1.0/sdmx/GetData/ exceeds 50.
  1: readSDMX(providerId = "KNOEMA", resource = "data", flowRef = "SADG2015", dsd = TRUE) at testthat/test_Data.R:36
  2: stop("HTTP request failed with status: ", h$value()["status"], " ", h$value()["statusMessage"])
  
  <simpleError in regexpr("<!DOCTYPE html>", content): object 'content' not found>
  testthat results ================================================================
  OK: 216 SKIPPED: 53 FAILED: 1
  1. Error: DSD is properly fetched by readSDMX when there is no dsdRef (using flowRef) (@test_Data.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 3.3.0 beta (2016-04-13 r70476)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Running examples in 'rvest-Ex.R' failed
The error most likely occurred in:

> ### Name: html
> ### Title: Parse an HTML page.
> ### Aliases: html read_xml.response read_xml.session
> ### Keywords: deprecated
> 
> ### ** Examples
> 
> # From a url:
> google <- read_html("http://google.com", encoding = "ISO-8859-1")
Error in open.connection(x, "rb") : Couldn't connect to server
Calls: read_html -> read_html.default
Execution halted
Found the following significant warnings:
  Warning: S3 methods 'anova.merMod', 'as.data.frame.boot', 'as.data.frame.thpr', 'as.data.frame.VarCorr.merMod', 'as.function.merMod', 'coef.lmList4', 'coef.merMod', 'confint.lmList4', 'confint.merMod', 'confint.thpr', 'densityplot.thpr', 'deviance.merMod', 'df.residual.merMod', 'dotplot.coef.mer', 'dotplot.ranef.mer', 'drop1.merMod', 'extractAIC.merMod', 'family.glmResp', 'family.lmResp', 'family.merMod', 'family.nlsResp', 'fitted.merMod', 'fixef.merMod', 'formula.lmList4', 'formula.merMod', 'getME.merMod', 'hatvalues.merMod', 'isGLMM.merMod', 'isLMM.merMod', 'isNLMM.merMod', 'isREML.merMod', 'log.thpr', 'logLik.merMod', 'model.frame.merMod', 'model.matrix.merMod', 'ngrps.factor', 'ngrps.merMod', 'nobs.merMod', 'plot.coef.mer', 'plot.lmList4.confint', 'plot.merMod', 'plot.ranef.mer', 'predict.merMod', 'print.merMod', 'print.ranef.mer', 'print.summary.merMod', 'print.VarCorr.merMod', 'profile.merMod', 'qqmath.merMod', 'qqmath.ranef.mer', 'ranef.merMod', 'refit.merMod', 'refitML.merMod', 'residua [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/Rz.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.5Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.2Mb
Missing or unexported object: 'ChemoSpec::readJDX'
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 6
  1. Failure: basic (@test-strip.R#13) 
  2. Failure: big (@test-strip.R#20) 
  3. Failure: libre (@test-strip.R#29) 
  4. Failure: abiword (@test-strip.R#39) 
  5. Failure: Japanese (cp932) (@test-strip.R#49) 
  6. Failure: Chinese and Korean (@test-strip.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  1. Failure: a subprocess can be spawned and killed (@test-subprocess.R#24) -----
  process_exists(handle) isn't false.
  
  
  testthat results ================================================================
  OK: 52 SKIPPED: 4 FAILED: 1
  1. Failure: a subprocess can be spawned and killed (@test-subprocess.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

The following object is masked from 'package:tibble':

    as_tibble

Warning: Removed 4160 rows containing non-finite values (stat_smooth).
Warning: Removed 4160 rows containing missing values (position_stack).
Getting data...

Warning in fun_transform(eval(parse(text = x)), OHLC = FALSE, ...) :
  missing values removed from data
Getting data...

Warning in value[[3L]](cond) :
  Error at stock symbol EMC during call to quantmod::getSymbols.
Quitting from lines 733-737 (tidyquant.Rmd) 
Error: processing vignette 'tidyquant.Rmd' failed with diagnostics:
`data` must be a tibble or data.frame.
Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/TROM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/WGCNA.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached
  testthat results ================================================================
  OK: 66 SKIPPED: 0 FAILED: 2
  1. Failure: normal usage (@test_caching_gathering.R#27) 
  2. Failure: setting cache file (@test_caching_gathering.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached
http://stats.grok.se/json/en/201510/Main_page

data from server was: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached


Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached
http://stats.grok.se/json/en/201511/Main_page

data from server was: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached


Quitting from lines 108-112 (using-wikipediatrend.Rmd) 
Error: processing vignette 'using-wikipediatrend.Rmd' failed with diagnostics:
need finite 'xlim' values
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   5.0Mb
BFD_Processor: no visible global function definition for 'levelplot'
BFD_Processor: no visible global function definition for 'corrplot'
FBA_solve: no visible global function definition for 'Rglpk_solve_LP'
PHPP: no visible global function definition for 'levelplot'
PHPP: no visible global function definition for 'persp3d'
PHPP: no visible global function definition for 'play3d'
PHPP: no visible global function definition for 'spin3d'
Found the following significant warnings:
  Warning: D:/temp/RtmpMPmczW/R.INSTALL4fc479ac73ed/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.2/ACEt.Rcheck/00install.out' for details.
clusters: no visible global function definition for 'write.matrix'
copNormal : pcopula: no visible global function definition for
  'pmvnorm'
copNormal : rcopula: no visible global function definition for
  'rmvnorm'
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
Namespaces in Imports field not imported from:
  'plotly' 'shinydashboard'
  All declared Imports should be used.
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
rCSL: no visible global function definition for 'ginv'
rCSL: no visible global function definition for 'expand'
rCSL: no visible global function definition for 'lu'
adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
ov.p.grid: no visible global function definition for 'cloud'
ov.p.grid: no visible global function definition for 'wireframe'
Namespace in Imports field not imported from: 'filehash'
  All declared Imports should be used.
checkDNAbcd: no visible global function definition for 'haplotype'
denoise: no visible global function definition for 'ebayesthresh'
denoise2: no visible global function definition for 'ebayesthresh'
denoisehetero: no visible global function definition for 'ebayesthresh'
denoisehetero2: no visible global function definition for
  'ebayesthresh'
denoiseheteromp: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop2: no visible global function definition for
  'ebayesthresh'
Namespaces in Imports field not imported from:
  'fields' 'knitr'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/agRee.Rcheck/00install.out' for details.
backfit.logistic.interaction: warning in glm(y ~ trt, family =
  "binomial", weight = wt): partial argument match of 'weight' to
  'weights'
backfit.logistic.main: warning in glm(y ~ 1, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.interaction: warning in glm(y ~ trt, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.main: warning in glm(y ~ 1, family = "binomial", weight = wt):
  partial argument match of 'weight' to 'weights'
backfit.cox.interaction: no visible global function definition for
  'coxph'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/AlignStat.Rcheck/00install.out' for details.
pedigree.summary: no visible global function definition for 'orderPed'
pedigree.summary: no visible global function definition for
  'calcInbreeding'
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
sigma.hat: no visible global function definition for 'sigmaHat'
Namespace in Imports field not imported from: 'unmarked'
  All declared Imports should be used.
Package required and available but unsuitable version: 'tcltk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LBI: warning in png(file = paste(graphout, ".png", sep = "")): partial
  argument match of 'file' to 'filename'
normalisation: warning in read.table(as.character(nom[i]), nrow = 1,
  skip = 1, sep = sep): partial argument match of 'nrow' to 'nrows'
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
plot,ANFIS : .local: no visible binding for global variable 'X'
varbin: no visible global function definition for 'boot'
parse.php.msgs: no visible global function definition for 'startsWith'
read.multiple.apache.access.log: no visible global function definition
  for 'endsWith'
read.multiple.apache.error.log: no visible global function definition
  for 'endsWith'
Running examples in 'ApacheLogProcessor-Ex.R' failed
The error most likely occurred in:

> ### Name: parse.php.msgs
> ### Title: Parses PHP mesages and store its parts in a data frame that
> ###   contains level, message, file, line number and referer.
> ### Aliases: parse.php.msgs
> 
> ### ** Examples
> 
> 
> #Loads the path of the erro log
> path <- system.file("examples", "error_log.log", package = "ApacheLogProcessor")
> 
> #Loads the error log to a data frame
> dfELog <- read.apache.error.log(path)
> 
> dfPHPMsgs <- parse.php.msgs(dfELog)
Error: could not find function "startsWith"
Execution halted
apple: no visible global function definition for 'ginv'
deri: no visible global function definition for 'ginv'
y.app: no visible global function definition for 'ginv'
bookTheme: no visible global function definition for 'trellis.par.set'
transparentTheme: no visible global function definition for
  'trellis.par.set'
upperp: no visible global function definition for 'ellipse'
upperp: no visible global function definition for 'panel.xyplot'
upperp: no visible global function definition for 'trellis.par.get'
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
apsrtableSummary.lrm: no visible binding for global variable 'est.exp'
pval.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'nmodels'
stars.note: no visible binding for global variable 'lev'
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for 'index'
ginv.zalphasfn: no visible global function definition for 'ginv'
tspsimplex_projection: no visible global function definition for
  'solve_TSP'
tspsimplex_projection: no visible global function definition for 'TSP'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.4Mb
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/arulesCBA.Rcheck/00install.out' for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    bin   11.7Mb
    misc   2.1Mb
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/arulesViz.Rcheck/00install.out' for details.
Asciidoc: no visible binding for global variable 'RweaveAsciidoc'
Org: no visible binding for global variable 'RweaveOrg'
Pandoc: no visible binding for global variable 'RweavePandoc'
ReST: no visible binding for global variable 'RweaveReST'
T2t: no visible binding for global variable 'RweaveT2t'
Textile: no visible binding for global variable 'RweaveTextile'
weaverAsciiFinish: no visible global function definition for
  'resetStorage'
weaverAsciiFinish: no visible binding for global variable 'cache_expr'
weaverAsciiRuncode: Error while checking: object 'weaverEvalWithOpt'
  not found
weaverAsciiSetup: no visible global function definition for 'log_debug'
weaverOrgSetup: no visible global function definition for 'log_debug'
weaverPandocSetup: no visible global function definition for
  'log_debug'
weaverReSTSetup: no visible global function definition for 'log_debug'
weaverT2tSetup: no visible global function definition for 'log_debug'
weaverTextileSetup: no visible global function definition for
  'log_debug'
CF: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities2'
CMD: no visible binding for global variable 'activities'
CMD: no visible global function definition for 'gridpts'
calc_box: no visible binding for global variable 'activities'
calc_box: no visible global function definition for 'wtd.var'
calc_sdd: no visible binding for global variable 'activities'
calc_sde: no visible binding for global variable 'activities'
distances: no visible binding for global variable 'centre'
distances: no visible binding for global variable 'activities'
mean_centre: no visible binding for global variable 'activities'
median_centre: no visible binding for global variable 'activities'
plot_box: no visible binding for global variable 'r.BOX'
plot_centres: no visible binding for global variable 'r.SDE'
plot_centres: no visible binding for global variable 'r.CF'
plot_centres: no visible binding for global variable 'r.median'
plot_centres: no visible binding for global variable 'r.CMD'
plot_centres: no visible binding for global variable 'r.CF2PTS'
plot_sdd: no visible binding for global variable 'r.SDD'
plot_sde: no visible binding for global variable 'r.SDE'
Missing link or links in documentation object 'is_s3_generic.Rd':
  '[utils]{isS3method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
my_uminp_method: no visible global function definition for 'pmvnorm'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/audio.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/auRoc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gpclib'
cv.compare.ggplot: no visible global function definition for 'ggplot'
cv.compare.ggplot: no visible global function definition for
  'aes_string'
cv.compare.ggplot: no visible global function definition for
  'facet_wrap'
cv.compare.ggplot: no visible global function definition for
  'scale_x_continuous'
cv.compare.ggplot: no visible global function definition for
  'scale_y_continuous'
cv.compare.ggplot: no visible global function definition for
  'coord_equal'
cv.compare.ggplot: no visible global function definition for
  'scale_color_gradient2'
cv.compare.ggplot: no visible global function definition for
  'scale_size_continuous'
cv.compare.ggplot: no visible global function definition for 'fortify'
cv.compare.ggplot: no visible global function definition for
  'geom_path'
cv.compare.ggplot: no visible global function definition for
  'geom_point'
Namespace in Imports field not imported from: 'EBImage'
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BACCT.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'osd'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bamdit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BANOVA.Rcheck/00install.out' for details.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: gcrma
Loading required package: preprocessCore
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayescount.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BayesMed.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayesmix.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
gibbs: no visible global function definition for 'permn'
hmflatlogit: no visible global function definition for 'rmnorm'
hmflatloglin: no visible global function definition for 'mvrnorm'
hmflatprobit: no visible global function definition for 'rmnorm'
hmnoinflogit: no visible global function definition for 'rmnorm'
hmnoinfloglin: no visible global function definition for 'mvrnorm'
hmnoinfprobit: no visible global function definition for 'rmnorm'
ACGaussian: no visible global function definition for 'ginv'
ACGaussian: no visible global function definition for 'rmvnorm'
ACt: no visible global function definition for 'ginv'
ACt: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'ginv'
MCGaussian: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'vec'
MCt: no visible global function definition for 'ginv'
MCt: no visible global function definition for 'rmvnorm'
MCt: no visible global function definition for 'vec'
NCGaussian: no visible global function definition for 'ginv'
NCGaussian: no visible global function definition for 'rmvnorm'
NCGaussian: no visible global function definition for 'rdiric'
NCt: no visible global function definition for 'ginv'
NCt: no visible global function definition for 'rmvnorm'
NCt: no visible global function definition for 'rdiric'
coef.Bayesthresh: no visible global function definition for 'mcmc'
lmerFactorList : <anonymous>: no visible binding for global variable
  'rBind'
lmerFactorList : <anonymous>: no visible global function definition for
  'drop0'
mkZt: no visible binding for global variable 'rBind'
predict.Bayesthresh: no visible global function definition for
  'rankMatrix'
random.effects: no visible global function definition for 'mcmc'
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
BPSpost2mcmc: no visible global function definition for 'mcmc'
CPPpost2mcmc: no visible global function definition for 'mcmc'
LittleMCAR: no visible global function definition for 'mlest'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BaySIC.Rcheck/00install.out' for details.
semimetric.deriv: no visible global function definition for
  'splineDesign'
BBRecap: no visible global function definition for 'arms'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
plot,BCDating-ts : .local: no visible binding for global variable
  'na.rm'
Running examples in 'BCEA-Ex.R' failed
The error most likely occurred in:

> ### Name: evppi
> ### Title: Expected Value of Perfect Partial Information (EVPPI) for
> ###   selected parameters
> ### Aliases: evppi evppi.default
> ### Keywords: Health economic evaluation Expected value of partial
> ###   information
> 
> ### ** Examples
> 
> # See Baio G., Dawid A.P. (2011) for a detailed description of the 
> # Bayesian model and economic problem
> #
> # Load the processed results of the MCMC simulation model
> data(Vaccine)
Warning: namespace 'rjags' is not available and has been replaced
by .GlobalEnv when processing object 'vaccine'
> # 
> # Runs the health economic evaluation using BCEA
> m <- bcea(e,c,ref=2,interventions=treats)
> #
> # Computes the EVPPI for a bunch of parameters
> inp <- CreateInputs(vaccine)
Error in CreateInputs(vaccine) : 
  You need to install the package 'R2jags'. Please run in your R terminal:
 install.packages('R2jags')
Execution halted
Running examples in 'BCEs0-Ex.R' failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
> print(m)
NULL
> plot(m)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Namespace in Imports field not imported from: 'inline'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readxl'
  All declared Imports should be used.
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/beanz.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:

  Warning: 'loadRcppModules' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Namespaces in Imports field not imported from:
  'Rcpp' 'chron' 'colorspace' 'gtable' 'htmltools' 'htmlwidgets'
  'httpuv' 'magrittr' 'munsell' 'plyr' 'scales' 'stringi' 'xtable'
  'yaml'
  All declared Imports should be used.
boxplot.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'value'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'samples'
bsgraph0.dist: no visible global function definition for 'addEdge'
bsgraph0.graphNEL: no visible global function definition for
  'getDefaultAttrs'
bsgraph0.graphNEL: no visible global function definition for 'agopen'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'value'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'algorithms'
mi: no visible global function definition for 'mi.plugin'
patch.relation_class_ids: no visible global function definition for
  'relation_is_strict_weak_order'
plot.DatasetCharacterization: no visible binding for global variable
  'characteristics'
plot.DatasetCharacterization: no visible binding for global variable
  'value'
plot.DatasetCharacterization: no visible binding for global variable
  'samples'
plot.DatasetCharacterization: no visible global function definition for
  'theme_text'
plot.TestResult: no visible binding for global variable 'samples'
plot.TestResult: no visible binding for global variable 'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'samples'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/benchr.Rcheck/00install.out' for details.
bI: no visible global function definition for 'mpfr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BEST.Rcheck/00install.out' for details.
betafam: no visible global function definition for 'glmnet'
cca.pertables : cca.var: no visible binding for global variable
  'cca.formula'
cca.pertables: no visible binding for global variable 'cca.formula'
rda.pertables : rda.var: no visible binding for global variable
  'rda.formula'
rda.pertables: no visible binding for global variable 'rda.formula'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/betategarch.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'FinTS' 'Rcpp' 'TSA' 'TTR' 'colorspace' 'fpp' 'fracdiff' 'gtable'
  'htmlwidgets' 'lmtest' 'normtest' 'quadprog' 'rugarch' 'scales'
  'stringi' 'testthat' 'timeDate' 'tseries' 'viridis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
maxstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
pvstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bife.Rcheck/00install.out' for details.
lasso.stars: no visible global function definition for 'glmnet'
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection : .local: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'fetch'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
ebayesthresh.wavelet.wd: no visible global function definition for
  'ebayesthresh'
hfdenoise: no visible global function definition for
  'ebayesthresh.wavelet'
negloglik.laplace: no visible global function definition for 'wfromt'
negloglik.laplace: no visible global function definition for
  'beta.laplace'
wandafromx: no visible global function definition for 'wfromt'
HLtest.Rsq: warning in pchisq(X2, 10 - 2, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
X2GOFtest.Rsq: warning in pnorm(abs(z), lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
Packages required and available but unsuitable versions:
  'spatstat' 'grDevices' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
dis: no visible binding for global variable 'sub.mat'
mat.dis: no visible binding for global variable 'sub.mat'
mmds.3D.plot: no visible global function definition for 'box3d'
mmds.3D.plot: no visible global function definition for 'axes3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BiSEp.Rcheck/00install.out' for details.
biwt.cor: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'covMcd'
Namespaces in Imports field not imported from:
  'glmnet' 'gtools' 'knitr' 'nnet' 'parallel' 'rJava' 'reshape'
  'rmarkdown' 'shinyjs'
  All declared Imports should be used.
'library' or 'require' calls in package code:
  'Matrix' 'sna'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
gplot1: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
gplot2: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
loadnetwork2: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
loadpajek: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
savecluster: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savematrix: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savenetwork: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savepajek: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savevector: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
check.these.par: no visible global function definition for
  'crit.fun.tmp'
check.these.par: no visible binding for global variable 'useM'
crit.fun: no visible global function definition for 'crit.fun.tmp'
crit.fun: no visible binding for global variable 'useM'
gen.crit.fun: no visible binding for global variable 's'
gplot1: no visible global function definition for 'gplot'
gplot2: no visible global function definition for 'gplot'
loadnetwork: no visible global function definition for 'Matrix'
loadnetwork2: no visible global function definition for 'Matrix'
opt.par: no visible global function definition for 'opt.par.tmp'
opt.random.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible binding for global variable 'm'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
      as.Date, as.Date.numeric
  
  trying URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Error in download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  : 
    cannot open URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Calls: test_check ... force -> source_file -> eval -> eval -> download.file
  In addition: Warning message:
  In download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  :
    InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
bmem.bs: no visible global function definition for 'sem'
bmem.em.rcov: no visible global function definition for 'cov.rob'
bmem.mi.cov: no visible global function definition for 'amelia'
bmem.sem: no visible global function definition for 'sem'
bmem.sobel: no visible global function definition for 'sem'
power.basic: no visible global function definition for 'simulateData'
power.basic: no visible global function definition for 'lavaanNames'
power.basic : runonce: no visible global function definition for
  'simulateData'
power.basic: no visible global function definition for 'sfInit'
power.basic: no visible global function definition for 'sfLibrary'
power.basic: no visible binding for global variable 'lavaan'
power.basic: no visible global function definition for 'sfLapply'
power.boot: no visible global function definition for 'simulateData'
power.boot: no visible global function definition for 'lavaanNames'
power.boot : runonce: no visible global function definition for
  'simulateData'
power.boot : runonce: no visible global function definition for
  'bootstrapLavaan'
power.boot: no visible global function definition for 'sfInit'
power.boot: no visible global function definition for 'sfLibrary'
power.boot: no visible binding for global variable 'lavaan'
power.boot: no visible global function definition for 'sfLapply'
summary.power: no visible global function definition for 'lavaanNames'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmeta.Rcheck/00install.out' for details.
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmlm.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'compiler'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Boom.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
alleleEnrichment.lp: no visible global function definition for
  'make.lp'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.column'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.type'
alleleEnrichment.lp: no visible global function definition for
  'set.objfn'
alleleEnrichment.lp: no visible global function definition for
  'set.constr.type'
alleleEnrichment.lp: no visible global function definition for
  'set.rhs'
alleleEnrichment.lp: no visible global function definition for
  'lp.control'
alleleEnrichment.lp: no visible global function definition for
  'get.variables'
getGenotypes : <anonymous>: no visible global function definition for
  'genotype'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/boral.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'rgdal' 'tidyr'
  All declared Imports should be used.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

const.cor.list: no visible global function definition for
  'wave.correlation'
const.var.list: no visible global function definition for
  'wave.variance'
wave.trans: no visible global function definition for 'dwt'
wave.trans: no visible global function definition for 'modwt'
wave.trans: no visible global function definition for 'brick.wall'
confint.profile.brglm: no visible global function definition for
  'profConfint'
profile.brglm: no visible global function definition for 'profileModel'
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
BOOTSimpsonD : BSimpson: no visible global function definition for
  'estSimpsonf'
BOOTSimpsonR : BSimpson: no visible global function definition for
  'estSimpsonf'
CIGLM: no visible global function definition for 'univariate_calpha'
CIGLM: no visible global function definition for 'adjusted_calpha'
EDA: no visible global function definition for 'kurtosis'
EDA: no visible global function definition for 'skewness'
bs.design: no visible global function definition for 'spline.des'
Packages required and available but unsuitable versions:
  'BoomSpikeSlab' 'Boom' 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BTSPAS.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
CADFpvalues: no visible binding for global variable 'coeffs_ct'
CADFpvalues: no visible binding for global variable 'coeffs_c'
CADFpvalues: no visible binding for global variable 'coeffs_nc'
estmodel: no visible global function definition for 'dynlm'
estmodel: no visible global function definition for 'punitroot'
estmodel: no visible global function definition for 'kernHAC'
plot.CADFtest: no visible global function definition for
  'jarque.bera.test'
MH: no visible global function definition for 'rmvnorm'
computer.model: no visible global function definition for 'rmvnorm'
model.inadequacy: no visible global function definition for 'rmvnorm'
prob.psi1: no visible global function definition for 'dmvnorm'
prob.psi2: no visible global function definition for 'dmvnorm'
prob.theta: no visible global function definition for 'dmvnorm'
sample.theta: no visible global function definition for 'rmvnorm'
bestBy: no visible global function definition for 'dbConnect'
bestBy: no visible global function definition for 'dbDriver'
bestBy: no visible global function definition for 'dbWriteTable'
bestBy: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbListFields'
dbWriteTable2: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbSendQuery'
dbWriteTable2: no visible global function definition for 'dbColumnInfo'
dbWriteTable2: no visible global function definition for
  'dbClearResult'
dbWriteTable2: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbConnect'
groupBy: no visible global function definition for 'dbDriver'
groupBy: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbGetQuery'
spie: no visible global function definition for 'grid.newpage'
spie: no visible global function definition for 'pushViewport'
spie: no visible global function definition for 'viewport'
spie: no visible global function definition for 'grid.layout'
spie: no visible global function definition for 'dataViewport'
spie: no visible global function definition for 'grid.circle'
spie: no visible global function definition for 'gpar'
spie: no visible global function definition for 'grid.polygon'
spie: no visible global function definition for 'grid.rect'
spie: no visible global function definition for 'stringWidth'
spie: no visible global function definition for 'stringHeight'
spie: no visible global function definition for 'grid.text'
spie: no visible global function definition for 'grid.lines'
spie: no visible global function definition for 'unit'
spie: no visible global function definition for 'upViewport'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
File 'CausalGAM/R/zzz.R':
  .onAttach calls:
    cat("##\n## CausalGAM Package\n")
    cat("## Copyright (C) 2009", " Adam Glynn and Kevin Quinn\n",     sep = "")
    require(gam, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CCTpack.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cda.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'RCurl' 'rgdal'
  All declared Imports should be used.
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
centrality: no visible global function definition for 'vcount'
centrality: no visible global function definition for 'degree'
centrality: no visible global function definition for 'betweenness'
cepa.all.parallel.by.snow: no visible global function definition for
  'makeCluster'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterCall'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterApply'
cepa.all.parallel.by.snow: no visible global function definition for
  'stopCluster'
generate.pathway: no visible global function definition for
  'graph.edgelist'
pathway.nodes: no visible global function definition for 'vcount'
pathway.nodes: no visible global function definition for
  'get.vertex.attribute'
plot.igraph2: no visible binding for global variable 'layout.random'
plot.igraph2: no visible global function definition for 'V'
plot.igraph2: no visible global function definition for 'E'
plot.igraph2: no visible global function definition for 'get.edgelist'
plot.igraph2: no visible global function definition for 'ecount'
plotGraph: no visible global function definition for 'V'
plotGraph: no visible global function definition for 'V<-'
plotGraph: no visible global function definition for 'E'
plotGraph: no visible global function definition for 'E<-'
plotGraph : layout.method: no visible global function definition for
  'layout.reingold.tilford'
radiality: no visible global function definition for 'shortest.paths'
radiality: no visible global function definition for 'vcount'
radiality: no visible global function definition for 'diameter'
reach: no visible global function definition for 'E'
reach: no visible global function definition for 'shortest.paths'
report: no visible global function definition for 'write.graph'
spread: no visible global function definition for 'E'
spread: no visible global function definition for 'shortest.paths'
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for 'gen.beta'
plotCVcggd: no visible binding for global variable 'cv'
plotCVcggd: no visible binding for global variable 'cv.error'
predict.cggd: no visible binding for global variable 'max.tk'
predict.cggd: no visible global function definition for 'gen.beta'
L2L1ExpandFit: no visible global function definition for
  'L2L1PathExtract'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Hartree2Joule: no visible binding for global variable
  'universalConstants'
Hertz2Joule: no visible binding for global variable
  'universalConstants'
Joule2Hartree: no visible binding for global variable
  'universalConstants'
Joule2Hertz: no visible binding for global variable
  'universalConstants'
Joule2Kelvin: no visible binding for global variable
  'universalConstants'
Joule2centimeterMinusOne: no visible binding for global variable
  'universalConstants'
Joule2electronVolt: no visible binding for global variable
  'universalConstants'
Joule2kiloCaloriePerMole: no visible binding for global variable
  'universalConstants'
Joule2kiloJoulePerMole: no visible binding for global variable
  'universalConstants'
Kelvin2Joule: no visible binding for global variable
  'universalConstants'
LandauZener: no visible binding for global variable
  'universalConstants'
LandauZenerProbability: no visible binding for global variable
  'universalConstants'
Marcus: no visible binding for global variable 'universalConstants'
MarcusLevichJortner: no visible binding for global variable
  'universalConstants'
centimeterMinusOne2Joule: no visible binding for global variable
  'universalConstants'
electronVolt2Joule: no visible binding for global variable
  'universalConstants'
kiloCaloriePerMole2Joule: no visible binding for global variable
  'universalConstants'
kiloJoulePerMole2Joule: no visible binding for global variable
  'universalConstants'
DPfitSamples: no visible global function definition for 'mclapply'
getCCF: no visible global function definition for 'mclapply'
getDiploidOrigin: no visible global function definition for 'mclapply'
getSegChr.CBS: no visible global function definition for 'mclapply'
getSegPurity: no visible global function definition for 'mclapply'
downloadMaster: no visible global function definition for
  'getURLContent'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cheddar.Rcheck/00install.out' for details.
Running examples in 'chipPCR-Ex.R' failed
The error most likely occurred in:

> ### Name: amptest
> ### Title: Class '"amptest"'
> ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
> ###   show.amptest show,amptest-method plot.amptest plot,amptest-method
> ###   plot,amptest,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Compare a positive and a negative amplification reaction.
> # First simulate positive reaction (fluo.pos) and than the 
> # negative reaction (fluo.neg).
> # Simulation of an amplifiaction curve with some noise and a high signal.
> 
> fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
> ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
+ 		      noiselevel = 0.15)
Error in validObject(.Object) : 
  invalid class "amptest" object: superclass "replValueSp" not defined in the environment of the object's class
Calls: amptester -> new -> initialize -> initialize -> validObject
Execution halted
chngpt.test.2: no visible global function definition for 'startsWith'
sim.chngpt: no visible global function definition for 'startsWith'
sim.my: no visible global function definition for 'endsWith'
sim.my: no visible global function definition for 'startsWith'
Running examples in 'chngpt-Ex.R' failed
The error most likely occurred in:

> ### Name: chngpt.test
> ### Title: Change Point Tests
> ### Aliases: antoch.test chngpt.test plot.chngpt.test
> 
> ### ** Examples
> 
> 
> dat=sim.chngpt("sigmoid4", type="step", n=200, seed=1, beta=1, alpha=-1, x.distr="norm", e.=4)
Loading required namespace: mvtnorm
Error in sim.chngpt("sigmoid4", type = "step", n = 200, seed = 1, beta = 1,  : 
  could not find function "startsWith"
Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  chngpt unit testing - 2 test functions, 2 errors, 0 failures
  ERROR in test.chngpt.test: Error in sim.chngpt("sigmoid4", type = "step", n = 250, seed = 1, beta = 0,  : 
    could not find function "startsWith"
  ERROR in test.chngptm: Error in sim.chngpt("sigmoid2", type = "hinge", n = 250, seed = 1, beta = log(0.4),  : 
    could not find function "startsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 2)
  
  Execution halted
correctData: no visible global function definition for 'wd'
correctData: no visible global function definition for 'threshold'
correctData: no visible binding for global variable 'madmad'
correctData: no visible global function definition for 'wr'
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
print.rao.spacing.test: no visible binding for global variable
  'rao.table'
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignCcmst: no visible binding for global variable 'citccmst'
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/classify.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: eval(expr, envir, enclos)
  6: samplerate2d(tb$torigin)
  7: rbind(sample.rate.table, data.frame(item = stname2longname(code2stname(i)), hiccode = as.number(StdId(i)), 
         sr = sr))
  8: rbind(deparse.level, ...)
  9: stop("numbers of columns of arguments do not match")
  
  testthat results ================================================================
  OK: 207 SKIPPED: 0 FAILED: 1
  1. Error: calculate 2D sample rate (@test_report.r#36) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
cfly_dist: no visible global function definition for 'ggplot'
cfly_dist: no visible global function definition for 'aes_string'
cfly_dist: no visible global function definition for 'geom_density'
cfly_dist: no visible global function definition for 'facet_grid'
cfly_fluct: no visible global function definition for 'ggplot'
cfly_fluct: no visible global function definition for 'aes_string'
cfly_fluct: no visible global function definition for 'geom_tile'
cfly_fluct: no visible global function definition for
  'scale_y_discrete'
cfly_fluct: no visible global function definition for
  'scale_x_discrete'
cfly_fluct: no visible global function definition for 'theme'
cfly_pcp: no visible global function definition for 'ggplot'
cfly_pcp: no visible global function definition for 'aes_string'
cfly_pcp: no visible global function definition for 'geom_line'
cfly_pcp: no visible global function definition for 'facet_wrap'
som_iterate: no visible global function definition for 'unit.distances'
Package required but not available: 'OpenImageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
BHI: no visible global function definition for 'getGO'
BHI: no visible binding for global variable 'dropECode'
BSI: no visible global function definition for 'getGO'
BSI: no visible binding for global variable 'dropECode'
vClusters: no visible global function definition for 'Mclust'
vClusters: no visible global function definition for 'som'
Error in re-building vignettes:
  ...
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:tools':

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
ControlCharts: no visible global function definition for
  'com.log.density'
COBRA : COBRA.lars: no visible global function definition for 'lars'
COBRA : COBRA.lars: no visible global function definition for
  'predict.lars'
COBRA : COBRA.tree: no visible global function definition for 'tree'
COBRA : COBRA.ridge: no visible global function definition for
  'linearRidge'
COBRA : COBRA.randomForest: no visible global function definition for
  'randomForest'
COBRA: no visible global function definition for 'sfInit'
COBRA: no visible global function definition for 'sfLibrary'
COBRA: no visible global function definition for 'sfExportAll'
COBRA: no visible global function definition for 'sfSapply'
COBRA: no visible global function definition for 'sfStop'
autocorr1: no visible global function definition for 'is.mcmc'
autocorr1: no visible global function definition for 'as.mcmc'
autocorr1: no visible global function definition for 'autocorr'
bridgestat.diag: no visible global function definition for
  'is.mcmc.list'
bridgestat.diag: no visible global function definition for 'as.mcmc'
bridgestat.diag: no visible global function definition for 'nvar'
bridgestat.diag: no visible global function definition for 'varnames'
bridgestat.diag: no visible global function definition for 'niter'
bridgestat.diag: no visible global function definition for
  'spectrum0.ar'
transient.test: no visible global function definition for 'as.mcmc'
coloc.abf.snpStats: no visible global function definition for
  'single.snp.tests'
coloc.abf.snpStats: no visible global function definition for
  'col.summary'
fillin: no visible global function definition for 'col.summary'
fillin: no visible global function definition for 'snp.imputation'
fillin: no visible global function definition for 'impute.snps'
plot,colocPCs-missing : .local: no visible binding for global variable
  'object'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
splitTrainTest: warning in ts(dat[1:numTrain], start = props[1], freq =
  props[3]): partial argument match of 'freq' to 'frequency'
splitTrainTest: warning in ts(dat[(numTrain + 1):length(dat)], start =
  (props[1] + numTrain/props[3]), freq = props[3]): partial argument
  match of 'freq' to 'frequency'
plot.msc : showResults: no visible global function definition for
  'rgl.open'
plot.msc : showResults: no visible global function definition for
  'rgl.clear'
plot.msc : showResults: no visible global function definition for
  'rgl.bg'
plot.msc : showResults: no visible global function definition for
  'rgl.light'
plot.msc : showResults: no visible global function definition for
  'rgl.bbox'
plot.msc : showResults: no visible global function definition for
  'rgl.surface'
plot.msc : showResults: no visible global function definition for
  'rgl.spheres'
plot.msc : showResults: no visible global function definition for
  'axes3d'
plot.msc : showResults: no visible global function definition for
  'title3d'
plot.msc : showResults: no visible global function definition for
  'rgl.viewpoint'
plot.msc: no visible global function definition for 'xyplot'
plot.msc : mypanel: no visible global function definition for
  'panel.fill'
plot.msc : mypanel: no visible global function definition for
  'panel.grid'
plot.msc : mypanel: no visible global function definition for
  'panel.levelplot'
plot.msc: no visible global function definition for 'levelplot'
plot.msc : <anonymous>: no visible global function definition for
  'axis.default'
plot.msc : <anonymous>: no visible global function definition for
  'panel.text'
plot.msc: no visible global function definition for 'shingle'
plot.msc: no visible global function definition for 'strip.custom'
Running examples in 'compareDF-Ex.R' failed
The error most likely occurred in:

> ### Name: compare_df
> ### Title: Compare Two dataframes
> ### Aliases: compare_df
> 
> ### ** Examples
> 
> old_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 3))
> new_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 4))
> ctable = compare_df(new_df, old_df, c("var1"))
Creating comparison table...
Loading required namespace: htmlTable
Creating HTML table for first 100 rows
Error in compare_df(new_df, old_df, c("var1")) : 
  Assertion failed. One of the following must apply:
 * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
 * check_character(css.cell): Must be of type 'character', not
 * 'data.frame'
Calls: compare_df ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Creating comparison table...
  Loading required namespace: htmlTable
  Creating HTML table for first 100 rows
  Error in test_check("compareDF") : 
    Assertion failed. One of the following must apply:
   * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
   * check_character(css.cell): Must be of type 'character', not
   * 'data.frame'
  Calls: test_check ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
compareODM: no visible global function definition for 'xmlRoot'
compareODM: no visible global function definition for 'xmlTreeParse'
compareODM: no visible global function definition for 'xmlChildren'
compareODM: no visible global function definition for 'xmlAttrs'
compareODM: no visible global function definition for 'xmlValue'
dcomplnorm: no visible global function definition for 'grad'
pcomplnorm: no visible global function definition for 'grad'
qcomplnorm: no visible global function definition for 'grad'
arrows3D.default: no visible global function definition for 'texts3d'
arrows3D.default: no visible global function definition for
  'segments3d'
axis3D: no visible global function definition for 'bbox3d'
biplot3D.default: no visible global function definition for 'points3d'
biplot3D.default: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'par3d'
plot3D.acomp: no visible global function definition for 'points3d'
plot3D.acomp: no visible global function definition for 'lines3d'
plot3D.acomp: no visible global function definition for 'texts3d'
plot3D.acomp: no visible global function definition for 'rgl.viewpoint'
plot3D.acomp: no visible global function definition for 'bbox3d'
plot3D.default: no visible global function definition for 'rgl.bbox'
plot3D.rcomp: no visible global function definition for 'points3d'
plot3D.rcomp: no visible global function definition for 'lines3d'
plot3D.rcomp: no visible global function definition for 'texts3d'
plot3D.rcomp: no visible global function definition for 'rgl.viewpoint'
plot3D.rcomp: no visible global function definition for 'bbox3d'
plot3D.rmult: no visible global function definition for 'points3d'
plot3D.rmult: no visible global function definition for 'par3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CompQuadForm.Rcheck/00install.out' for details.
dhpareto: no visible global function definition for 'pgpd'
dhpareto: no visible global function definition for 'dgpd'
hpareto.gamma: no visible global function definition for 'pgpd'
phpareto: no visible global function definition for 'pgpd'
qhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'pgpd'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
Namespaces in Imports field not imported from:
  'Hmisc' 'MASS' 'geepack'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Error in re-building vignettes:
  ...
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
Namespaces in Imports field not imported from:
  'Rtsne' 'scatterplot3d'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/CorrectOverloadedPeaks.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'xtable'
  All declared Imports should be used.
Package in Depends field not imported from: 'calibrate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'circle'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'calibrate'
cosinor_analyzer: no visible binding for global variable 'vitamind'
AntiAR: no visible global function definition for 'first.last'
BootTOS: no visible global function definition for 'ewspec'
BootTOS : bsfn: no visible global function definition for 'LSWsim'
BootTOS : bsfn: no visible global function definition for 'ewspec'
EWSsmoothRM: no visible global function definition for 'accessD'
EWSsmoothRM: no visible global function definition for 'putD'
LCTS: no visible global function definition for 'ewspec'
LCTSres: no visible global function definition for 'ewspec'
coeftofn: no visible global function definition for 'wd'
coeftofn: no visible global function definition for 'wr'
findstysols: no visible global function definition for 'IsPowerOfTwo'
lacv: no visible global function definition for 'ewspec'
lacv: no visible global function definition for 'PsiJmat'
cotrend.default: no visible global function definition for 'coredata'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
calcz02: no visible global function definition for 'coxph'
covTest: no visible global function definition for 'Surv'
CoxBoost: no visible global function definition for 'Matrix'
cv.CoxBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'Matrix'
plot.coxr: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
cpa : OpenX: no visible global function definition for 'tclvalue'
cpa : OpenX: no visible global function definition for 'tkgetOpenFile'
cpa : OpenV: no visible global function definition for 'tclvalue'
cpa : OpenV: no visible global function definition for 'tkgetOpenFile'
cpa : OpenA: no visible global function definition for 'tclvalue'
cpa : OpenA: no visible global function definition for 'tkgetOpenFile'
cpa : Close: no visible global function definition for 'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkmessageBox'
cpa : OnOK: no visible global function definition for 'tclvalue'
cpa : OnOK: no visible global function definition for 'tktoplevel'
cpa : OnOK: no visible global function definition for 'tclVar'
cpa : OnOK: no visible global function definition for 'tkentry'
cpa : OnOK: no visible global function definition for 'tkgrid'
cpa : OnOK: no visible global function definition for 'tklabel'
cpa : OnOK : Save: no visible global function definition for 'tclvalue'
cpa : OnOK : Save: no visible global function definition for
  'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkbutton'
cpa : OnOK: no visible global function definition for 'tkbind'
cpa : OnOK: no visible global function definition for 'tkfocus'
cpa: no visible global function definition for 'tktoplevel'
cpa: no visible global function definition for 'tkwm.title'
cpa: no visible global function definition for 'tkbutton'
cpa: no visible global function definition for 'tkgrid'
cpa: no visible global function definition for 'tklabel'
cpa: no visible global function definition for 'tkfocus'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/crmPack.Rcheck/00install.out' for details.
getUrlsCRN: no visible global function definition for 'getURL'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: 'httpcode'
  All declared Imports should be used.
GMLDfct: no visible global function definition for 'clusterApplyLB'
SNPgenmap: no visible binding for global variable 'RutgersMapB36'
doGeneDrops: no visible global function definition for 'write.pedfile'
doGeneDrops: no visible global function definition for 'GeneDrops'
doGeneDrops: no visible global function definition for 'read.pedfile'
flagAllPairs: no visible global function definition for 'showLabels'
flagPairs: no visible global function definition for 'showLabels'
gendrp: no visible global function definition for 'clusterApply'
get.ellipse: no visible global function definition for 'ellipse'
parfile.fitLD: no visible global function definition for
  'write.pedfile'
parfile.fitLD: no visible global function definition for
  'write.parfile'
parfile.fitLD: no visible global function definition for 'FitGMLD'
parfile.noLD: no visible global function definition for 'write.parfile'
snpfilter: no visible global function definition for 'row.summary'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CuCubes.Rcheck/00install.out' for details.
cudiaDet: no visible global function definition for 'rdirichlet'
cudiaDet: no visible global function definition for 'lm.ridge'
getoptimalalpha: no visible global function definition for 'gcvplot'
.klogreg: no visible global function definition for 'Matrix'
.klogreg: no visible global function definition for 'kernelMatrix'
.klogreg: no visible global function definition for 'Diagonal'
.klogreg.predict: no visible global function definition for
  'kernelMult'
.krr: no visible global function definition for 'kernelMatrix'
.krr: no visible global function definition for 'Matrix'
.krr.predict: no visible global function definition for 'kernelMatrix'
constructSVMLearner : learn.svm: no visible global function definition
  for 'ksvm'
constructSVRLearner : learn.svr: no visible global function definition
  for 'ksvm'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
initialize,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
updateD2C,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
compute,DAG.network : .local: no visible global function definition for
  'numNodes'
compute,DAG.network : .local: no visible global function definition for
  'inEdges'
initialize,D2C : .local: no visible binding for global variable 'i'
initialize,D2C : .local: no visible global function definition for
  'nodes'
initialize,D2C : .local: no visible global function definition for
  'subGraph'
initialize,D2C : .local: no visible global function definition for
  'inEdges'
initialize,simulatedDAG : .local: no visible binding for global
  variable 'i'
initialize,simulatedDAG : .local: no visible global function definition
  for 'edges'
updateD2C,D2C : .local: no visible binding for global variable 'i'
updateD2C,D2C : .local: no visible global function definition for
  'nodes'
updateD2C,D2C : .local: no visible global function definition for
  'subGraph'
updateD2C,D2C : .local: no visible global function definition for
  'inEdges'
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
Daim: no visible global function definition for 'mclapply'
Daim: no visible global function definition for 'clusterSetRNGStream'
Daim: no visible global function definition for 'clusterEvalQ'
Daim: no visible global function definition for 'clusterApplyLB'
The following files are already in R: 'jss.bst', 'jss.cls'
Please remove them from your package.
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
meta,SftpLocation : .local: no visible global function definition for
  'basicTextGatherer'
meta,SftpLocation : .local: no visible binding for global variable
  'isdir'
meta,SftpLocation : .local: no visible binding for global variable
  'name'
put,BlogPostTarget-Blogger : .local: no visible global function
  definition for 'toJSON'
Package suggested but not available for checking: 'nanotime'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
plot.pcobiplot: no visible binding for global variable 'sveg'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible binding for global variable 'distEqCut'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dclone.Rcheck/00install.out' for details.
Plot.triangle: no visible global function definition for 'cloud'
Plot.triangle: no visible binding for global variable 'panel.3dbars'
Plot.triangle: no visible global function definition for 'level.colors'
Plot.triangle: no visible global function definition for 'do.breaks'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
+ ClusterSizeContribution = "POP8")
[1] 1 1
> 
> #Display results
> ny.cl1
           x       y size      minDateCluster      maxDateCluster statistic
88  409430.4 4720092    9 1972-01-01 01:00:00 1972-01-01 01:00:00  5.861204
119 404710.7 4768346   20 1972-01-01 01:00:00 1972-01-01 01:00:00  3.160591
          pvalue      risk cluster
88  0.0006175202 0.5869176    TRUE
119 0.0119304026 0.4882633    TRUE
> 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  11.95 0.35 15.37 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dcmle.Rcheck/00install.out' for details.
plot,attribute.class-missing : .local: no visible binding for global
  variable 'attr.number'
plot,attribute.class-missing : .local: no visible binding for global
  variable 'mean.attr'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'attr.profile.number'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'mean.attr.profile'
summary,attribute.class : .local: no visible binding for global
  variable 'value'
summary,attribute.profile.class : .local: no visible binding for global
  variable 'max.class'
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
.factorAnalysisRunFunction: no visible global function definition for
  'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeFactorAnalysisDialog: no visible binding for global variable
  'SimpleRDialog'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'addComponent'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableListWidget'
makeFactorAnalysisDialog: no visible binding for global variable
  'CheckBoxesWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'toJava'
makeListExampleDialog: no visible binding for global variable
  'ListWidget'
makeListExampleDialog: no visible global function definition for
  'setSize'
makeListExampleDialog: no visible binding for global variable
  'AddRemoveButtons'
makeListExampleDialog: no visible binding for global variable
  'SimpleRDialog'
makeListExampleDialog: no visible global function definition for
  'addComponent'
makeListExampleDialog: no visible global function definition for
  'toJava'
makeScatterPlotDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
'library' or 'require' call to 'UScensus2010' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'UScensus2010'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'JavaGD' 'OpenStreetMap' 'maptools' 'rgdal' 'scales' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.containedBy: no visible global function definition for
  'projectMercator'
.makeCensusDialog: no visible global function definition for 'J'
.makeCensusDialog: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jengine'
.onLoad: no visible global function definition for 'J'
.subsetLines: no visible global function definition for
  'projectMercator'
.subsetPoints: no visible global function definition for
  'projectMercator'
.subsetPoly: no visible global function definition for
  'projectMercator'
spatialBubblePlot: no visible global function definition for
  'coordinates'
spatialChoropleth: no visible global function definition for
  'manual_pal'
spatialChoropleth: no visible global function definition for
  'gradient_n_pal'
spatialChoropleth: no visible global function definition for 'cscale'
spatialColoredPoints: no visible global function definition for
  'manual_pal'
spatialColoredPoints: no visible global function definition for
  'gradient_n_pal'
spatialColoredPoints: no visible global function definition for
  'cscale'
spatialTextPlot: no visible global function definition for
  'coordinates'
.CompareRunFunction: no visible global function definition for
  'execute'
.KMRunFunction: no visible global function definition for 'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeCompareDialog: no visible binding for global variable
  'SimpleRDialog'
makeCompareDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeCompareDialog: no visible global function definition for
  'addComponent'
makeCompareDialog: no visible binding for global variable
  'SingleVariableWidget'
makeCompareDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeCompareDialog: no visible global function definition for 'toJava'
makeKMDialog: no visible binding for global variable 'SimpleRDialog'
makeKMDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeKMDialog: no visible global function definition for 'addComponent'
makeKMDialog: no visible binding for global variable
  'SingleVariableWidget'
makeKMDialog: no visible binding for global variable 'TextAreaWidget'
makeKMDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeKMDialog: no visible binding for global variable 'TextFieldWidget'
makeKMDialog: no visible global function definition for 'toJava'
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
bpstrip: no visible binding for global variable 'panel.polygon'
bpstrip: no visible binding for global variable 'panel.segments'
bpstrip: no visible global function definition for
  'current.panel.limits'
bpstrip: no visible global function definition for 'trellis.par.get'
cistrip: no visible binding for global variable 'panel.points'
cistrip: no visible binding for global variable 'panel.segments'
denstrip: no visible binding for global variable 'panel.rect'
denstrip: no visible binding for global variable 'panel.segments'
denstrip: no visible global function definition for
  'current.panel.limits'
denstrip: no visible global function definition for 'trellis.par.get'
denstrip.legend: no visible binding for global variable 'panel.polygon'
denstrip.legend: no visible binding for global variable
  'panel.segments'
denstrip.legend: no visible binding for global variable 'panel.text'
denstrip.legend: no visible global function definition for
  'current.panel.limits'
denstrip.legend: no visible global function definition for
  'trellis.last.object'
denstrip.legend: no visible global function definition for
  'trellis.par.get'
sectioned.density: no visible binding for global variable 'panel.rect'
sectioned.density: no visible global function definition for
  'current.panel.limits'
sectioned.density: no visible global function definition for
  'trellis.par.get'
vwstrip: no visible binding for global variable 'panel.polygon'
vwstrip: no visible binding for global variable 'panel.segments'
vwstrip: no visible global function definition for
  'current.panel.limits'
vwstrip: no visible global function definition for 'trellis.par.get'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DEploid.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.4Mb
Missing link or links in documentation object 'StrRep.Rd':
  'strrep'

See section 'Cross-references' in the 'Writing R Extensions' manual.
compute.p.values: no visible global function definition for 'ash2'
draw.single.detsel.graph: no visible global function definition for
  'ash2'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin   3.7Mb
    doc   1.7Mb
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
sectionview,function : .local: warning in sectionview.fun(fun = model,
  dim = dim, center = center, axis = axis, npoints = npoints, col =
  col, mfrow = mfrow, Xname = Xname, yname = yname, Xscale = Xscale,
  yscale = yscale, xlim = xlim, ylim = ylim, title = title, ...):
  partial argument match of 'col' to 'col_surf'
view,character-function : .local: warning in sectionview.fun(fun =
  model, dim = dim, center = center, axis = axis, npoints =
  ifelse(is.null(npoints), 100, npoints), col = col, mfrow = mfrow,
  Xname = Xname, yname = yname, Xscale = Xscale, yscale = yscale, xlim
  = xlim, ylim = ylim, title = title, ...): partial argument match of
  'col' to 'col_surf'
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'uniroot.all'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.3Mb
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'coordinates'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
EdgelistFromIgraph: no visible global function definition for
  'get.adjacency'
EdgelistFromIgraph: no visible global function definition for 'V'
EdgelistFromIgraph: no visible global function definition for 'vcount'
IgraphFromEdgelist: no visible global function definition for
  'graph.adjacency'
IgraphFromEdgelist: no visible global function definition for 'V'
IgraphFromEdgelist: no visible global function definition for 'V<-'
MeasureNetworkInformation: no visible binding for global variable
  'betweenness'
MeasureNetworkInformation: no visible global function definition for
  'vcount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'ecount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'delete.edges'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'E'
RelativeNetworkInformation: no visible binding for global variable
  'betweenness'
RssSuggestedNetwork: no visible global function definition for
  'get.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'is.directed'
RssSuggestedNetwork: no visible global function definition for 'vcount'
RssSuggestedNetwork: no visible global function definition for
  'graph.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'graph.density'
plot.discrimARTs: no visible global function definition for 'grid.text'
plot.discrimARTs: no visible global function definition for 'gpar'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
momIntegrated: multiple local function definitions for 'ddist' with
  different formal arguments
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    include  18.9Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.2Mb
hip: no visible global function definition for 'adiag'
.addEq: no visible global function definition for '.Eq'
.addSt: no visible global function definition for '.St'
plot.compExp: no visible global function definition for 'grid.newpage'
plot.compExp: no visible global function definition for 'pushViewport'
plot.compExp: no visible global function definition for 'viewport'
plot.compExp: no visible global function definition for 'grid.layout'
plot.compExp: no visible global function definition for 'bwplot'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.grid'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.bwplot'
plot.compExp: no visible global function definition for 'upViewport'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DNAprofiles.Rcheck/00install.out' for details.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Namespaces in Imports field not imported from:
  'GOstats' 'caTools' 'fdrtool'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
.randomize: no visible global function definition for '[.coded.data'
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.2/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-32~1.5/bin/Rscript", argv=0x000000000A90CCC0, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x000000000A6B6898, errors=0x000000000A85B4E0) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
dpmixsim: no visible global function definition for 'clara'
postkcluster: no visible global function definition for 'clara'
readsliceimg: no visible global function definition for 'readNIfTI'
depratio: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
drm: warning in match.call(expand = FALSE): partial argument match of
  'expand' to 'expand.dots'
Namespace in Imports field not imported from: 'shapefiles'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dSVA.Rcheck/00install.out' for details.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
filt: no visible global function definition for 'wavDaubechies'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dynamichazard.Rcheck/00install.out' for details.
bootstrapCI: no visible global function definition for 'lpepa'
dynamicCorrelation: no visible global function definition for 'lpepa'
PredictPropen,modelObjFit-data.frame : .local: no visible global
  function definition for 'level'
PlotPotential: no visible global function definition for 'aes'
PlotPotential: no visible global function definition for 'geom_tile'
PlotPotential: no visible global function definition for
  'scale_fill_gradient'
PlotPotential: no visible global function definition for 'stat_contour'
PlotPotential: no visible global function definition for 'xlab'
PlotPotential: no visible global function definition for 'ylab'
PlotPotential: no visible global function definition for 'labs'
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2' 'scales' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  'base64encode'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/EasyMARK.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: compare(object, expected, ...)
  3: EnsRoca(fcst4, obs2)
  4: count2prob(ens, type = 4)
  5: stopifnot(is.wholenumber(rowSums(x)))
  6: stop(sprintf(ngettext(length(r), "%s is not TRUE", "%s are not all TRUE"), ch), call. = FALSE, 
         domain = NA)
  
  testthat results ================================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Error: ROC area values (@test_Roc.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
decdfHT: possible error in findInterval(x[i], ecdfHT.fit$xsort,
  rightmost.closed = TRUE, all.inside = TRUE, left.open = FALSE):
  unused argument (left.open = FALSE)
Running examples in 'ecdfHT-Ex.R' failed
The error most likely occurred in:

> ### Name: pecdfHT
> ### Title: Compute cdf, pdf, quantiles, and simulate from a fitted
> ###   distribution
> ### Aliases: decdfHT pecdfHT qecdfHT recdfHT
> 
> ### ** Examples
> 
> x <- rcauchy(1000)
> a <- ecdfHT( x, show.plot=FALSE )
> fit <- ecdfHT.fit( c(.1,.9), a, add.to.plot=FALSE )
> pecdfHT( -3:3, fit )
[1] 0.08621799 0.12705058 0.23166862 0.47955015 0.72400844 0.82998740 0.87927967
> decdfHT( -3:3, fit )
Error in findInterval(x[i], ecdfHT.fit$xsort, rightmost.closed = TRUE,  : 
  unused argument (left.open = FALSE)
Calls: decdfHT -> findInterval
Execution halted
Package required and available but unsuitable version: 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ecipex: no visible binding for global variable 'nistiso'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
.echCusum1: no visible global function definition for 'xcusum.arl'
.echCusum2: no visible global function definition for 'xcusum.arl'
.echEwma1: no visible global function definition for 'xewma.arl'
.echEwma2: no visible global function definition for 'xewma.arl'
echCusum: no visible global function definition for 'xcusum.arl'
echEwma: no visible global function definition for 'xewma.arl'
ecoCusum: no visible global function definition for 'xcusum.arl'
ecoEwma: no visible global function definition for 'xewma.arl'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/eggCounts.Rcheck/00install.out' for details.
Y_impute: no visible binding for global variable 'pp_zq'
Y_impute: no visible binding for global variable 'Ranks'
Y_impute: no visible binding for global variable 'Z'
eigenmodel_setup: no visible binding for global variable 'Y'
rUL_fc: no visible binding for global variable 'Z'
rUL_fc: no visible binding for global variable 'X'
rUL_fc: no visible binding for global variable 'b'
rUL_fc: no visible binding for global variable 'UL'
rUL_fc: no visible binding for global variable 'R'
rUL_fc: no visible binding for '<<-' assignment to 'mean_u'
rUL_fc: no visible binding for global variable 'var_u'
rUL_fc: no visible binding for global variable 'pp_mu'
rUL_fc: no visible binding for global variable 'pm_mu'
rUL_fc: no visible binding for global variable 'n'
rUL_fc: no visible binding for global variable 'mean_u'
rUL_fc: no visible binding for global variable 'pp_l'
rZ_fc: no visible binding for global variable 'X'
rZ_fc: no visible binding for global variable 'b'
rZ_fc: no visible binding for global variable 'UL'
rZ_fc: no visible binding for global variable 'pp_zq'
rZ_fc: no visible binding for global variable 'Ranks'
rZ_fc: no visible binding for global variable 'uRanks'
rZ_fc: no visible binding for global variable 'n'
rb_fc: no visible binding for global variable 'Z'
rb_fc: no visible binding for global variable 'UL'
rb_fc: no visible binding for global variable 'pm_b'
rb_fc: no visible binding for global variable 'xtx'
rb_fc: no visible binding for global variable 'pp_b'
rb_fc: no visible binding for global variable 'tx'
cluster.segment: no visible global function definition for 'knn'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
ei.MD.bayes: warning in BayesMDei2(formula, data, total = total,
  lambda1 = lambda1, lambda2 = lambda2, tune.alpha = tune.alpha,
  tune.beta = tune.beta, start.alpha = start.alphas, start.betas =
  start.betas, sample = sample, thin = thin, burnin = burnin, verbose =
  verbose, ret.beta = ret.beta, ret.mcmc = ret.mcmc, usrfun = usrfun):
  partial argument match of 'start.alpha' to 'start.alphas'
tuneMD: warning in ei.MD.bayes(formula, covariate = covariate, data =
  data, sample = sample, thin = thin, burnin = burnin, tune = tl, ...):
  partial argument match of 'tune' to 'tune.list'
bayes.regress : truncMVRnorm: no visible global function definition for
  'mvrnorm'
bayes.regress: no visible binding for global variable 'mvrnorm'
cover.plot: no visible global function definition for 'is.mcmc'
density.plot.lambdaMD: no visible global function definition for
  'is.mcmc'
density.plot.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
lambda.MD: no visible global function definition for 'is.mcmc'
lambda.MD: no visible global function definition for 'mcpar'
mergeMD: no visible global function definition for 'mcmc'
print.eiMD: no visible global function definition for 'is.mcmc'
read.betas: no visible global function definition for 'as.mcmc'
summary.eiMD: no visible global function definition for 'is.mcmc'
summary.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
BaB: no visible binding for global variable 'calc.pairwise.e_p'
BaB: no visible global function definition for 'weight.function'
BaB: no visible global function definition for 'compute.stark.t'
LKPBound: no visible binding for global variable 'calc.pairwise.e_p'
LKPBound: no visible global function definition for 'weight.function'
LKPBound: no visible global function definition for 'compute.stark.t'
eqValBound: no visible binding for global variable 'calc.pairwise.e_p'
eqValBound: no visible global function definition for 'weight.function'
eqValBound: no visible global function definition for 'compute.stark.t'
getEbsMargin: no visible global function definition for 'is.elec.data'
getEbsMargin: no visible global function definition for
  'maximumMarginBound'
makeStratObj: no visible global function definition for 'is.elec.data'
makeStratObj: no visible global function definition for
  'maximumMarginBound'
strat.elec.data: no visible global function definition for 'elec.data'
takeOutZeroMMB: no visible global function definition for
  'maximumMarginBound'
withReplaceBound: no visible binding for global variable
  'calc.pairwise.e_p'
withReplaceBound: no visible global function definition for
  'weight.function'
withReplaceBound: no visible global function definition for
  'compute.stark.t'
Namespaces in Imports field not imported from:
  'prettyunits' 'ratelimitr' 'rgdal'
  All declared Imports should be used.
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
################################################################################

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
################################################################################

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Warning: namespace 'embryogrowth' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.2/embryogrowth.Rcheck/00install.out' for details.
File 'EMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Evolutionary Monte Carlo Package (EMC)\n",     "##\n", "## Functionality: random walk Metropolis, general Metropolis-Hastings\n",     "## parallel tempering, target oriented EMC (TOEMC), temperature ladder\n",     "## construction and placement\n", "##\n", "## Use: \"help(package = EMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.

CigarShapedFuncGenerator1 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
CigarShapedFuncGenerator2 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
VShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
WShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : logTarDensFunc: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : propNewFunc: no visible global function
  definition for 'mvrnorm'
twentyModeFuncGenerator : logTarDensFunc : <anonymous>: no visible
  global function definition for 'dmvnorm'
uniModeFuncGenerator : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  'data.Normalization'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
MFFetch: no visible global function definition for 'melt'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
fmmst.contour.3d: no visible global function definition for 'plot3d'
fmmst.contour.3d: no visible global function definition for 'points3d'
Error in re-building vignettes:
  ...
Quitting from lines 119-144 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
ENMCA : fn: no visible global function definition for 'assignCluster'
ENMCA : fn: no visible global function definition for 'catdes'
ENMCA : fn: no visible global function definition for 'plot.MCA'
ENdensity: no visible global function definition for 'kde2d'
ENlisib: no visible global function definition for 'plot.MCA'
MCA2: no visible global function definition for 'tab.disjonctif'
MCA2: no visible global function definition for 'PCA'
MCA2: no visible global function definition for 'CA'
MCA2: no visible global function definition for 'plot.MCA'
XvsYbarplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
XvsYbarplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
XvsYbarplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 0.4 +
  (cont[j]/max) * 0.6, v = 1, 1, 1): unused argument (1)
barplot_sweave : set.X: no visible binding for global variable 'X'
chisq.function: no visible global function definition for 'coltable'
col.barplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
col.barplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
col.barplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
p_inertia: no visible global function definition for 'MCA'
tab_chi2: no visible global function definition for 'coltable'
KM.plot.ade : plot.box.ade: no visible global function definition for
  'axis.break'
KM.plot.ade: no visible global function definition for 'survfit'
KM.plot.ade: no visible global function definition for 'survdiff'
a.form.ade: no visible global function definition for 'cylindrect'
a.form.ade : sub.ellipse.ade : gradient.rect.ade: no visible global
  function definition for 'color.gradient'
box.plot.ade : a.draw.box: no visible global function definition for
  'cylindrect'
box.plot.wtd : wtd.sd: no visible global function definition for
  'wtd.var'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.mean'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.quantile'
box.plot.wtd : a.draw.box: no visible global function definition for
  'cylindrect'
histogram.ade: no visible global function definition for
  'weighted.hist'
pr2 : fa22: no visible global function definition for 'Anova'
eqs2lavaan: no visible binding for global variable 'r'
topoplot: no visible global function definition for 'interp'
esgplotshocks: no visible global function definition for 'geom_point'
esgplotshocks: no visible global function definition for 'aes'
esgplotshocks: no visible global function definition for 'theme'
esgplotshocks: no visible global function definition for
  'element_blank'
esgplotshocks: no visible global function definition for
  'scale_color_manual'
esgplotshocks: no visible global function definition for 'geom_density'
esgplotshocks: no visible global function definition for
  'scale_fill_manual'
esgplotshocks: no visible global function definition for 'coord_flip'
esgplotts: no visible global function definition for 'xlab'
esgplotts: no visible global function definition for 'ylab'
esgplotts: no visible global function definition for 'theme'
iqr_cell: no visible global function definition for 'wtd.quantile'
mean_sd_cell: no visible global function definition for 'wtd.mean'
mean_sd_cell: no visible global function definition for 'wtd.var'
mode_cell: no visible global function definition for 'wtd.table'
quantile_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.mean'
stat_cell: no visible global function definition for 'wtd.var'
stat_cell: no visible global function definition for 'wtd.table'
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
read_eventdata : read_ed_file: warning in read.csv(d, sep = sep, head =
  head, strip.white = TRUE, colClasses = "character"): partial argument
  match of 'head' to 'header'
ees: no visible global function definition for 'zoo'
eesPlot: no visible global function definition for 'index'
gen.data: no visible global function definition for 'index'
gen.data: no visible global function definition for 'coredata'
get.clusters.formatted: no visible global function definition for 'xts'
get.clusters.formatted: no visible global function definition for 'zoo'
inference.Ecar: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for
  'boot.ci'
phys2eventtime : timeshift: no visible global function definition for
  'index'
phys2eventtime : timeshift: no visible global function definition for
  'zoo'
phys2eventtime: no visible global function definition for 'zoo'
phys2eventtime: no visible global function definition for 'na.locf'
sumstat: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'apply.yearly'
yearly.exevent.summary: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'index<-'
yearly.exevent.summary: no visible global function definition for
  'as.yearmon'
yearly.exevent.summary: no visible global function definition for
  'index'
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
expectreg.boost: no visible global function definition for 'mclapply'
expectreg.boost: no visible global function definition for
  'detectCores'
laws: no visible global function definition for 'mclapply'
laws: no visible global function definition for 'detectCores'
quant.boost: no visible global function definition for 'mclapply'
quant.boost: no visible global function definition for 'detectCores'
rb: no visible global function definition for 'cover.design'
ATEbounds: no visible global function definition for 'boot'
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
computeConstraints: no visible global function definition for
  'minmaxHelper'
coreCA: no visible global function definition for 'repmat'
coreMDS: no visible global function definition for 'repmat'
corePCA: no visible global function definition for 'repmat'
epGraphs: no visible global function definition for
  'createColorVectorsByDesign'
epGraphs: no visible global function definition for 'prettyPlot'
epGraphs: no visible global function definition for 'contributionBars'
makeNominalData: no visible global function definition for 'repmat'
mca.eigen.fix: no visible global function definition for 'repmat'
pcaSupplementaryColsPreProcessing: no visible global function
  definition for 'repmat'
pcaSupplementaryRowsPreProcessing: no visible global function
  definition for 'repmat'
rowNorms: no visible global function definition for 'repmat'
supplementalProjection: no visible global function definition for
  'repmat'
node.age: no visible global function definition for 'is.binary.tree'
node.age: no visible global function definition for 'multi2di'
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for 'ripras'
Namespace in Imports field not imported from: 'affy'
  All declared Imports should be used.
extfunnel: no visible global function definition for 'meta.summaries'
misc : q: no visible global function definition for 'name'
Namespace in Imports field not imported from: 'FactoMineR'
  All declared Imports should be used.
bayesQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
bayesQR: warning in matrix(beta, nc = 1): partial argument match of
  'nc' to 'ncol'
factorQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
factorQR: warning in matrix(rnorm(nObs * nFact), nr = nObs): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nr' to
  'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nc' to
  'ncol'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nc' to 'ncol'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * nFact), nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * xLength), nc = xLength): partial
  argument match of 'nc' to 'ncol'
plot.bayesQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
plot.factorQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
as.FAMTdata: no visible global function definition for 'impute.knn'
nbfactors : bivprob : <anonymous>: no visible global function
  definition for 'biv.nt.prob'
File 'fANCOVA/R/onload.R':
  .onLoad calls:
    packageStartupMessage("fANCOVA 0.5-1 loaded")

See section 'Good practice' in '?.onAttach'.
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Namespace in Imports field not imported from: 'whisker'
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
mis.cluster: no visible global function definition for 'permn'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fcros.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fdasrvf.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/feather.Rcheck/00install.out' for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'base' 'graphics' 'stats'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ncdf4' 'rgeos'
  All declared Imports should be used.
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.halton'
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.sobol'
EasyExpressCertificate: no visible global function definition for
  'CashOrNothingOption'
EasyExpressCertificate: no visible global function definition for
  'GBSOption'
ExpressCertificate: no visible global function definition for
  'GBSOption'
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
garchFit: no visible binding for global variable 'dem2gbp'
fitted,fGARCH : .local: no visible binding for global variable 'fit'
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Error in re-building vignettes:
  ...
Loading required package: RSQLite
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/filesstrings.Rcheck/00install.out' for details.
FinTS.stats: no visible global function definition for 'skewness'
FinTS.stats: no visible global function definition for 'kurtosis'
Unitroot: no visible global function definition for 'adfTest'
Unitroot: no visible global function definition for 'unitrootTest'
plotArmaTrueacf: no visible global function definition for 'polynomial'
summary.fHTEST: no visible global function definition for 'padf'
fem.estep: no visible global function definition for 'ginv'
fem.loglik: no visible global function definition for 'ginv'
fstep.GramSc: no visible global function definition for 'ginv'
fstep.fisher: no visible global function definition for 'ginv'
fstep.qiao: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'enet'
fstep.sparse: no visible global function definition for 'predict.enet'
FitARMA: no visible global function definition for 'PacfDL'
FitARMA: no visible global function definition for 'GetARMeanMLE'
FitARMA: no visible global function definition for
  'BackcastResidualsAR'
FitARMA: no visible global function definition for 'LjungBoxTest'
GetFitARMA: no visible global function definition for 'LoglikelihoodAR'
GetFitARMA: no visible global function definition for 'ChampernowneD'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfToAR'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfDL'
GetFitARMA : EntropyARMA: no visible global function definition for
  'FastLoglikelihoodAR'
GetFitARMA: no visible global function definition for 'PacfToAR'
InformationMatrixARMA: no visible global function definition for
  'InvertibleQ'
TacvfARMA: no visible global function definition for 'InvertibleQ'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FIT.Rcheck/00install.out' for details.
saveMarkerModels: no visible global function definition for
  'registerDoMC'
saveMarkerModels: no visible global function definition for '%dopar%'
saveMarkerModels: no visible global function definition for 'foreach'
start.plot: no visible global function definition for 'emf'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/flan.Rcheck/00install.out' for details.
getDifferentCluster: no visible global function definition for
  'solve_LSAP'
plot,FLXboot-missing : .local: no visible global function definition
  for 'rmvnorm'
plot,flexmix-missing : .local: no visible binding for global variable
  'cluster'
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
flip.adjust : <anonymous>: no visible global function definition for
  'adjusted'
mf.flux: no visible global function definition for 'runsd'
fmt.default: no visible global function definition for 'loessFit'
fmt.default: no visible global function definition for
  'trigammaInverse'
analyse.list: no visible binding for '<<-' assignment to 'files'
analyse.list: no visible binding for global variable 'files'
analyse.list: no visible binding for '<<-' assignment to 'foodweb'
analyse.list: no visible binding for '<<-' assignment to 'name'
analyse.list: no visible binding for global variable 'foodweb'
analyse.list: no visible binding for global variable 'name'
analyse.list: no visible binding for global variable 'indices'
analyse.seq: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'name'
analyse.single: no visible binding for global variable 'name'
analyse.single: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'levels.l'
analyse.single: no visible binding for global variable 'S'
analyse.single: no visible binding for global variable 'omn.l'
calculate.metrics: no visible binding for '<<-' assignment to 'S'
calculate.metrics: no visible binding for global variable 'S'
calculate.metrics: no visible binding for '<<-' assignment to 'indices'
calculate.metrics: no visible binding for global variable 'indices'
plotweb: no visible binding for global variable 'foodweb'
plotweb: no visible binding for global variable 'S'
INFCvpe: no visible binding for global variable 'INFCstats'
INFCvpe: no visible binding for global variable 'INFCdomain'
fwdglm: warning in glm.fit(x = x[bsb, ], y = y[bsb], w = weights[bsb],
  offset = obsb, family = family, control = glm.control(epsilon =
  epsilon, maxit = maxit)): partial argument match of 'w' to 'weights'
lmsglm : subset.median: warning in glm.fit(x[bsb, ], ybsb, family =
  family, w = weights[bsb], offset = obsb, control =
  glm.control(epsilon = epsilon, maxit = maxit)): partial argument
  match of 'w' to 'weights'
lmsglm: warning in glm.fit(x[bsb, ], y[bsb], family = family, w =
  weights[bsb], offset = obsb, control = glm.control(epsilon = epsilon,
  maxit = maxit)): partial argument match of 'w' to 'weights'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fractal.random: no visible global function definition for 'flog.debug'
fractal.random: no visible global function definition for 'xts'
fractal.uniform: no visible global function definition for 'flog.debug'
fractal.uniform: no visible global function definition for 'xts'
getPortfolioPrices: no visible binding for global variable
  'holidayNYSE'
getPortfolioPrices: no visible binding for global variable
  'sampleInitiators'
getPortfolioPrices: no visible global function definition for
  'anylength'
getPortfolioPrices: no visible binding for global variable
  'sampleGenerators'
getPortfolioPrices: no visible global function definition for 'index<-'
getPortfolioPrices: no visible global function definition for
  'anynames<-'
getTradingDates: no visible binding for global variable 'holidayNYSE'
getTradingDates: no visible global function definition for
  'timeSequence'
getTradingDates: no visible global function definition for 'isBizday'
getTradingDates: no visible global function definition for 'anylength'
next.seeds: no visible global function definition for 'flog.debug'
ou.process: no visible global function definition for 'xts'
plotReturns: no visible global function definition for 'Delt'
expandSlash : <anonymous>: no visible global function definition for
  'makeInteraction'
predict.FRBmultireg: no visible global function definition for
  'predict.mlm'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'textxy'
chgbasismat: no visible global function definition for 'splineDesign'
coef.freekt: no visible global function definition for 'splineDesign'
fitted.freekt: no visible global function definition for 'splineDesign'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FREGAT.Rcheck/00install.out' for details.
Bell : nways: no visible global function definition for 'setparts'
Bell: no visible global function definition for 'restrictedparts'
CalIncLapInt: no visible global function definition for 'is.whole'
CalIncLapInt: no visible global function definition for 'mpfr'
CalIncLapInt: no visible global function definition for 'chooseMpfr'
lrtest.frontier: no visible binding for global variable
  'lrtest.default'
Namespaces in Imports field not imported from:
  'R.utils' 'grDevices' 'graphics' 'matrixStats' 'stats'
  All declared Imports should be used.
.alignment: warning in lm(Y ~ X, dat = fr): partial argument match of
  'dat' to 'data'
.alignment: warning in lm(as.formula(form), dat = fr): partial argument
  match of 'dat' to 'data'
display.tests: no visible binding for global variable 'parameter.list'
display.tests: no visible binding for global variable 'sigs'
display.tests: no visible binding for global variable 'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'parameter.list'
run.analysis: no visible binding for global variable 'centers'
run.cluster.matrix: no visible binding for global variable 'amps'
run.cluster.matrix: no visible binding for global variable
  'clust.constant'
run.cluster.matrix: no visible binding for global variable 'spect.base'
run.lrg.peaks: no visible binding for global variable 'spect.base'
fugeR.sfRun: no visible global function definition for 'sfInit'
fugeR.sfRun: no visible global function definition for 'sfLibrary'
fugeR.sfRun: no visible global function definition for 'sfExport'
fugeR.sfRun: no visible global function definition for 'sfLapply'
fugeR.sfRun: no visible global function definition for 'sfStop'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'FunCluster/R/FunCluster.R':
  .First.lib calls:
    cat(paste("\nThis is FunCluster package version ", f.version,     " maintained by Corneliu Henegar.\n\n", "FunCluster(wd='', org='HS', go.direct=FALSE, clusterm='cc', compare='common.correl.genes',\n",     "\tcorr.met='greedy', corr.th=0.85, two.lists=TRUE, restrict=FALSE, alpha=0.05,\n",     "\tlocation=FALSE, details=FALSE)\n\n", sep = ""))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial argument
  match of 'label' to 'labels'
MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
  argument match of 'label' to 'labels'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
  'nrow'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
  'ncol'
dualpathFusedX.mod: no visible global function definition for
  'graph.adjacency'
dualpathFusedX.mod: no visible global function definition for
  'clusters'
dualpathFusedX.mod: no visible global function definition for 'ginv'
dualpathFusedX.mod: no visible global function definition for
  'subcomponent'
dualpathFusedX.mod: no visible global function definition for 'rBind'
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable 'nn'
plotMF: no visible global function definition for 'interpSpline'
fxreturns: no visible binding for global variable 'FXRatesCHF'
gbreakpoints: no visible global function definition for '%dopar%'
gbreakpoints: no visible global function definition for 'foreach'
DBNScoreStep1: no visible global function definition for 'rlm'
DBNScoreStep2: no visible global function definition for 'rlm'
GAMBoost: no visible global function definition for 'Matrix'
cv.GAMBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
gen.likelihood: no visible global function definition for 'startsWith'
getPEF: no visible global function definition for 'startsWith'
Running examples in 'gamlss-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.likelihood
> ### Title: A function to generate the likelihood function from a GAMLSS
> ###   object
> ### Aliases: gen.likelihood
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(aids)
> m1 <- gamlss(y~x+qrt, data=aids, family=NBI)
GAMLSS-RS iteration 1: Global Deviance = 492.7119 
GAMLSS-RS iteration 2: Global Deviance = 492.6375 
GAMLSS-RS iteration 3: Global Deviance = 492.6373 
> logL<-gen.likelihood(m1)
Error in gen.likelihood(m1) : could not find function "startsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gamsel.Rcheck/00install.out' for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
gboot: no visible global function definition for 'boot'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gbs2ploidy.Rcheck/00install.out' for details.
IsValidGDELT: no visible global function definition for 'md5sum'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.2Mb
Running examples in 'gemtc-Ex.R' failed
The error most likely occurred in:

> ### Name: mtc.hy.prior
> ### Title: Set priors for the heterogeneity parameter
> ### Aliases: mtc.hy.prior mtc.hy.empirical.lor
> 
> ### ** Examples
> 
> # NOTE: the mtc.run commands below are for illustrative purposes, such a small
> # number of iterations should obviously not be used in practice.
> 
> # set a uniform prior standard deviation
> model1 <- mtc.model(smoking, hy.prior=mtc.hy.prior("std.dev", "dunif", 0, 2))
> result <- mtc.run(model1, n.adapt=10, n.iter=10)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
arrange_probabel_phe: no visible global function definition for
  'databel'
as.genotype.snp.data: no visible global function definition for
  'genotype'
check.marker.internal: no visible global function definition for
  'qvalue'
extract.annotation.impute: no visible global function definition for
  'extract_text_file_columns'
extract.annotation.mach: no visible global function definition for
  'extract_text_file_columns'
impute2databel: no visible global function definition for
  'get_temporary_file_name'
impute2databel: no visible global function definition for
  'text2databel'
impute2databel: no visible global function definition for
  'get_dimnames'
impute2databel: no visible global function definition for 'apply2dfo'
impute2databel: no visible global function definition for 'databel'
impute2databel: no visible global function definition for
  'set_dimnames<-'
impute2databel: no visible global function definition for 'disconnect'
impute2mach: no visible global function definition for 'get_dimnames'
impute2mach: no visible global function definition for 'disconnect'
mach2databel: no visible global function definition for
  'get_temporary_file_name'
mach2databel: no visible global function definition for 'text2databel'
mach2databel: no visible global function definition for 'get_dimnames'
minimac2databel: no visible global function definition for
  'get_temporary_file_name'
minimac2databel: no visible global function definition for
  'text2databel'
minimac2databel: no visible global function definition for
  'get_dimnames'
polygenic: no visible global function definition for 'ginv'
polygenic_hglm: no visible global function definition for 'hglm'
polygenic_hglm: no visible global function definition for 'ginv'
scan.haplo: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'score.sim.control'
header.info: no visible global function definition for 'mmap'
header.info: no visible global function definition for 'char'
header.info: no visible global function definition for 'is.mmap'
header.info: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'mmap'
read.bin: no visible global function definition for 'char'
read.bin: no visible global function definition for 'is.mmap'
read.bin: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'uint8'
GeneFeST: no visible global function definition for 'as.mcmc'
NCPUS: no visible global function definition for 'detectCores'
NCPUS: no visible global function definition for 'makeCluster'
importance: no visible global function definition for 'clusterExport'
importance: no visible global function definition for 'clusterEvalQ'
importance: no visible global function definition for 'parApply'
importance: no visible global function definition for 'stopCluster'
parallelFindBest: no visible global function definition for 'parApply'
parallelSignatureFinder: no visible global function definition for
  'parApply'
puttingAllTogether: no visible global function definition for
  'makeCluster'
puttingAllTogether: no visible global function definition for
  'stopCluster'
seedsFinder: no visible global function definition for 'clusterExport'
seedsFinder: no visible global function definition for 'clusterEvalQ'
seedsFinder: no visible global function definition for 'parApply'
seedsFinder: no visible global function definition for 'stopCluster'
signatureFinder: no visible global function definition for
  'clusterExport'
signatureFinder: no visible global function definition for
  'clusterEvalQ'
signatureFinder: no visible global function definition for
  'stopCluster'
testGE: no visible global function definition for 'clusterExport'
testGE: no visible global function definition for 'parApply'
testGE: no visible global function definition for 'stopCluster'
groupGenotype: no visible global function definition for 'mapLevels<-'
groupGenotype: no visible global function definition for 'as.levelsMap'
bandwidthselect: no visible global function definition for 'dpik'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.0Mb
Package suggested but not available for checking: 'sf'
Namespace in Imports field not imported from: 'agricolae'
  All declared Imports should be used.
gTree: no visible global function definition for 'ctree'
gTree: no visible global function definition for 'ctree_control'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gets.Rcheck/00install.out' for details.
gexmap : gexgraph: warning in axis(side = 2, at = min:max, tick = TRUE,
  lab = c(rep(min:max, 1)), cex.axis = 1): partial argument match of
  'lab' to 'labels'
gexmap : gexgraph: warning in axis(side = 1, at = seq(1, (may + 1), by
  = 5), tick = TRUE, lab = c(seq(0, may, by = 5)), cex.axis = 1):
  partial argument match of 'lab' to 'labels'
Namespace in Imports field not imported from: 'plotly'
  All declared Imports should be used.
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespaces in Imports field not imported from:
  'dplyr' 'ggmap' 'gridExtra' 'scales' 'tnet'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ggdmc.Rcheck/00install.out' for details.
Running examples in 'ggforce-Ex.R' failed
The error most likely occurred in:

> ### Name: facet_zoom
> ### Title: Facet data for zoom with context
> ### Aliases: facet_zoom
> 
> ### ** Examples
> 
> # Zoom in on the versicolor species on the x-axis
> ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) +
+     geom_point() +
+     facet_zoom(x = Species == "versicolor")
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 336-339 (Visual_Guide.Rmd) 
Error: processing vignette 'Visual_Guide.Rmd' failed with diagnostics:
INTEGER() can only be applied to a 'integer', not a 'NULL'
Execution halted
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'XML' 'mapproj' 'moonBook'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'NHANES' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
prepare_Rd: geom_bar.Rd:94: unknown macro '\aesthetics'
prepare_Rd: geom_bin2d.Rd:76: unknown macro '\aesthetics'
prepare_Rd: geom_boxplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_contour.Rd:78: unknown macro '\aesthetics'
prepare_Rd: geom_count.Rd:66: unknown macro '\aesthetics'
prepare_Rd: geom_density.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_density_2d.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_dotplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_errorbarh.Rd:59: unknown macro '\aesthetics'
prepare_Rd: geom_hex.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_jitter.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_linerange.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_map.Rd:60: unknown macro '\aesthetics'
prepare_Rd: geom_path.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_point.Rd:90: unknown macro '\aesthetics'
prepare_Rd: geom_polygon.Rd:62: unknown macro '\aesthetics'
prepare_Rd: geom_qq.Rd:68: unknown macro '\aesthetics'
prepare_Rd: geom_quantile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_ribbon.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_rug.Rd:70: unknown macro '\aesthetics'
prepare_Rd: geom_segment.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_smooth.Rd:107: unknown macro '\aesthetics'
prepare_Rd: geom_spoke.Rd:61: unknown macro '\aesthetics'
prepare_Rd: geom_text.Rd:91: unknown macro '\aesthetics'
prepare_Rd: geom_tile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_violin.Rd:89: unknown macro '\aesthetics'
prepare_Rd: stat_function.Rd:68: unknown macro '\aesthetics'
prepare_Rd: stat_summary.Rd:78: unknown macro '\aesthetics'
prepare_Rd: stat_unique.Rd:58: unknown macro '\aesthetics'
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespace in Imports field not imported from: 'randomForest'
  All declared Imports should be used.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'gibbs.met/R/firstlib.R':
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
panel.pyramid: no visible global function definition for
  'trellis.par.get'
panel.pyramid: no visible global function definition for
  'current.panel.limits'
panel.pyramid: no visible global function definition for 'panel.abline'
panel.pyramid: no visible global function definition for 'panel.rect'
pyramid2.formula: no visible global function definition for
  'lattice.getOption'
pyramid2.formula: no visible global function definition for
  'is.shingle'
pyramid2.formula: no visible global function definition for
  'as.factorOrShingle'
useOuterStrips2 : new.strip: no visible global function definition for
  'strip.default'
useOuterStrips2 : new.strip.left: no visible global function definition
  for 'strip.default'
glm.fit2: no visible binding for global variable 'n'
el.CSW: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'llogp'
el.owen: no visible global function definition for 'llogpp'
el.owen: no visible global function definition for 'llog'
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  21.2Mb
glmnet.cr: no visible global function definition for 'glmnet'
glmpath.cr: no visible global function definition for 'glmpath'
predict.coxpath: no visible global function definition for 'coxph'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
predict.gnm: no visible binding for global variable 'eliminate'
cumres.lvmfit : myres: no visible global function definition for 'vars'
cumres.lvmfit: no visible global function definition for 'iid'
GOGANPA: no visible global function definition for 'GSE.Test.Main'
selectRho: no visible global function definition for
  'scaleFreeFitIndex'
goest,Goestica : .local: no visible global function definition for
  'fastICA'
Namespace in Imports field not imported from: 'googleCloudStorageR'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'roxygen2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca: no visible global function definition for 'scatterplot3d'
gpCovGrads: no visible global function definition for 'diag.spam'
gpUpdateAD: no visible global function definition for 'diag.spam'
gpUpdateKernels: no visible global function definition for 'diag.spam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gpuR.Rcheck/00install.out' for details.
Errors in running code in vignettes:
when running code in 'GRAN-Overview.Rnw'
  ...
Building 0 packages
starting migrateToFinalRepo 2017-02-11 18:28:19
Built 0 packages

  When sourcing 'GRAN-Overview.R':
Error: dims [product 0] do not match the length of object [1]
No traceback available 
> proc.time()
   user  system elapsed 
   1.13    0.43   22.86
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/graphql.Rcheck/00install.out' for details.
GrassmannOptim : <anonymous>: no visible global function definition for
  'expm'
GrassmannOptim : <anonymous>: no visible global function definition for
  'Matrix'
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
GriegSmith: no visible global function definition for 'is.ppp'
grouped: no visible binding for global variable 'n'
lL.gaussian: no visible binding for global variable 'p'
lL.gaussian: no visible binding for global variable 'X'
lL.gaussian: no visible binding for global variable 'qb'
lL.gaussian: no visible binding for global variable 'qa'
lL.logistic: no visible binding for global variable 'p'
lL.logistic: no visible binding for global variable 'X'
lL.logistic: no visible binding for global variable 'qb'
lL.logistic: no visible binding for global variable 'qa'
lL.t: no visible binding for global variable 'p'
lL.t: no visible binding for global variable 'X'
lL.t: no visible binding for global variable 'qb'
lL.t: no visible binding for global variable 'df.'
lL.t: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'p'
sc.gaussian: no visible binding for global variable 'X'
sc.gaussian: no visible binding for global variable 'qb'
sc.gaussian: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'qb.'
sc.gaussian: no visible binding for global variable 'qa.'
sc.logistic: no visible binding for global variable 'p'
sc.logistic: no visible binding for global variable 'X'
sc.logistic: no visible binding for global variable 'qb'
sc.logistic: no visible binding for global variable 'qa'
sc.logistic: no visible binding for global variable 'qb.'
sc.logistic: no visible binding for global variable 'qa.'
sc.t: no visible binding for global variable 'p'
sc.t: no visible binding for global variable 'X'
sc.t: no visible binding for global variable 'qb'
sc.t: no visible binding for global variable 'df.'
sc.t: no visible binding for global variable 'qa'
sc.t: no visible binding for global variable 'qb.'
sc.t: no visible binding for global variable 'qa.'
GSA: no visible global function definition for 'impute.knn'
plotgsCP: no visible global function definition for 'opts'
plotgsPower: no visible global function definition for 'opts'
qplotit: no visible global function definition for 'opts'
Namespace in Imports field not imported from: 'rrcov'
  All declared Imports should be used.
gee_wrap: no visible global function definition for 'gee'
geeglm_wrap: no visible global function definition for 'geeglm'
Found the following possibly unsafe calls:
File 'gtools/R/unByteCode.R':
  unlockBinding(name, env = env)
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-32\unhbox\voidb@x \penalty \@M \ {}1.
5/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Namespace in Imports field not imported from: 'rvest'
  All declared Imports should be used.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
AIC: no visible global function definition for 'hash'
AIC: no visible global function definition for 'values'
AIC: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'hash'
ODS.ror: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'keys'
ODS.ror: no visible global function definition for 'values'
ODS.ror: no visible global function definition for 'read.tree'
ODS.ror: no visible global function definition for 'nodelabels'
cc.sim: no visible global function definition for 'hash'
cc.sim: no visible global function definition for 'values<-'
cc.sim: no visible global function definition for 'values'
collapse: no visible global function definition for 'hash'
collapse: no visible global function definition for 'values<-'
collapse: no visible global function definition for 'keys'
collapse: no visible global function definition for 'values'
deletion: no visible global function definition for 'hash'
deletion: no visible global function definition for 'values<-'
deletion: no visible global function definition for 'keys'
deletion: no visible global function definition for 'values'
grp.list: no visible global function definition for 'hash'
grp.list: no visible global function definition for 'values'
Found the following significant warnings:
  readstat/stata/readstat_dta_read.c:181:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:366:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:584:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:831:21: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/3.2/haven.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'hms'
  All declared Imports should be used.
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: warning in symnum(correl, abbr.col = NULL): partial
  argument match of 'abbr.col' to 'abbr.colnames'
tlm: no visible binding for global variable 'response'
tlm: no visible binding for global variable 'dofse'
tscore: no visible binding for global variable 'response'
Btilde: no visible global function definition for 'bs'
hgam: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'grplasso'
hgam.fit: no visible global function definition for 'grpl.control'
hrisk: no visible binding for global variable 'mclapply'
hrisk : <anonymous>: no visible global function definition for
  'lambdamax'
plot.hrisk: no visible global function definition for 'plot3d'
plot.hrisk: no visible global function definition for 'levelplot'
gcline.fn: no visible global function definition for 'multinom'
Namespace in Imports field not imported from: 'quantmod'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
hand1: no visible binding for global variable 'name1'
hotelling.stat: no visible global function definition for 'cov.shrink'
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
get.pdf: no visible global function definition for 'dmvnorm'
hsmm.sim: no visible global function definition for 'rmvnorm'
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
humarray version 1.1

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
humarray version 1.1

The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
humarray version 1.1

See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
humarray version 1.1

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
humarray version 1.1

humarray version 1.1

humarray version 1.1
humarray version 1.1

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error in re-building vignettes:
  ...
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 153-159 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
replacement has 0 rows, data has 4973
Execution halted
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
hybridMC: no visible global function definition for 'mcmc'
Running examples in 'HydeNet-Ex.R' failed
The error most likely occurred in:

> ### Name: HydePosterior
> ### Title: Posterior Distributions of a Decision Network
> ### Aliases: HydePosterior
> 
> ### ** Examples
> 
> data(PE, package="HydeNet")
> Net <- HydeNetwork(~ wells + 
+                      pe | wells + 
+                      d.dimer | pregnant*pe + 
+                      angio | pe + 
+                      treat | d.dimer*angio + 
+                      death | pe*treat,
+                      data = PE) 
>   
>                  
> compiledNet <- compileJagsModel(Net, n.chains=5)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library("testthat")
  > library("HydeNet")
  Loading required package: nnet
  > 
  > test_check("HydeNet")
  Error: .onLoad failed in loadNamespace() for 'rjags', details:
    call: fun(libname, pkgname)
    error: The environment variable JAGS_HOME is set to
  c:/Program Files/JAGS/JAGS-4.0.0
  but no JAGS installation can be found there
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: nnet
Quitting from lines 314-325 (DecisionNetworks.Rmd) 
Error: processing vignette 'DecisionNetworks.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
hydromod: no visible global function definition for 'ggof'
plot_out: no visible global function definition for 'zoo'
plot_out: no visible global function definition for 'ggof'
plot_params.default: no visible global function definition for
  'vioplot'
plot_params.default: no visible global function definition for
  'hydropairs'
hyperbCvMTestPValue: no visible binding for global variable
  'hyperbWSqTable'
momIntegrated : ddist: no visible global function definition for 'dvg'
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
fitter.gen.rParam.uniform: no visible global function definition for
  '%do%'
fitter.gen.rParam.uniform: no visible global function definition for
  'foreach'
hzar.chain.doSeq: no visible global function definition for 'mcmc'
hzar.chain.doSeq: no visible global function definition for 'thin'
hzar.dataGroup.null: no visible global function definition for 'mcmc'
hzar.doChain.multi: no visible global function definition for '%dopar%'
hzar.doChain.multi: no visible global function definition for 'foreach'
hzar.doChain.multi: no visible global function definition for '%do%'
hzar.doFit: no visible global function definition for 'MCMCmetrop1R'
hzar.doFit.multi: no visible global function definition for '%dopar%'
hzar.doFit.multi: no visible global function definition for 'foreach'
hzar.doFit.multi: no visible global function definition for '%do%'
hzar.eval.clineLL: no visible global function definition for '%dopar%'
hzar.eval.clineLL: no visible global function definition for 'foreach'
hzar.eval.clineLL: no visible global function definition for '%do%'
hzar.fit2DataGroup: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'as.mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'thin'
hzar.profile.dataGroup: no visible global function definition for
  'equal.count'
hzar.profile.dataGroup: no visible global function definition for
  'foreach'
hzar.profile.dataGroup: no visible global function definition for
  '%dopar%'
hzar.profile.dataGroup: no visible global function definition for
  '%do%'
optimizeTrace: no visible global function definition for 'as.mcmc'
Namespaces in Imports field not imported from:
  'Rcpp' 'ggplot2' 'pander'
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.9Mb
TrainIBHM: no visible global function definition for 'enableJIT'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ibmdbR.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   1.2Mb
NB: this package is only installed for sub-architecture 'x64'
str_match_all: possible error in regexec(pattern, x, perl = perl,
  useBytes = useBytes): unused argument (perl = perl)
str_pair_match : <anonymous>: possible error in regexec(pattern =
  pattern, text = x, perl = perl, useBytes = useBytes): unused argument
  (perl = perl)
Running the tests in 'tests/test-current-no-comorbid.R' failed.
Last 13 lines of output:
  unused argument (perl = perl)
  1: expect_identical(chapter_to_desc_range.icd10("jack (A10-A20)"), list(Jack = c(start = "A10", 
         end = "A20"))) at testthat/test-current-util.R:135
  2: identical(object, expected)
  3: chapter_to_desc_range.icd10("jack (A10-A20)")
  4: .chapter_to_desc_range(x, re_major = re_icd10_major_bare)
  5: str_match_all(x, re_code_range)
  6: regmatches(x, regexec(pattern, x, perl = perl, useBytes = useBytes))
  7: regexec(pattern, x, perl = perl, useBytes = useBytes)
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
plot.ICEepmap: no visible global function definition for 'contourplot'
plotHeatmap: no visible global function definition for 'bluered'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.levelplot'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.abline'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.levelplot'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.abline'
plotHeatmap: no visible global function definition for 'levelplot'
tune.iCluster2: no visible binding for global variable 'glp'
tune.iCluster2: no visible global function definition for 'mclapply'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(ids)
  > 
  > test_check("ids")
  1. Failure: functional interface (@test-adjective-animal.R#64) -----------------
  all(grepl(re, x)) isn't true.
  
  
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: functional interface (@test-adjective-animal.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
agent_returnGridResolution: no visible global function definition for
  'xmlAttrs'
agent_returnIVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnJVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnKVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnSimIteration: no visible global function definition for
  'xmlAttrs'
agent_returnSimTime: no visible global function definition for
  'xmlAttrs'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlSize'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlAttrs'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlSize'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlName'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlAttrs'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlSize'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlAttrs'
env_returnSimIteration: no visible global function definition for
  'xmlAttrs'
env_returnSimTime: no visible global function definition for 'xmlAttrs'
env_returnSoluteGridIVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridJVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridKVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridRes: no visible global function definition for
  'xmlAttrs'
env_returnSpecifiedSoluteData: no visible global function definition
  for 'xmlSize'
env_soluteProductionRateOverTime: no visible global function definition
  for 'xmlValue'
readSimResultFile: no visible global function definition for
  'xmlTreeParse'
readSimResultFile: no visible global function definition for 'xmlRoot'
simpsonIndex: no visible global function definition for 'diversity'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  12.8Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs      6.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
select.lines: warning in symbols(long[segment[1:2]], lat[segment[1:2]],
  cir = c(1, 0.1), add = TRUE, col = 8): partial argument match of
  'cir' to 'circles'
IMIS: no visible global function definition for 'sample.prior'
IMIS: no visible global function definition for 'prior'
IMIS: no visible global function definition for 'likelihood'
IMIS : posterior: no visible global function definition for 'prior'
IMIS : posterior: no visible global function definition for
  'likelihood'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ImportExport.Rcheck/00install.out' for details.
FctReducedNodevalues: no visible global function definition for
  'cfunction'
TotalVar: no visible global function definition for 'lp'
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
heal_data: no visible global function definition for 'optimum_k'
heal_data: no visible global function definition for 'optimum_w'
heal_data: no visible global function definition for 'pred_for_w'
initialize,Image : .local: no visible global function definition for
  'readJPEG'
initialize,Image : .local: no visible global function definition for
  'readPNG'
initialize,Image : .local: no visible global function definition for
  'read.bmp'
initialize,OrthIm : .local: no visible binding for global variable
  'obj'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
infer,coxph : .local: no visible global function definition for
  'sandwich'
infer,glm : .local: no visible global function definition for
  'sandwich'
infer,lm : .local: no visible global function definition for 'sandwich'
infer,lme : .local: no visible global function definition for
  'fixed.effects'
infer,mer : .local: no visible binding for global variable 'fm1'
est.expDeath : surv_p: no visible global function definition for
  'survfit'
function1: no visible global function definition for 'coxph.detail'
var.expDeath : surv_p: no visible global function definition for
  'survfit'
getFixEF.onePhase: no visible global function definition for
  'fractions'
getFixEF.twoPhase: no visible global function definition for
  'fractions'
getVcCoefMS.onePhase: no visible global function definition for
  'fractions'
getVcCoefMS.onePhase : <anonymous>: no visible global function
  definition for 'fractions'
getVcCoefMS.twoPhase: no visible global function definition for
  'fractions'
getVcCoefMS.twoPhase : <anonymous>: no visible global function
  definition for 'fractions'
projMat: no visible global function definition for 'ginv'
trtProkMat: no visible global function definition for 'ginv'
Package required and available but unsuitable version: 'Rmixmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
boot.compute.fj: no visible global function definition for
  'supplementaryCols'
epCA.inference.battery : permute.components.ca: no visible global
  function definition for 'epCA'
epCA.inference.battery: no visible global function definition for
  'epCA'
epGPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epGPCA'
epGPCA.inference.battery: no visible global function definition for
  'epGPCA'
epMCA.inference.battery : permute.components.mca: no visible global
  function definition for 'epMCA'
epMCA.inference.battery: no visible global function definition for
  'makeNominalData'
epMCA.inference.battery: no visible global function definition for
  'epMCA'
epPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epPCA'
epPCA.inference.battery: no visible global function definition for
  'epPCA'
inGraphs: no visible global function definition for
  'createColorVectorsByDesign'
inGraphs: no visible global function definition for
  'calculateConstraints'
inGraphs: no visible global function definition for 'prettyPlot'
inGraphs: no visible global function definition for 'prettyBars'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'insideRODE/R/zzz.r':
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
cgrad: no visible global function definition for 'res'
doshade: no visible global function definition for 'projection'
doshade: no visible global function definition for 'extent'
doshade: no visible global function definition for 'res'
doshade: no visible global function definition for 'raster'
doshade: no visible global function definition for 'extent<-'
Namespace in Imports field not imported from: 'prodlim'
  All declared Imports should be used.
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'hessian'
f.grovest3 : f.est: no visible global function definition for 'survfit'
Namespace in Imports field not imported from: 'png'
  All declared Imports should be used.
summary,ipdlme: warning in pt(abs(stat), df = object@df, lower =
  FALSE): partial argument match of 'lower' to 'lower.tail'
.getListRegObjects: no visible global function definition for 'rmvnorm'
.getListRegObjectsFec: no visible global function definition for
  'rmvnorm'
diagnosticsPmatrix: no visible global function definition for
  'dtruncnorm'
sampleVitalRateObj: no visible global function definition for
  'rdirichlet'
sampleVitalRateObj: no visible global function definition for 'rmvnorm'
simulateCarlina: no visible global function definition for 'rmvnorm'
growth,numeric-numeric-data.frame-growthObjTruncIncr: no visible global
  function definition for 'dtruncnorm'
growthCum,numeric-numeric-data.frame-growthObjTruncIncr: no visible
  global function definition for 'ptruncnorm'
plot.htest: no visible global function definition for
  'normal.and.t.dist'
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
convert_edgeList_to_graph: no visible global function definition for
  'ftM2graphNEL'
convert_edgeList_to_graph: no visible global function definition for
  'graph.data.frame'
convert_graph_to_edgeList: no visible global function definition for
  'edgeWeights'
convert_graph_to_edgeList: no visible global function definition for
  'get.edgelist'
convert_graph_to_edgeList: no visible global function definition for
  'E'
summary_graph: no visible global function definition for
  'connectedComp'
summary_graph: no visible global function definition for 'subGraph'
summary_graph: no visible global function definition for 'clusters'
summary_graph: no visible global function definition for 'subgraph'
summary_graph: no visible binding for global variable
  'layout.fruchterman.reingold'
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
IS: no visible global function definition for 'mclapply'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/IUPS.Rcheck/00install.out' for details.
clusterVCV: no visible global function definition for 'estfun'
covc: no visible global function definition for 'sandwich'
ftest: no visible global function definition for 'vcovHC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jagsUI.Rcheck/00install.out' for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for 'invalid'
.getJavaGDObject: no visible global function definition for '.jmkref'
JavaGD: no visible global function definition for '.jinit'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jmotif.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'BayesFactor' 'GGally' 'GPArotation' 'PMCMR' 'afex' 'car' 'lsmeans'
  'lsr' 'multcomp' 'psych' 'vcd' 'vcdExtra'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import 'lme4::sigma' by 'nlme::sigma' when loading 'joineRML'
See 'd:/Rcompile/CRANpkg/local/3.2/joineRML.Rcheck/00install.out' for details.
JointRegBC.default: no visible global function definition for 'fdHess'
JointRegBC.default: no visible global function definition for 'ginv'
JOP: no visible global function definition for 'dglm'
JOP: no visible global function definition for 'gosolnp'
JOP: no visible global function definition for 'solnp'
Found the following significant warnings:
  Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
See 'd:/Rcompile/CRANpkg/local/3.2/JWileymisc.Rcheck/00install.out' for details.
KappaV: no visible global function definition for 'over'
plot,kaps-missing : .local: no visible global function definition for
  'locfit.censor'
kcirt.fitMSS: no visible global function definition for 'sfInit'
kcirt.fitMSS: no visible global function definition for 'sfExport'
kcirt.fitMSS: no visible global function definition for 'sfIsRunning'
kcirt.fitMSS: no visible global function definition for 'sfStop'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'cluster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller: no visible global function definition for 'daisy'
theme_ms: possible error in theme(axis.text = element_text(size =
  rel(0.8)), axis.ticks = element_line(colour = "black"), legend.key =
  element_rect(colour = "grey80"), panel.background = element_rect(fill
  = "white", colour = NA), panel.border = element_rect(fill = NA,
  colour = "grey50"), panel.grid.major = element_line(colour =
  "grey90", size = 0.2), panel.grid.minor = element_line(colour =
  "grey98", size = 0.5), strip.background = element_rect(fill =
  "grey80", colour = "grey50"), strip.background = element_rect(fill =
  "grey80", : formal argument "strip.background" matched by multiple
  actual arguments
theme_ms: possible error in colour = "grey50")): formal argument
  "strip.background" matched by multiple actual arguments
kobe2sm,data.frame : .local: no visible global function definition for
  'kobe2smFn'
kobe,data.frame-missing : .local : <anonymous>: no visible global
  function definition for 'kobeFn'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.0Mb
Package in Depends field not imported from: 'Sejong'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'rJava:::.jniInitialized'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.KoNLPEnv'
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
plot.krls: no visible global function definition for 'histogram'
readSelexFile: no visible global function definition for 'startsWith'
ROC.offset: no visible global function definition for 'pData'
ROC.offset: no visible global function definition for 'exprs'
ROC.voting: no visible global function definition for 'pData'
ROC.voting: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for
  'featureNames'
bootstrap.ktsp: no visible global function definition for 'pData'
ktspcalc: no visible global function definition for 'exprs'
ktspcalc: no visible global function definition for 'featureNames'
ktspcalc: no visible global function definition for 'pData'
ktspcalc2: no visible global function definition for 'exprs'
ktspcalc2: no visible global function definition for 'featureNames'
ktspcalc2: no visible global function definition for 'pData'
predict.ktsp: no visible global function definition for 'featureNames'
predict.ktsp: no visible global function definition for 'exprs'
updatePackages: possible error in available.packages(repos = repos):
  unused argument (repos = repos)
Errors in running code in vignettes:
when running code in 'variablekey.Rnw'
  ...
Warning in file(outfile, "w") :
  cannot open file 'plots/t-Roptions.R': No such file or directory

  When tangling 'variablekey.Rnw':
Error: cannot open the connection
Execution halted
cv.l2boost: no visible global function definition for 'detectCores'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
BSL: no visible global function definition for 'read.asciigrid'
PIF: no visible global function definition for 'read.asciigrid'
clouds: no visible global function definition for 'read.asciigrid'
geoshift: no visible global function definition for 'bbox'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeList.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeVis.Rcheck/00install.out' for details.
birthdeathSim: no visible global function definition for 'sim.bdtree'
birthdeathSim: no visible binding for global variable 'drop.tip'
birthdeathSim : fx: no visible global function definition for
  'branching.times'
getBtimes: no visible global function definition for 'read.tree'
getBtimes: no visible global function definition for 'is.ultrametric'
getBtimes: no visible global function definition for 'branching.times'
getBtimes.batch : btfx: no visible global function definition for
  'branching.times'
getBtimes.batch: no visible global function definition for 'read.tree'
getBtimes.batch: no visible binding for global variable
  'branching.times'
mccrTest: no visible global function definition for 'sim.bdtree'
mccrTest: no visible global function definition for 'drop.tip'
mccrTest: no visible global function definition for 'read.tree'
mccrTest: no visible binding for global variable 'gammaStat'
plotNodeNumbers.phylo: no visible global function definition for
  'plot.phylo'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include   4.3Mb
    libs      2.0Mb
Tkp: no visible global function definition for 'is.spam'
addObservations: no visible global function definition for 'bbox'
addObservations: no visible global function definition for 'as.ppp'
addObservations: no visible global function definition for 'nncross'
addQuantVar: no visible global function definition for 'bbox'
addQuantVar: no visible global function definition for 'as.ppp'
addQuantVar: no visible global function definition for 'nncross'
areaRegion: no visible global function definition for 'areapl'
editLattice: no visible global function definition for 'card'
formLattice: no visible global function definition for 'dnearneigh'
makeTmatrix: no visible global function definition for 'as.spam.listw'
makeTmatrix: no visible global function definition for 'nb2listw'
makeTmatrix: no visible global function definition for 'diag.spam'
makeTmatrix: no visible global function definition for 'nb2mat'
nodeFilling: no visible global function definition for 'inout'
nodeFilling: no visible global function definition for 'as.points'
plot.formLatticeOutput: no visible global function definition for
  'card'
predict.NparRegOut: no visible global function definition for 'bbox'
predict.NparRegOut: no visible global function definition for 'as.ppp'
predict.NparRegOut: no visible global function definition for 'nncross'
removeHole: no visible global function definition for 'inout'
lbfit.par : loglogistic.fit.optim : loglik.lb.loglogis: no visible
  global function definition for 'pllogis'
optim.const.ordi: no visible binding for global variable 'k'
LD.Measures: no visible global function definition for 'mclapply'
Fisher1sided: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
HWE2sided.table: warning in round(xtable, d = 4): partial argument
  match of 'd' to 'digits'
LD2sided.pvals: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(dprime, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(delta2, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(dprime, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(delta2, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(xtable, d = 3): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(ztable, d = 3): partial argument
  match of 'd' to 'digits'
leafletProxy: no visible global function definition for 'startsWith'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library(testthat)
  > library(leaflet)
  > 
  > test_check("leaflet")
  Error in library(sf) : there is no package called 'sf'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 41 SKIPPED: 0 FAILED: 0
  Execution halted
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
File 'LeLogicielR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(utils::packageDescription("LeLogicielR",     lib.loc = libname), appendLF = TRUE)

See section 'Good practice' in '?.onAttach'.
gap.default: no visible global function definition for 'makeCluster'
gap.default: no visible global function definition for 'clusterEvalQ'
gap.default: no visible global function definition for 'clusterApply'
gap.default: no visible global function definition for 'clusterCall'
gap.default: no visible global function definition for 'stopCluster'
lga.default: no visible global function definition for 'makeCluster'
lga.default: no visible global function definition for 'clusterEvalQ'
lga.default: no visible global function definition for 'clusterApplyLB'
lga.default: no visible global function definition for 'stopCluster'
rlga.default: no visible global function definition for 'makeCluster'
rlga.default: no visible global function definition for 'clusterEvalQ'
rlga.default: no visible global function definition for
  'clusterApplyLB'
rlga.default: no visible global function definition for 'stopCluster'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.3Mb
estimate_LC_pdf_state: no visible global function definition for
  'huge.select'
estimate_LC_pdf_state: no visible global function definition for 'huge'
search_knn: no visible global function definition for 'ann'
LICurvature.default: no visible global function definition for 'ginv'
Namespaces in Imports field not imported from:
  'Rcpp' 'rgeos'
  All declared Imports should be used.
Running examples in 'lidR-Ex.R' failed
The error most likely occurred in:

> ### Name: lastrees
> ### Title: Individual tree segmentation
> ### Aliases: lastrees
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Tree.laz", package="lidR")
> las = readLAS(LASfile, XYZonly = TRUE, filter = "-drop_z_below 0")
> 
> # compute a canopy image
> chm = grid_canopy(las, res = 0.5, subcircle = 0.1, na.fill = "knnidw", k = 4)
[using inverse distance weighting]
> chm = as.raster(chm)
> 
> # smoothing post-process (e.g. 2x mean)
> kernel = matrix(1,3,3)
> chm = raster::focal(chm, w = kernel, fun = mean)
> chm = raster::focal(chm, w = kernel, fun = mean)
> raster::plot(chm, col = height.colors(50)) # check the image
> 
> # segmentation (default parameters but th = 4 + extra output)
> extra = lastrees(las, "dalponte2016", chm, th = 4, extra = TRUE)
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector
Calls: lastrees -> dalponte2012 -> matrix -> as.vector
Execution halted
.N: no visible global function definition for 'mpfr'
LIHNPSD_prepare_data: no visible global function definition for
  'skewness'
LIHNPSD_prepare_data: no visible global function definition for
  'kurtosis'
LIHNPSD_standardfit_test: no visible global function definition for
  'skewness'
LIHNPSD_standardfit_test: no visible global function definition for
  'kurtosis'
LihnBetaPoly: no visible global function definition for 'Const'
LihnBetaPoly: no visible global function definition for 'getPrec'
LihnTildeFunction: no visible global function definition for 'Const'
LihnTildeFunction: no visible global function definition for 'getPrec'
prepare.LIHNPSD : D: no visible global function definition for 'mpfr'
prepare.LIHNPSD: no visible global function definition for 'Const'
psdunittest.LIHNPSD: no visible global function definition for
  'sintegral'
rawcdf.LIHNPSD : cdf: no visible global function definition for 'erf'
rawcdf.LIHNPSD : cdf: no visible global function definition for
  'T.Owen'
rawsn.LIHNPSD: no visible global function definition for 'erf'
standardfit.LIHNPSD: no visible global function definition for
  'skewness'
standardfit.LIHNPSD: no visible global function definition for
  'kurtosis'
standardfit.LIHNPSD: no visible global function definition for 'optimx'
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
solveLP: no visible global function definition for 'lp'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/lira.Rcheck/00install.out' for details.
ave.sorted: warning in matrix(y[lens == i], nr = i): partial argument
  match of 'nr' to 'nrow'
ave.sorted: warning in matrix(weights[lens == i], nr = i): partial
  argument match of 'nr' to 'nrow'
liso.adaptive: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.backfit: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.maxlamb: no visible global function definition for 'pava'
pavareg: no visible global function definition for 'pava'
pavaregorig: no visible global function definition for 'pava'
lle_sound: no visible binding for global variable 'lle_wave'
plot_lle: no visible global function definition for 'plot3d'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs       2.1Mb
    testdata   1.5Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
Namespace in Imports field not imported from: 'boot'
  All declared Imports should be used.
File 'lmmlasso/R/zzz.R':
  .onAttach calls:
    cat("----------------------------------------------------------------------",     "This is a test release of the package 'lmmlasso'. If you have any questions or problems, do not hesitate to contact the author.",     "----------------------------------------------------------------------",     sep = "\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

LambdaInv: no visible global function definition for 'quad.tform'
MLloglik: no visible global function definition for 'quad.form'
MLpdSym: no visible global function definition for 'triang'
MLpdSym: no visible global function definition for 'vecli'
MLpdSymLambda: no visible global function definition for 'quad.tform'
MLsigmaZPsiZt: no visible global function definition for 'quad.tform'
ObjFunction : tResLRes: no visible global function definition for
  'quad.form'
covStartingValues : optimize3: no visible global function definition
  for 'quad.form.inv'
lmmlasso.default: no visible global function definition for 'optL1'
lmmlasso.default: no visible global function definition for 'optL2'
lmmlasso.default: no visible global function definition for 'vecli'
lmmlasso.default: no visible global function definition for 'triang'
lfbas: no visible global function definition for 'basis'
EMmixlcd: no visible global function definition for 'hc'
EMmixlcd: no visible global function definition for 'hclass'
interactive2D: no visible global function definition for 'tktoplevel'
interactive2D: no visible global function definition for 'tclVar'
interactive2D : plotdens: no visible global function definition for
  'tclvalue'
interactive2D: no visible global function definition for 'tkrplot'
interactive2D : densplot: no visible global function definition for
  'tkrreplot'
interactive2D: no visible global function definition for 'tkscale'
interactive2D: no visible global function definition for 'tklabel'
interactive2D: no visible global function definition for 'tkpack'
plot.LogConcDEAD: no visible global function definition for 'open3d'
plot.LogConcDEAD: no visible global function definition for 'par3d'
plot.LogConcDEAD: no visible global function definition for 'surface3d'
plot.LogConcDEAD: no visible global function definition for
  'decorate3d'
plot.LogConcDEAD: no visible global function definition for
  'rgl.surface'
plot.LogConcDEAD: no visible global function definition for 'plot3d'
Namespace in Imports field not imported from: 'distr'
  All declared Imports should be used.
Package in Depends field not imported from: 'logcondens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LCLRCImode: no visible global function definition for 'preProcess'
Local_LL.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalNormalize'
MLE.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalF'
activeSetLogCon: no visible global function definition for 'preProcess'
activeSetLogCon: no visible global function definition for
  'LocalNormalize'
activeSetLogCon: no visible global function definition for 'LocalMLE'
activeSetLogCon: no visible global function definition for
  'LocalConvexity'
activeSetLogCon: no visible global function definition for 'LocalF'
activeSetLogCon : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : Fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode: no visible global function definition for
  'preProcess'
activeSetLogCon.mode: no visible global function definition for
  'LocalNormalize'
activeSetLogCon.mode: no visible global function definition for
  'LocalF'
activeSetLogCon.mode : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode : fhat.f: no visible global function definition
  for 'evaluateLogConDens'
activeSetLogCon.mode : Fhat.f: no visible global function definition
  for 'evaluateLogConDens'
estimateLRdistn: no visible global function definition for 'preProcess'
intECDFfn : Y: no visible global function definition for 'intECDF'
intFfn: multiple local function definitions for 'H' with different
  formal arguments
logConDens: no visible global function definition for
  'evaluateLogConDens'
x2z: no visible global function definition for 'LocalNormalize'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
LogrankA: no visible global function definition for 'is.Surv'
predict.KernS: no visible global function definition for 'chkDots'
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
print.summary.lqa: warning in printCoefmat(coefs, P.value = FALSE,
  has.Pvalue = FALSE): partial argument match of 'P.value' to
  'P.values'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/lqr.Rcheck/00install.out' for details.
example.ls2w: no visible global function definition for 'lda'
Namespace in Imports field not imported from: 'tcltk2'
  All declared Imports should be used.
lsplsCv: no visible global function definition for 'cvsegments'
orthlspls.fit: no visible binding for global variable 'oscorespls.fit'
orthlsplsCv: no visible binding for global variable 'oscorespls.fit'
lss: no visible binding for global variable 'response'
lss.betag: no visible global function definition for 'l1fit'
gauher: no visible binding for global variable 'gh'
vcov.gpcm: no visible global function definition for 'ginv'
vcov.grm: no visible global function definition for 'ginv'
get.Z.HWP: no visible global function definition for 'is.genotype'
get.Z.HWP: no visible global function definition for 'allele.count'
get.lambda: no visible global function definition for 'is.genotype'
get.lambda: no visible global function definition for 'heterozygote'
luca: no visible global function definition for 'is.genotype'
luca: no visible global function definition for 'genotype'
luca: no visible global function definition for 'Surv'
luca: no visible global function definition for 'coxph.fit'
luca: no visible global function definition for 'coxph.control'
Error in re-building vignettes:
  ...
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
Loading required package: coda
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there

Quitting from lines 269-293 (lucid_printing.Rmd) 
Error: processing vignette 'lucid_printing.Rmd' failed with diagnostics:
could not find function "jags.model"
Execution halted
LVMMCOR.default: no visible global function definition for 'fdHess'
LVMMCOR.default: no visible global function definition for 'ginv'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates<-'
project.M3.1.to.M3.2: no visible global function definition for
  'proj4string<-'
project.M3.1.to.M3.2: no visible global function definition for 'CRS'
project.M3.1.to.M3.2: no visible global function definition for
  'spTransform'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates'
Namespaces in Imports field not imported from:
  'Rcpp' 'cmprsk' 'colorspace' 'etm' 'fracdiff' 'gtable' 'munsell'
  'numDeriv' 'plyr' 'quadprog' 'scales' 'timeDate' 'tseries' 'zoo'
  All declared Imports should be used.
installed size is 41.0Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  34.0Mb
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
MalletLDA: no visible global function definition for '.jnew'
mallet.doc.topics: no visible global function definition for
  '.jevalArray'
mallet.import: no visible global function definition for 'J'
mallet.import: no visible global function definition for '.jnew'
mallet.import: no visible global function definition for '.jcast'
mallet.subset.topic.words: no visible global function definition for
  '.jevalArray'
mallet.topic.words: no visible global function definition for
  '.jevalArray'
mallet.word.freqs: no visible global function definition for
  '.jevalArray'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'anova.gam'
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/maps/libs/i386/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/maps/libs/x64/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: 'gpclib'
aa.account: no visible binding for global variable 'last'
cashflow.portfolio.bond: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for 'last'
connectTheDots: no visible global function definition for 'first'
current.market: no visible global function definition for 'last'
findMaxMat: no visible global function definition for 'lambert_W0'
market.rate: no visible global function definition for 'last'
plot.history.market: no visible global function definition for
  'sort.data.frame'
print.account: no visible binding for global variable 'last'
build.eqn.tex: no visible global function definition for 'str_detect'
build.eqn.tex: no visible global function definition for 'str_trim'
get.mat.tex : tmp.fun: no visible global function definition for
  'latexTranslate'
get.mat.tex : tmp.fun.2: no visible global function definition for
  'str_replace_all'
get.mat.tex: no visible global function definition for 'latexTabular'
get.mat.tex: no visible global function definition for
  'str_replace_all'
parameters.time.varying: no visible global function definition for
  'str_detect'
parameters.time.varying: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for
  'str_detect'
toLatex.marssMODEL: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for 'str_sub'
toLatex.marssMODEL: no visible global function definition for 'sys'
toLatex.marssMODEL: no visible global function definition for
  'str_replace'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.8Mb
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
mbmdr : Regresion: no visible global function definition for 'logistf'
laugreen: no visible global function definition for 'lp'
relabel : min.perm.labels: no visible global function definition for
  'lp.transport'
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'thin'
mcgibbsit: no visible global function definition for 'nvar'
mcgibbsit: no visible global function definition for 'mcmc'
mcgibbsit: no visible global function definition for 'mcmc.list'
mcgibbsit: no visible global function definition for 'varnames'
mcgibbsit: no visible global function definition for 'niter'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mcPAFit.Rcheck/00install.out' for details.
I2.MCPerm: no visible global function definition for 'rma'
I2.MCPerm: no visible global function definition for 'rma.mh'
I2.MCPerm: no visible global function definition for 'rma.peto'
I2.TradPerm: no visible global function definition for 'rma'
I2.TradPerm: no visible global function definition for 'rma.mh'
I2.TradPerm: no visible global function definition for 'rma.peto'
Q.MCPerm: no visible global function definition for 'rma'
Q.MCPerm: no visible global function definition for 'rma.mh'
Q.MCPerm: no visible global function definition for 'rma.peto'
Q.TradPerm: no visible global function definition for 'rma'
Q.TradPerm: no visible global function definition for 'rma.mh'
Q.TradPerm: no visible global function definition for 'rma.peto'
meta: no visible global function definition for 'rma'
meta: no visible global function definition for 'rma.mh'
meta: no visible global function definition for 'rma.peto'
meta.MCPerm: no visible global function definition for 'rma'
meta.MCPerm: no visible global function definition for 'rma.mh'
meta.MCPerm: no visible global function definition for 'rma.peto'
meta.TradPerm: no visible global function definition for 'rma'
meta.TradPerm: no visible global function definition for 'rma.mh'
meta.TradPerm: no visible global function definition for 'rma.peto'
geoshape: no visible global function definition for 'coordinates'
geoshape: no visible global function definition for 'ppp'
geoshape: no visible global function definition for 'nncross'
gmmlogit: no visible global function definition for 'poly2nb'
gmmlogit: no visible global function definition for 'nb2mat'
gmmprobit: no visible global function definition for 'poly2nb'
gmmprobit: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'coordinates'
makew: no visible global function definition for 'poly2nb'
makew: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'knearneigh'
makew: no visible global function definition for 'knn2nb'
qregsim1: no visible global function definition for 'brewer.pal'
qregspiv: no visible global function definition for 'poly2nb'
qregspiv: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'poly2nb'
sarml: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'nb2listw'
sarml: no visible global function definition for 'eigenw'
smooth12: no visible global function definition for 'nn2'
splogit: no visible global function definition for 'poly2nb'
splogit: no visible global function definition for 'nb2mat'
splogit: no visible global function definition for 'hccm'
spprobit: no visible global function definition for 'poly2nb'
spprobit: no visible global function definition for 'nb2mat'
spprobit: no visible global function definition for 'hccm'
spprobitml : makevar: no visible global function definition for
  'poly2nb'
spprobitml : makevar: no visible global function definition for
  'nb2mat'
File 'medSTC/libs/i386/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.o'
File 'medSTC/libs/x64/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'RGtk2' 'RNifti' 'cairoDevice' 'gtools' 'jsonlite'
  All declared Imports should be used.
codomToPropShared: no visible global function definition for
  'df2genind'
codomToPropShared: no visible global function definition for
  'propShared'
mgLandscape: no visible global function definition for 'SpatialPoints'
mgQuick: no visible global function definition for 'distm'
mgQuick: no visible binding for global variable 'distMeeus'
metacor.DSL: no visible global function definition for 'metaplot'
metacor.OP: no visible global function definition for 'hyperg_2F1'
metacor.OP: no visible global function definition for 'metaplot'
CDF.rop : <anonymous> : <anonymous>: no visible global function
  definition for 'dmnom'
MetaDE.impute: no visible global function definition for 'impute.knn'
cal.logrank : get.stat: no visible global function definition for
  'coxph'
cal.p.logrank : get.p: no visible global function definition for
  'coxph'
get.RP: no visible binding for global variable 'na.rm'
get.RP: no visible global function definition for 'NaReplace2'
Error in re-building vignettes:
  ...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/metamisc.Rcheck/00install.out' for details.
.MetaSparsePCA: no visible global function definition for '%do%'
.MetaSparsePCA: no visible global function definition for 'foreach'
.MetaSparsePCA: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'registerDoMC'
DropDupGenes: no visible global function definition for 'startWorkers'
DropDupGenes: no visible global function definition for 'registerDoSMP'
DropDupGenes: no visible global function definition for '%dopar%'
DropDupGenes: no visible global function definition for 'foreach'
DropDupGenes: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'stopWorkers'
MetaPCA: no visible global function definition for 'PCAgrid'
PlotPC2D: no visible global function definition for 'cov.mve'
PlotPC2D: no visible global function definition for 'ellipse'
PreprocessMetaAnalysis: no visible global function definition for
  '%do%'
PreprocessMetaAnalysis: no visible global function definition for
  'foreach'
PreprocessMetaAnalysis: no visible global function definition for
  'iter'
PreprocessMetaAnalysis: no visible binding for global variable 'dat'
PreprocessMetaAnalysis: no visible global function definition for
  'impute.knn'
requireAll: no visible global function definition for 'biocLite'
downloadAEMETcurrentday: no visible global function definition for
  'startsWith'
downloadAEMETcurrentday: no visible global function definition for
  'endsWith'
QCRep: warning in axis(1, at = 0:axislen, lab = 0:axislen, cex.axis =
  0.7, tcl = -0.2): partial argument match of 'lab' to 'labels'
QCplot: warning in axis(1, at = 1:lenRow, lab = 1:lenRow, cex.axis =
  0.7): partial argument match of 'lab' to 'labels'
AltReg: no visible global function definition for 'lme'
BA.est: no visible global function definition for 'lmeControl'
MCmcmc: no visible global function definition for 'jags.model'
MCmcmc: no visible global function definition for 'bugs'
MCmcmc: no visible global function definition for 'read.bugs'
VC.est: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lme'
VC.est.fixed: no visible global function definition for 'pdIdent'
VC.est.fixed: no visible global function definition for 'varIdent'
VC.est.fixed: no visible global function definition for 'pdDiag'
VC.est.fixed: no visible global function definition for 'pdSymm'
VC.est.random: no visible global function definition for 'lmeControl'
VC.est.random: no visible global function definition for 'lme'
VC.est.random: no visible global function definition for 'pdBlocked'
VC.est.random: no visible global function definition for 'pdIdent'
VC.est.random: no visible global function definition for 'varIdent'
VC.est.random: no visible global function definition for 'ranef'
VC.est.random: no visible global function definition for 'pdDiag'
find.mean: no visible global function definition for 'varnames'
find.vars: no visible global function definition for 'varnames'
pairs.MCmcmc: no visible global function definition for 'varnames'
subset.MCmcmc : char.2.num: no visible global function definition for
  'varnames'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
eventpois: no visible global function definition for 'dsort'
FoM.FitBinnedSampleRepeatErrors : local.fit.function: no visible global
  function definition for 'rlm'
RevNet.JacobianMethod : RevNet.FirstEstimate: no visible global
  function definition for 'lm.ridge'
dbgpd_bilog: no visible global function definition for 'pbvevd'
dbgpd_negbilog: no visible global function definition for 'pbvevd'
dtgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psilog: no visible global function definition for 'image.plot'
dtgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psineglog: no visible global function definition for 'image.plot'
mgpd_init: no visible global function definition for 'fgev'
ml_bilog: no visible global function definition for 'pbvevd'
ml_negbilog: no visible global function definition for 'pbvevd'
pbgpd_bilog: no visible global function definition for 'pbvevd'
pbgpd_ct: no visible global function definition for 'pbvevd'
pbgpd_negbilog: no visible global function definition for 'pbvevd'
ptgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psilog: no visible global function definition for 'image.plot'
ptgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psineglog: no visible global function definition for 'image.plot'
inbar: no visible global function definition for 'spplot'
inbox: no visible global function definition for 'spplot'
indot: no visible global function definition for
  'SpatialPointsDataFrame'
indot: no visible global function definition for 'coordinates'
indot: no visible global function definition for 'CRS'
indot: no visible global function definition for 'bubble'
inhist: no visible global function definition for 'spplot'
inline: no visible global function definition for 'spplot'
inmap: no visible global function definition for
  'SpatialPointsDataFrame'
inmap: no visible global function definition for 'coordinates'
inmap: no visible global function definition for 'CRS'
inmap: no visible global function definition for 'bubble'
inmap: no visible global function definition for 'spplot'
inpie: no visible global function definition for 'spplot'
inscatter: no visible global function definition for 'spplot'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
lrtest.aidsEst: no visible binding for global variable 'lrtest.default'
quadFuncEst: no visible global function definition for 'plm'
quadFuncEst: no visible global function definition for 'fixef'
Running examples in 'micropan-Ex.R' failed
The error most likely occurred in:

> ### Name: entrezDownload
> ### Title: Downloading genome data
> ### Aliases: entrezDownload
> 
> ### ** Examples
> 
> # Accession numbers for the chromosome and plasmid of Buchnera aphidicola, strain APS
> entrezDownload( accession="BA000003.2,AP001071.1", out.file="Buchnera_aphidicola_APS.fsa" )
Downloading genome...Warning in url(adr, open = "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in url(adr, open = "rt") : cannot open the connection
Calls: entrezDownload -> url
Execution halted
MigClim.genClust: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for
  'dataframe2asc'
MigClim.migrate: no visible global function definition for
  'writeRaster'
MigClim.migrate: no visible global function definition for 'cellStats'
MigClim.plot: no visible global function definition for 'raster'
MigClim.plot: no visible global function definition for 'ymax'
MigClim.plot: no visible global function definition for 'ymin'
MigClim.plot: no visible global function definition for 'xmax'
MigClim.plot: no visible global function definition for 'xmin'
summary.MImixresult: warning in qt(alpha/2, object$df, lower = FALSE):
  partial argument match of 'lower' to 'lower.tail'
Namespaces in Imports field not imported from:
  'DiceDesign' 'MaxPro' 'doSNOW'
  All declared Imports should be used.
minPtest: no visible global function definition for 'sfIsRunning'
minPtest: no visible global function definition for 'sfInit'
minPtest: no visible global function definition for 'sfLibrary'
minPtest: no visible global function definition for 'sfExport'
minPtest: no visible global function definition for 'sfClusterApplyLB'
minPtest: no visible global function definition for 'mclapply'
minPtest: no visible global function definition for 'sfStop'
Namespaces in Imports field not imported from:
  'MASS' 'cluster' 'dendextend' 'npmv' 'utils'
  All declared Imports should be used.
change_family,missing-proportion-family : .local: no visible binding
  for global variable '.identity_transformation'
fit_model,missing-multilevel_missing_data.frame : .local: no visible
  binding for global variable 'X'
image,mi : .local: no visible global function definition for 'Matrix'
image,missing_data.frame : .local: no visible global function
  definition for 'Matrix'
mi,grouped-binary-clogit : .local: no visible global function
  definition for 'untangle.specials'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
image3d: no visible global function definition for 'clear3d'
image3d: no visible global function definition for 'sprites3d'
image3d: no visible global function definition for 'points3d'
slices3d : mkimg: no visible global function definition for 'tkrplot'
slices3d : mkscale : f: no visible global function definition for
  'tclvalue'
slices3d : mkscale : f: no visible global function definition for
  'tkrreplot'
slices3d : mkscale : f: no visible global function definition for
  'tkconfigure'
slices3d : mkscale: no visible global function definition for 'tkframe'
slices3d : mkscale: no visible global function definition for 'tkscale'
slices3d : mkscale: no visible global function definition for 'tklabel'
slices3d : mkscale: no visible global function definition for 'tkgrid'
slices3d : move: no visible global function definition for 'tkbind'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkwinfo'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkrreplot'
slices3d : move : <anonymous>: no visible global function definition
  for 'tclvalue<-'
slices3d: no visible global function definition for 'tktoplevel'
slices3d: no visible global function definition for 'tktitle<-'
slices3d: no visible binding for global variable 'tclVar'
slices3d: no visible global function definition for 'tkgrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/miscF.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
missForest: no visible global function definition for 'idiv'
dmvgt: no visible global function definition for 'dmvt'
rmvgt: no visible global function definition for 'rmvt'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
anova.mix: warning in pchisq(dchisq, ddf, low = FALSE): partial
  argument match of 'low' to 'lower.tail'
Namespace in Imports field not imported from: 'rjags'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  OK: 26 SKIPPED: 0 FAILED: 9
  1. Error: Wolves ex works (@test_ex1_wolves.R#33) 
  2. Error: Geese ex works (@test_ex2_geese.R#27) 
  3. Error: Lake ex works (@test_ex3_lake.R#27) 
  4. Error: Palmyra ex works (@test_ex4_palmyra.R#27) 
  5. Error: Killer whale ex works (@test_ex5_killerwhale.R#28) 
  6. Error: Snail ex works (@test_ex6_snail.R#27) 
  7. Error: Storm-petrel ex works (@test_ex7_stormpetrel.R#27) 
  8. Error: Cladocera ex works (@test_ex8_cladocera.R#31) 
  9. Error: Isopod ex works (@test_ex9_isopod.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
.DNA.connectivitylist : .fun_conn_idx: no visible global function
  definition for 'attach.big.matrix'
.DNA.distance: no visible global function definition for
  'as.big.matrix'
.checkadjmatrix: no visible global function definition for
  'is.big.matrix'
.filterLowCorrelation: no visible global function definition for
  'is.big.matrix'
.network.differences : .fun_distance: no visible global function
  definition for 'attach.big.matrix'
.uniqueTissues: no visible global function definition for 'str_sub'
geneRanker: no visible global function definition for 'RankingTstat'
geneRanker: no visible global function definition for 'RankingFC'
geneRanker: no visible global function definition for 'RankingWilcoxon'
geneRanker: no visible global function definition for
  'RankingBaldiLong'
geneRanker: no visible global function definition for
  'RankingShrinkageT'
geneRanker: no visible global function definition for 'RankingSam'
geneRanker: no visible global function definition for
  'RankingSoftthresholdT'
geneRanker: no visible global function definition for 'RankingLimma'
geneRanker: no visible global function definition for 'toplist'
mlegp: no visible global function definition for 'sfLapply'
mleurDiag: no visible global function definition for 'shapiroTest'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/MLID.Rcheck/00install.out' for details.
do.estimate.mlogit: no visible global function definition for 'maxLik'
get.mnl.data: no visible global function definition for 'abind'
imageplot.mlogit: no visible global function definition for
  'imageplot.bma'
listGenoToTable: no visible binding for global variable 'dummy'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mlVAR.Rcheck/00install.out' for details.
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/mmap.Rcheck/00install.out' for details.
mmm: no visible global function definition for 'gee'
.Oarray_to_MB: no visible global function definition for 'is.Oarray'
.gunter: no visible global function definition for 'minmax'
.gunter: no visible global function definition for 'compositions'
MM: no visible global function definition for 'minmax'
MM_allsamesum: no visible global function definition for 'quad.tform'
MM_allsamesum_A: no visible global function definition for 'minmax'
MM_allsamesum_A: no visible global function definition for 'tr'
MM_allsamesum_A: no visible global function definition for 'quad.tform'
MM_differsums: no visible global function definition for 'quad.tform'
MM_single: no visible global function definition for 'quad.form'
NormC: no visible global function definition for 'compositions'
as.array.gunter_MB: no visible global function definition for 'Oarray'
expected_suffstats: no visible global function definition for
  'compositions'
optimizer: no visible global function definition for 'minmax'
optimizer_allsamesum: no visible global function definition for
  'minmax'
suffstats: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for
  'compositions'
gunter,matrix: no visible global function definition for 'minmax'
gunter,matrix: no visible global function definition for 'compositions'
biplot.character: no visible global function definition for 'opts'
biplot.character: no visible global function definition for
  'theme_blank'
distributionplot.factor: no visible global function definition for
  'opts'
distributionplot.factor: no visible global function definition for
  'theme_text'
scatterplot: no visible global function definition for 'opts'
scatterplot: no visible global function definition for 'theme_text'
timeplot: no visible global function definition for 'opts'
clusval: no visible global function definition for 'std.ext'
clusval: no visible global function definition for 'confusion.matrix'
clusval: no visible global function definition for 'similarity.index'
clusval: no visible global function definition for 'clv.Jaccard'
clusval: no visible global function definition for 'clv.Folkes.Mallows'
predict_baseline: no visible global function definition for 'knn1'
predict_cclust: no visible global function definition for 'cclust'
predict_kmeans: no visible global function definition for 'knn1'
predict_single: no visible global function definition for 'agnes'
predict_single: no visible global function definition for 'knn1'
contour.hmac: no visible global function definition for 'kde2d'
modalclust: no visible global function definition for 'mclapply'
phmac: no visible global function definition for 'mclapply'
File 'modeest/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\nThis is package 'modeest' written by P. PONCET.\nFor a complete list of functions, use 'library(help = \"modeest\")' or 'help.start()'.\n")

See section 'Good practice' in '?.onAttach'.

.mlv.fisk: no visible global function definition for 'pfisk'
.mlv.frechet: no visible global function definition for 'pfrechet'
.mlv.gev: no visible global function definition for 'pgev'
.mlv.gh: no visible global function definition for 'pgh'
.mlv.gompertz: no visible global function definition for 'pgompertz'
.mlv.gpd: no visible global function definition for 'pgpd'
.mlv.gumbel: no visible global function definition for 'pgumbel'
.mlv.hyp: no visible global function definition for 'phyp'
.mlv.koenker: no visible global function definition for 'pkoenker'
.mlv.kumar: no visible global function definition for 'pkumar'
.mlv.laplace: no visible global function definition for 'plaplace'
.mlv.nig: no visible global function definition for 'pnig'
.mlv.paralogistic: no visible global function definition for
  'pparalogistic'
.mlv.pareto: no visible global function definition for 'ppareto'
.mlv.rayleigh: no visible global function definition for 'prayleigh'
.mlv.rweibull: no visible global function definition for 'prweibull'
.mlv.stable: no visible global function definition for 'pstable'
ghMode: no visible global function definition for 'qgh'
ghMode: no visible binding for global variable 'dgh'
nigMode: no visible global function definition for 'qnig'
nigMode: no visible binding for global variable 'dnig'
stableMode: no visible binding for global variable 'dstable'
Namespace in Imports field not imported from: 'broom'
  All declared Imports should be used.
byteint2bit: no visible global function definition for 'digitsBase'
extract_bit: no visible global function definition for 'digitsBase'
get_bitgrid: no visible global function definition for 'raster'
get_bitgrid: no visible global function definition for 'coordinates'
get_bitgrid: no visible global function definition for 'extract'
get_bitgrid_2bits: no visible global function definition for 'raster'
get_bitgrid_2bits: no visible global function definition for
  'coordinates'
get_bitgrid_2bits: no visible global function definition for 'extract'
make_cloudcount_product: no visible global function definition for
  'CRS'
make_cloudcount_product: no visible global function definition for
  'proj4string'
make_cloudcount_product: no visible global function definition for
  'extent'
make_cloudcount_product: no visible global function definition for
  'coordinates<-'
make_cloudcount_product: no visible global function definition for
  'SpatialPixelsDataFrame'
make_cloudcount_product: no visible global function definition for
  'coordinates'
numslist_to_grd: no visible global function definition for 'CRS'
numslist_to_grd: no visible global function definition for
  'proj4string'
numslist_to_grd: no visible global function definition for 'extent'
numslist_to_grd: no visible global function definition for
  'coordinates<-'
numslist_to_grd: no visible global function definition for
  'SpatialPixelsDataFrame'
numslist_to_grd: no visible global function definition for
  'coordinates'
yearday_to_date: no visible global function definition for 'mdy.date'
yearday_to_date: no visible global function definition for 'date.mdy'
yearmonthday_to_julianday: no visible global function definition for
  'mdy.date'
Package required and available but unsuitable version: 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/morse.Rcheck/00install.out' for details.
mMap: no visible binding for global variable 'facet'
mScatter: no visible binding for global variable 'facet'
mUniplot: no visible binding for global variable 'facet'
Package required and available but unsuitable version: 'slam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
GetExampleData: no visible binding for global variable 'MPINetData'
Getenvir: no visible binding for global variable 'MPINetData'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/mpMap.Rcheck/00install.out' for details.
CR_calcLD: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle<-'
fill: no visible global function definition for 'lowerTriangle<-'
fill: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle'
findqtl2: no visible global function definition for 'dilation'
fit.mpqtl: no visible global function definition for 'wald.test'
mpIM: no visible global function definition for 'stepAIC'
mpIM: no visible global function definition for 'wald.test'
mpcalcld: no visible global function definition for 'lowerTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle'
mpestrf: no visible global function definition for 'lowerTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle'
mporder : <anonymous>: no visible global function definition for
  'seriate'
mporder: no visible binding for global variable 'get_order'
mpprob: no visible global function definition for 'happy'
mpprob: no visible global function definition for 'hdesign'
plot.mapcomp: no visible global function definition for 'xyplot'
plot.mpcross: no visible global function definition for
  'upperTriangle<-'
plot.mpcross: no visible global function definition for 'upperTriangle'
plot.mpcross: no visible global function definition for
  'lowerTriangle<-'
plot.mpcross: no visible global function definition for 'lowerTriangle'
plot.mpcross: no visible global function definition for 'heatmap_2'
mpmcorrelogram: no visible global function definition for
  'mantel.partial'
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
plot.mpm: warning in symbols(ss[isel, 1], ss[isel, 2], circle =
  sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg = colors[2]):
  partial argument match of 'circle' to 'circles'
plot.mpm: warning in symbols(ll[ii, 1], ll[ii, 2], square = sqs, inches
  = FALSE, lwd = 3, add = TRUE, fg = colors[2 + iGroup[i]]): partial
  argument match of 'square' to 'squares'
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
MRsurvival: no visible global function definition for 'rmvnorm'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/msBP.Rcheck/00install.out' for details.
kgml_i: no visible global function definition for 'xmlTreeParse'
kgml_i: no visible global function definition for 'xmlRoot'
kgml_i: no visible global function definition for 'xmlAttrs'
list2xml: no visible global function definition for 'xmlNode'
list2xml: no visible global function definition for 'append.xmlNode'
read_pathway: no visible global function definition for 'xmlTreeParse'
read_pathway: no visible global function definition for 'xmlRoot'
read_pathway: no visible global function definition for 'xmlToList'
read_pathway: no visible global function definition for 'xmlAttrs'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasy.Rcheck/00install.out' for details.
MS.DataCreation: no visible global function definition for 'tclvalue'
MS.DataCreation: no visible global function definition for
  'tkchooseDirectory'
MS.clust: no visible global function definition for 'tk_choose.files'
MS.test.clust: no visible global function definition for
  'tk_choose.files'
MSeasyToARISTO: no visible global function definition for
  'tk_choose.files'
MSeasyToMSP: no visible global function definition for
  'tk_choose.files'
SearchNIST: no visible global function definition for 'tclvalue'
SearchNIST: no visible global function definition for
  'tkchooseDirectory'
SearchNIST: no visible global function definition for 'tk_choose.files'
trans.ASCII: no visible global function definition for 'tclvalue'
trans.ASCII: no visible global function definition for
  'tkchooseDirectory'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasyTkGUI.Rcheck/00install.out' for details.
dialog.MS.clust: no visible binding for global variable
  'Agilent_quantF_MSclust'
dialog.MS.test.clust: no visible binding for global variable
  'Data_testclust'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
[,MSM.fitted-character-missing-missing : .local: warning in switch(EXP
  = i, CondMean = return(x@CondMean), error = return(x@error), Likel =
  return(x@Likel), margLik = return(x@margLik), filtProb =
  return(x@filtProb), smoProb = return(x@smoProb), states =
  return(apply(x@smoProb, 1, which.max)), smoTransMat =
  return(x@smoTransMat), logLikel = return(x@logLikel), stop("Error:",
  i, "is not a MSM.fitted slot")): partial argument match of 'EXP' to
  'EXPR'
[,MSM.glm-character-missing-missing : .local: warning in switch(EXP =
  i, call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), transMat = return(x@transMat), iniProb =
  return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), family = return(x@family), stop("Error:", i,
  "is not a MSM slot")): partial argument match of 'EXP' to 'EXPR'
[,MSM.lm-character-missing-missing : .local: warning in switch(EXP = i,
  call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), std = return(x@std), transMat = return(x@transMat),
  iniProb = return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), stop("Error:", i, "is not a MSM slot")):
  partial argument match of 'EXP' to 'EXPR'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36516L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
plmm.mtk: no visible global function definition for 'stepAIC'
File 'mtsdi/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste("This is 'mtsdi' library", ver, sep = " "))

See section 'Good practice' in '?.onAttach'.
getFlights: no visible binding for global variable 'htmlTreeParse'
getFlights: no visible binding for global variable 'xpathSApply'
getFlights: no visible binding for global variable 'xmlAttrs'
getFlights: no visible binding for global variable 'free'
plot.routes : a: no visible global function definition for
  'gcIntermediate'
routes: no visible global function definition for 'distHaversine'
routes: no visible global function definition for 'gcIntermediate'
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/multinet.Rcheck/00install.out' for details.
genoudRob: no visible global function definition for 'genoud'
showmap: no visible binding for global variable 'landmask'
File 'multxpert/R/zzz.R':
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

pdunnett: no visible global function definition for 'GenzBretz'
qdunnett: no visible global function definition for 'GenzBretz'
Plot.pca.score: no visible global function definition for 'dataEllipse'
Plot.plsda: no visible global function definition for 'dataEllipse'
explore.data: no visible global function definition for 'T2.test'
oplsda: no visible global function definition for 'dataEllipse'
ostocsy: no visible global function definition for 'colorpanel'
outlier: no visible global function definition for 'pdist'
plsda: no visible global function definition for 'plsr'
stocsy: no visible global function definition for 'colorpanel'
stocsy.1d: no visible global function definition for 'rich.colors'
ystand: no visible global function definition for 'spatial.signs'
ystand: no visible global function definition for 'spatial.rank'
mvtmeta_fe: no visible global function definition for 'combinations'
mvtsplot: no visible global function definition for 'brewer.pal'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   1.3Mb
quantile,cenmle-lognormal : .local: warning in formatC(100 * q, format
  = "fg", wid = 1): partial argument match of 'wid' to 'width'
summary,ros : .local: no visible global function definition for
  'plot.lm'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NanoStringNorm.Rcheck/00install.out' for details.
Package required but not available: 'RcppCCTZ'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NAPPA.Rcheck/00install.out' for details.
bcrm: no visible global function definition for 'startsWith'
getVarComponent.bcrm: no visible global function definition for
  'endsWith'
ncal.formula: no visible global function definition for 'startsWith'
plot.marginals: no visible global function definition for 'startsWith'
read.luminex.xls: no visible global function definition for
  'startsWith'
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  Number of test functions: 3 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 1 error, 0 failures
  ERROR in test.ncal: Error in getVarComponent.bcrm(fit) : could not find function "endsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (nCal-vignette.Rnw) 
Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
could not find function "endsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ndjson.Rcheck/00install.out' for details.
XH: no visible binding for global variable 'exprs'
XIs: no visible binding for global variable 'exprs'
cv.aep: no visible global function definition for 'mclapply'
cv.frsvm: no visible global function definition for 'mclapply'
cv.hubc: no visible global function definition for 'mclapply'
cv.pac: no visible global function definition for 'mclapply'
cv.stsvm: no visible global function definition for 'mclapply'
probeset2pathway: no visible binding for global variable
  'KEGGEXTID2PATHID'
probeset2pathwayTrain: no visible binding for global variable
  'KEGGEXTID2PATHID'
spanbound: no visible global function definition for 'param'
spanbound: no visible global function definition for 'error'
spanbound: no visible global function definition for 'kernelf'
spanbound: no visible global function definition for 'b'
svm.predict: no visible global function definition for 'b'
macros/struct_test.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'struct_test.Rd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/NetRep.Rcheck/00install.out' for details.
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'lower' to
  'lower.tail'
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'log' to
  'log.p'
bentlerParameters: no visible global function definition for
  'wireframe'
bentlerParameters: no visible global function definition for
  'contourplot'
bentlerParameters: no visible global function definition for
  'levelplot'
corFA: no visible global function definition for 'ginv'
iterativePrincipalAxis: no visible global function definition for
  'ginv'
parallel: no visible global function definition for 'mvrnorm'
parallel: no visible global function definition for 'ginv'
principalAxis: no visible global function definition for 'ginv'
structureSim: no visible global function definition for 'sim.structure'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    CppCode   1.7Mb
    R         2.4Mb
    include   3.6Mb
    libs      1.3Mb
Error in re-building vignettes:
  ...
Error in deriv.default(firstd, "x") : 
  invalid expression in 'FindSubexprs'
Error : object 'x' not found
Error : object 'x' not found
Loading required package: Ryacas
d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\yacas.exe and/or d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\scripts.dat not found
run yacasInstall() without arguments to installation yacas.

Attaching package: 'Ryacas'

The following object is masked from 'package:Deriv':

    Simplify

Quitting from lines 428-442 (nlsr-derivs.Rmd) 
Error: processing vignette 'nlsr-derivs.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
denoiseperm: no visible global function definition for 'ebayesthresh'
add.test: no visible global function definition for 'ace'
ll.order: no visible global function definition for 'locfit.raw'
ll.order: no visible global function definition for 'dat'
predict.ll.order: no visible global function definition for
  'locfit.raw'
algorithm,NMFStrategyOctave : .local: no visible global function
  definition for 'fstop'
evar,ANY : .local: no visible binding for global variable 'Biobase'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'n'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'RNGobj'
rss,matrix : .local: no visible binding for global variable 'Biobase'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/nonparaeff.Rcheck/00install.out' for details.
additive: no visible global function definition for 'lp'
ar.dual.dea: no visible global function definition for 'lp'
cost.dea: no visible global function definition for 'lp'
ddf: no visible global function definition for 'lp'
dea: no visible global function definition for 'lp'
direc.dea: no visible global function definition for 'lp'
dual.dea: no visible global function definition for 'lp'
effdea.b.f: no visible global function definition for 'convhulln'
effdea.b.f: no visible global function definition for 'lp'
faremalm2: no visible binding for global variable 'Lag'
int.dea: no visible global function definition for 'lp'
lp2: no visible global function definition for 'lp'
revenue.dea: no visible global function definition for 'lp'
sbm.tone: no visible global function definition for 'lp'
sbm.vrs: no visible global function definition for 'lp'
dist.plot.bar.plot: no visible global function definition for
  'rainbow_hcl'
dist.plot.hist.plot: no visible global function definition for
  'rainbow_hcl'
plot.stdf: no visible global function definition for 'rainbow_hcl'
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
normgam.fit: no visible global function definition for 'optimx'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'npde/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("     Loading library npde, version 2.0, August 2012\n         please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr\n")

See section 'Good practice' in '?.onAttach'.

npde.binning: no visible global function definition for 'Mclust'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
allsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for '<<-' assignment to 'NAwarning'
cfuinterpolation: no visible binding for global variable
  'measured_values'
disconestep: no visible binding for global variable 'measured_values'
disconestep: no visible binding for global variable 'psteps'
makepdfoutput: no visible binding for '<<-' assignment to 'textt'
npmpm: no visible binding for '<<-' assignment to 'inputsettings'
npmpm: no visible binding for global variable 'psteps'
npmpm: no visible binding for '<<-' assignment to 'cfu'
npmpm: no visible binding for '<<-' assignment to 'countwarnings'
npmpm: no visible binding for global variable 'cfu'
onestep: no visible binding for global variable 'measured_values'
onestep: no visible binding for global variable 'psteps'
simpleinterpolation: no visible binding for global variable
  'measured_values'
npqcmstest : boot.wild: no visible global function definition for 'rq'
npqcmstest : boot.wild.rademacher: no visible global function
  definition for 'rq'
npqcmstest : boot.iid: no visible global function definition for 'rq'
File 'NPsimex/R/onload.R':
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

See section 'Good practice' in '?.onAttach'.
npst: no visible global function definition for 'mclapply'
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
obliqueRF.default: no visible global function definition for
  'prediction'
obliqueRF.default: no visible global function definition for
  'performance'
pls_wrapper: no visible global function definition for 'kernelpls.fit'
ridge_slow_wrapper: no visible global function definition for
  'gen.ridge'
ridge_svd_wrapper: no visible global function definition for
  'gen.ridge'
svm_wrapper: no visible global function definition for 'svm'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/odbc.Rcheck/00install.out' for details.
isClosed: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbDisconnect'
odb.insert: no visible global function definition for 'dbSendQuery'
odb.insert: no visible global function definition for 'dbColumnInfo'
odb.open: no visible global function definition for 'JDBC'
odb.open: no visible global function definition for 'dbConnect'
odb.read: no visible global function definition for 'dbSendQuery'
odb.read: no visible global function definition for 'fetch'
odb.read: no visible global function definition for 'dbColumnInfo'
odb.tables: no visible global function definition for 'dbListTables'
odb.tables: no visible global function definition for 'dbSendQuery'
odb.tables: no visible global function definition for 'dbColumnInfo'
odb.write: no visible global function definition for 'dbSendUpdate'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         e$call <- sys.calls()[(frame + 11):(sys.nframe() - 2)]
         register_expectation(e, frame + 11, sys.nframe() - 2)
         signalCondition(e)
     }, "could not find function \"logi\"", quote(eval(expr, envir, enclos))) at testthat/test_odeintr.R:33
  2: eval(expr, envir, enclos)
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Error: compile_sys works (@test_odeintr.R#25) 
  2. Error: compile_implicit works (@test_odeintr.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
mapvar: no visible binding for global variable 'state.fips'
nearstn: no visible binding for global variable 'okstations'
nearstn: no visible binding for global variable 'Commissioned'
nearstn: no visible binding for global variable 'Decommissioned'
okmts: no visible binding for global variable 'okstations'
okmts: no visible binding for global variable 'TIME'
totalprecip: no visible binding for global variable 'TIME'
Namespaces in Imports field not imported from:
  'randomForest' 'ranger'
  All declared Imports should be used.
Packages suggested but not available for checking: 'RAppArmor' 'feather'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/OpenImageR.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.8Mb
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
File 'orderbook/R/AllGenerics.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

.animate.plot : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.animate.plot: no visible global function definition for 'barchart'
.plot.ob : new.yscale.components: no visible global function definition
  for 'yscale.components.default'
.plot.ob: no visible global function definition for 'xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.lines'
.plot.orders.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.orders.ob: no visible global function definition for 'xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.lines'
.plot.side.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.side.ob: no visible global function definition for 'barchart'
.plot.side.ob: no visible global function definition for
  'trellis.focus'
.plot.side.ob: no visible global function definition for 'grid.text'
.plot.side.ob: no visible global function definition for
  'trellis.unfocus'
.supply.demand.plot: no visible global function definition for 'xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.abline'
copy,orderbook : .local: no visible global function definition for
  'hash'
reset,orderbook: no visible global function definition for 'clear'
Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
boat3d: no visible global function definition for 'rgl.cur'
boat3d: no visible global function definition for 'open3d'
boat3d: no visible global function definition for 'clear3d'
boat3d: no visible global function definition for 'bg3d'
boat3d: no visible global function definition for 'rgl.set'
boat3d: no visible global function definition for 'triangles3d'
boat3d: no visible global function definition for 'quads3d'
boat3d: no visible global function definition for 'decorate3d'
boat3d: no visible global function definition for 'scatterplot3d'
zsuml2minucminf.loca.p: no visible global function definition for
  'ucminf'
zsumlpminucminf.loca.p: no visible global function definition for
  'ucminf'
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for 'lme'
est.lme : <anonymous>: no visible global function definition for
  'VarCorr'
srt : <anonymous>: no visible global function definition for
  'rowttests'
chebyshev.c.polynomials: no visible global function definition for
  'polynomial'
chebyshev.s.polynomials: no visible global function definition for
  'polynomial'
chebyshev.t.polynomials: no visible global function definition for
  'polynomial'
chebyshev.u.polynomials: no visible global function definition for
  'polynomial'
gegenbauer.polynomials: no visible global function definition for
  'polynomial'
ghermite.h.polynomials: no visible global function definition for
  'polynomial'
glaguerre.polynomials: no visible global function definition for
  'polynomial'
hermite.h.polynomials: no visible global function definition for
  'polynomial'
hermite.he.polynomials: no visible global function definition for
  'polynomial'
jacobi.g.polynomials: no visible global function definition for
  'polynomial'
jacobi.p.polynomials: no visible global function definition for
  'polynomial'
legendre.polynomials: no visible global function definition for
  'polynomial'
monic.polynomials: no visible global function definition for
  'polynomial'
orthogonal.polynomials: no visible global function definition for
  'polynomial'
orthonormal.polynomials: no visible global function definition for
  'polynomial'
polynomial.integrals: no visible global function definition for
  'integral'
schebyshev.t.polynomials: no visible global function definition for
  'polynomial'
schebyshev.u.polynomials: no visible global function definition for
  'polynomial'
slegendre.polynomials: no visible global function definition for
  'polynomial'
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Namespace in Imports field not imported from: 'bitops'
  All declared Imports should be used.
plot,OutlierDM-missing : .local: no visible binding for global variable
  'pch'
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'coxph'
[,ClassW : .local: warning in switch(EXP = i, u1 = {: partial argument
  match of 'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u2): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@w1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW : .local: warning in switch(EXP = i, u1 = {: partial
  argument match of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u2 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@w1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
clapply_cluster: no visible global function definition for
  'makeCluster'
clapply_cluster: no visible global function definition for
  'clusterSetRNGStream'
clapply_cluster: no visible global function definition for
  'clusterExport'
clapply_cluster: no visible global function definition for
  'clusterApply'
clapply_cluster: no visible global function definition for
  'clusterApplyLB'
clapply_cluster: no visible global function definition for
  'stopCluster'
md5sumString: no visible global function definition for 'md5sum'
writeRdocumentationToDir: no visible global function definition for
  'list_files_with_exts'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
par.nmds: no visible binding for global variable 'j'
par.spp.est: no visible binding for global variable 'i'
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
fitOR: no visible global function definition for 'multinom'
parpdist: no visible binding for global variable 'tmpx'
cv_nfold: no visible global function definition for 'cv.glmnet'
glmcvbeta: no visible global function definition for 'cv.glmnet'
Errors in running code in vignettes:
when running code in 'pasta_intro.Rmd'
  ...

  When running vignette 'pasta_intro.Rmd':
Error: No such vignette 'pasta_intro.Rmd'
Execution halted
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'read.dna'
oneway.plots: warning in dotchart(x = Y, groups = fac1, col = COL[2],
  pch = 1, xlab = deparse(substitute(Y)), xlim = YL, gdata = tapply(Y,
  fac1, mean), gpch = 17): partial argument match of 'col' to 'color'
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess


Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
draw: no visible global function definition for 'plotellipse'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
pen_or1: no visible global function definition for 'multiroot'
plot.pedigree: no visible global function definition for
  'align.pedigree'
plotPed: no visible global function definition for 'pedigree'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdBASE.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'pmclust'
Package required and available but unsuitable version: 'pbdBASE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdMPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdSLAP.Rcheck/00install.out' for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
xyplot.pbo: no visible global function definition for 'doubleYScale'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pcnetmeta.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  'car' 'sandwich'
  All declared Imports should be used.
genomesim : extractA: no visible global function definition for
  'is.genotype'
genomesim : extractA : <anonymous>: no visible global function
  definition for 'nallele'
phensim: no visible global function definition for 'rmvnorm'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
.replaceinf: no visible global function definition for 'fcn_values<-'
complexity.LASSO: no visible global function definition for 'profL1'
complexity.ipec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ipec.CoxBoost: no visible global function definition for
  'locfit'
complexity.mincv.CoxBoost: no visible global function definition for
  'cv.CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'locfit'
extract: no visible global function definition for 'findGlobals'
fit.CoxBoost: no visible global function definition for 'CoxBoost'
fit.LASSO: no visible global function definition for 'penalized'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

phantom : model: missing arguments not allowed in calls to 'c'
readData: no visible global function definition for 'read.image'
writeData: no visible global function definition for 'make.image'
writeData: no visible global function definition for 'write.image'
File 'pgam/R/zzz.r':
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Namespace in Imports field not imported from: 'quanteda'
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
bg.similarity.test: no visible global function definition for
  'sampleRandom'
bg.similarity.test: no visible global function definition for
  'coordinates'
bg.similarity.test: no visible global function definition for 'extract'
bg.similarity.test: no visible global function definition for
  'SpatialPoints'
bg.similarity.test : random.presence: no visible global function
  definition for 'sampleRandom'
bg.similarity.test : random.presence: no visible global function
  definition for 'coordinates'
bg.similarity.test: no visible global function definition for
  'writeRaster'
bg.similarity.test: no visible global function definition for
  'read.asciigrid'
di.enm: no visible global function definition for 'read.asciigrid'
niche.equivalency.test: no visible global function definition for
  'extract'
niche.equivalency.test: no visible global function definition for
  'SpatialPoints'
niche.equivalency.test: no visible global function definition for
  'sampleRandom'
niche.equivalency.test: no visible global function definition for
  'coordinates'
niche.equivalency.test: no visible global function definition for
  'writeRaster'
niche.equivalency.test: no visible global function definition for
  'read.asciigrid'
niche.overlap: no visible global function definition for
  'read.asciigrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PhyloMeasures.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
comm.phylo.qr: no visible global function definition for 'rq'
sppregs: no visible global function definition for 'brglm'
ARTP.GE: no visible global function definition for 'ARTP_pathway'
LR.cont.surv: no visible global function definition for 'coxph'
LR.inter.cat.surv: no visible global function definition for 'coxph'
LR.inter.cont.surv: no visible global function definition for 'coxph'
permutation.snp: no visible global function definition for 'sfInit'
permutation.snp: no visible global function definition for 'sfLibrary'
permutation.snp: no visible global function definition for
  'sfExportAll'
permutation.snp: no visible global function definition for 'sfLapply'
permutation.snp: no visible global function definition for 'sfStop'
fitaci: no visible global function definition for 'chkDots'
.var.ij: no visible global function definition for 'hcv'
.var.ij: no visible global function definition for 'h.select'
.var.ij: no visible global function definition for 'sm.regression'
LiStengos: no visible global function definition for 'h.select'
LiStengos: no visible global function definition for 'hcv'
LiStengos: no visible global function definition for 'sm.regression'
cal_df_gamma1: no visible global function definition for 'binning'
cal_df_gamma2: no visible global function definition for 'binning'
iteration: no visible global function definition for 'h.select'
iteration: no visible global function definition for 'hcv'
iteration: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'h.select'
plmm: no visible global function definition for 'Formula'
plmm.bs: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'sm.regression'
predict.plmm: no visible global function definition for 'Formula'
predict.plmm: no visible global function definition for 'sm.regression'
print.summary.plmm: no visible global function definition for 'Formula'
ranef.plmm: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'h.select'
select.h0: no visible global function definition for 'hcv'
var.plot: no visible global function definition for 'Formula'
var.plot: no visible global function definition for 'sm.regression'
wplmm: no visible global function definition for 'Formula'
Namespaces in Imports field not imported from:
  'hexbin' 'quantreg'
  All declared Imports should be used.
llla.mc: no visible global function definition for 'coxph'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.4Mb
cor.xl.ImputeData: no visible global function definition for
  'impute.knn'
pnmtrem1: no visible global function definition for 'ginv'
smooth: no visible global function definition for 'genoud'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
poLCA: no visible global function definition for 'ginv'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
Packages in Depends field not imported from:
  'mvtnorm' 'sfsmisc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
binBvn: no visible global function definition for 'pmvnorm'
hetcor.data.frame: no visible global function definition for 'nearcor'
Package unavailable to check Rd xrefs: 'gpclib'
plot.preplot.polywog: no visible global function definition for
  'persp3d'
siteocc: no visible global function definition for
  'is.positive.definite'
outputBottleSim: no visible binding for global variable 'final.vec'
outputBottleSim: no visible binding for global variable 'kvec'
portest : OneMonteCarlo: no visible global function definition for
  'garchFit'
portest: no visible global function definition for 'makeCluster'
portest: no visible global function definition for
  'clusterSetRNGStream'
portest: no visible global function definition for 'clusterEvalQ'
portest: no visible global function definition for 'clusterExport'
portest: no visible global function definition for 'clusterCall'
portest: no visible global function definition for 'parSapply'
portest: no visible global function definition for 'stopCluster'
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

getSimTrades,stiFromSignal-orderable-portfolio-simData-logical :
  .local: no visible binding for global variable 'shares'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.freq'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.errors'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.type'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.summary.interface'
loadIn,simResultSinglePeriod-character-missing : .local: no visible
  binding for global variable 'x'
plot,simResult-missing: no visible global function definition for
  'xyplot'
runSim,portfolioSim-logical : .local: no visible binding for global
  variable 'id'
runSim,portfolioSim-logical : .local: no visible global function
  definition for 'updateSummary'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PottsUtils.Rcheck/00install.out' for details.
ExampleModels: no visible binding for global variable 'ExampleData'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/prevalence.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'graphics' 'stats'
  All declared Imports should be used.
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
LR.pvalue: warning in matrix(c(y1, y2, (n1 - y1), (n2 - y2)), nr = 2,
  dimnames = list(c("treat", "control"), c("Success", "No success"))):
  partial argument match of 'nr' to 'nrow'
profilelike.gls: no visible global function definition for 'gls'
profilelike.lme: no visible global function definition for 'lme'
profilelike.polr: no visible global function definition for 'polr'
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.4Mb
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
IndividualPROC: no visible global function definition for 'survfit'
optim.two.stage.appr: no visible global function definition for
  'mvrnorm'
optim.two.stage.group: no visible global function definition for
  'mvrnorm'
optim.two.stage.single: no visible global function definition for
  'mvrnorm'
power.group.cost: no visible global function definition for 'mvrnorm'
power.single.cost: no visible global function definition for 'mvrnorm'
predict.protoclass: no visible global function definition for 'knn1'
Missing or unexported object: 'tools::nonS3methods'
Namespaces in Imports field not imported from:
  'forecast' 'knitr'
  All declared Imports should be used.
learnParameters: no visible global function definition for
  'coordinates'
makePrediction: no visible global function definition for 'coordinates'
spatialPredict.psgp: no visible global function definition for
  'coordinates'
spatialPredict.psgp: no visible global function definition for
  'makeCluster'
spatialPredict.psgp: no visible global function definition for
  'registerDoParallel'
spatialPredict.psgp: no visible global function definition for
  'clusterEvalQ'
spatialPredict.psgp: no visible global function definition for
  '%dopar%'
spatialPredict.psgp: no visible global function definition for
  'foreach'
spatialPredict.psgp: no visible global function definition for
  'stopCluster'
spatialPredict.psgp: no visible global function definition for
  'SpatialPointsDataFrame'
spatialPredict.psgp: no visible global function definition for 'bbox'
spatialPredict.psgp: no visible global function definition for
  'proj4string<-'
spatialPredict.psgp: no visible global function definition for
  'proj4string'
test.problem : g: no visible global function definition for 'grad'
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
testCatEffectBoot: no visible global function definition for 'boot'
bootstrap_inference: no visible global function definition for
  'makeCluster'
bootstrap_inference: no visible global function definition for
  '%dopar%'
bootstrap_inference: no visible global function definition for
  'foreach'
bootstrap_inference: no visible global function definition for
  'stopCluster'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PurBayes.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PVAClone.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RSVGTipsDevice'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible binding for global variable 'Type'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.qrfactor : sp.label: no visible global function definition for
  'coordinates'
plot.qrfactor: no visible global function definition for 'spplot'
plot.qrfactor: no visible global function definition for 'bpy.colors'
plot.qrfactor: no visible global function definition for 'readOGR'
rq: no visible global function definition for 'readOGR'
Namespace in Imports field not imported from: 'xts'
  All declared Imports should be used.
tailprob: warning in pchisq(t, df, low = FALSE): partial argument match
  of 'low' to 'lower.tail'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    contrib   3.6Mb
    doc       2.9Mb
plot,cvpen : .local: no visible binding for global variable 'lambda1'
plot,cvpen : .local: no visible binding for global variable 'lambda2'
plot,cvpen : .local: no visible binding for global variable 'serr'
plot,cvpen : .local: no visible binding for global variable 'xval'
plot,cvpen : .local: no visible binding for global variable
  'lambda.choice'
plot,quadrupen : .local: no visible binding for global variable
  'variables'
plot,stability.path : .local: no visible binding for global variable
  'variables'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/QuantTools.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'afex' 'data.table' 'dplyr' 'lmerTest'
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/R2jags.Rcheck/00install.out' for details.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
allpossregs.formula: no visible global function definition for
  'regsubsets'
allpossregs.lm: no visible global function definition for 'regsubsets'
reg3d: no visible global function definition for 'rgl.open'
reg3d: no visible global function definition for 'rgl.bg'
reg3d: no visible global function definition for 'rgl.material'
reg3d: no visible global function definition for 'rgl.lines'
reg3d: no visible global function definition for 'rgl.spheres'
reg3d: no visible global function definition for 'rgl.surface'
reg3d: no visible global function definition for 'rgl.texts'
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
BinBam: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
BinBam: no visible global function definition for 'seqlengths'
makeGCContentData: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
makeGCContentData: no visible global function definition for
  'seqlengths'
makeGCContentPerPos: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
freq: no visible global function definition for 'melt'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.freq: no visible global function definition for 'melt'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'polynomial'
bef.get.categories_for: no visible binding for global variable 'id'
bef.portal.get.categories_for: no visible binding for global variable
  'id'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rblpapi.Rcheck/00install.out' for details.
bn2nbn: no visible binding for global variable 'bn.fit'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8mn: no visible global function definition for 'mvrnorm'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
install_version: no visible global function definition for
  'install_url'
circlesSize: no visible global function definition for 'bbox'
discretVar: no visible global function definition for 'classIntervals'
discretVar: no visible global function definition for 'brewer.pal'
frameAutoSize: no visible global function definition for 'bbox'
mapChoroTypo: no visible global function definition for
  'readShapeSpatial'
mapChoropleth: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for 'coordinates'
mapCirclesChoro: no visible global function definition for
  'readShapeSpatial'
mapCirclesChoro: no visible global function definition for
  'coordinates'
mapCirclesTypo: no visible global function definition for
  'readShapeSpatial'
mapCirclesTypo: no visible global function definition for 'coordinates'
northArrowDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
northArrowDisplay: no visible global function definition for
  'layout.north.arrow'
scalebarDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
scalebarDisplay: no visible global function definition for
  'layout.scale.bar'
typo: no visible global function definition for 'brewer.pal'
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
.onAttach: no visible global function definition for 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
bigraphe0: no visible global function definition for 'qgraph'
bisummarize0: no visible global function definition for 'dudi.coa'
chalandise.DEP0: no visible global function definition for 'map'
histbackback0: no visible global function definition for 'mgp.axis'
mapAFC: no visible global function definition for 'scatter'
mapAFC: no visible global function definition for 'dudi.coa'
multivariate0: no visible global function definition for 'dudi.mix'
plotCat2: no visible global function definition for 's.class'
plotLikert1: no visible global function definition for 'trellis.device'
plotLikert1: no visible global function definition for 'dotplot'
plotLikert1: no visible global function definition for 'simpleKey'
plotMissing: no visible global function definition for 'whatis'
plotNum: no visible global function definition for 's.corcircle'
plotTabCont0: no visible global function definition for 'assoc'
plotTabCont0: no visible binding for global variable 'shading_hcl'
plotTabCont0: no visible global function definition for 'corresp'
sortAnova: no visible global function definition for 'Anova'
statMissing: no visible global function definition for 'whatis'
vpAFC: no visible global function definition for 'dudi.coa'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcmdrPlugin.RMTCJags.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppBlaze.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppCCTZ.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs      1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppHMM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppOctave.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       6.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.3Mb
    libs      1.9Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    include   4.3Mb
    lib      21.3Mb
    libs      3.8Mb
sumry_categorical: no visible global function definition for 'freq'
prepare_Rd: Rdpack-package.Rd:154: unknown macro '\insertRef'
prepare_Rd: Rdpack-package.Rd:156: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:89: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:91: unknown macro '\insertRef'
macros/refmacros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'refmacros.Rd'
Package suggested but not available for checking: 'RSelenium'
Namespaces in Imports field not imported from:
  'R6' 'hms'
  All declared Imports should be used.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.6Mb
Namespaces in Imports field not imported from:
  'devtools' 'dplyr' 'magrittr' 'plyr' 'reshape2'
  All declared Imports should be used.
Error in re-building vignettes:
  ...

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Quitting from lines 47-64 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
object 'x' not found
Execution halted
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Namespaces in Imports field not imported from:
  'igraph' 'rJava'
  All declared Imports should be used.
REEMtree: no visible binding for global variable 'SubsetVector'
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
macros/macros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'macros.Rd'
wcr: no visible global function definition for 'ginv'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
relaxo: no visible global function definition for 'lars'
cross: no visible binding for global variable 'is.Surv'
is.numeric.and.not.surv: no visible global function definition for
  'is.Surv'
remix: no visible global function definition for 'is.formula'
remix : <anonymous>: no visible global function definition for
  'is.Surv'
remix: no visible binding for global variable 'is.Surv'
remix: no visible global function definition for 'llply'
summarize.by: no visible global function definition for 'dlply'
summarize.by: no visible global function definition for '.'
summarize.data.frame.by: no visible global function definition for
  'dlply'
survival: no visible global function definition for 'survfit'
survival: no visible global function definition for 'daply'
survival: no visible global function definition for '.'
test.survival.logrank: no visible global function definition for
  'survdiff'
GlobTestMissing: no visible global function definition for 'lme'
TestStatSimple: no visible global function definition for 'ginv'
reshapeGUI: no visible global function definition for 'gwindow'
reshapeGUI: no visible global function definition for 'gnotebook'
reshapeGUI: no visible global function definition for 'size<-'
reshapeGUI: no visible global function definition for 'ggroup'
reshapeGUI: no visible global function definition for 'gtable'
reshapeGUI: no visible global function definition for 'addSpring'
reshapeGUI: no visible global function definition for 'gbutton'
reshapeGUI: no visible global function definition for 'glabel'
reshapeGUI: no visible global function definition for 'gedit'
reshapeGUI: no visible global function definition for 'gcheckbox'
reshapeGUI: no visible global function definition for 'gdf'
reshapeGUI: no visible global function definition for 'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerClicked'
reshapeGUI : <anonymous>: no visible global function definition for
  'gmessage'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue<-'
reshapeGUI : <anonymous>: no visible global function definition for
  'delete'
reshapeGUI : <anonymous>: no visible global function definition for
  'add'
reshapeGUI : <anonymous>: no visible global function definition for
  'gdf'
reshapeGUI : <anonymous>: no visible global function definition for
  'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerChanged'
updateMeltCodeBox: no visible global function definition for 'svalue<-'
findCredentials: no visible global function definition for 'startsWith'
Running examples in 'restfulr-Ex.R' failed
The error most likely occurred in:

> ### Name: RestContainer-class
> ### Title: RestContainer
> ### Aliases: class:RestContainer RestContainer-class RestContainer
> ###   [,RestContainer-method [<-,RestContainer-method
> ###   $,RestContainer-method [[,RestContainer-method
> ###   $<-,RestContainer-method [[<-,RestContainer-method
> ###   show,RestContainer-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> apache <- RestContainer("http://wiki.apache.org")
Error in which(startsWith(uri, as.character(names(config)))) : 
  could not find function "startsWith"
Calls: RestContainer -> container -> RestUri -> findCredentials -> which
Execution halted
mat2coo: no visible global function definition for 'as.matrix.coo'
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    gdal       3.0Mb
    libs      23.7Mb
    pictures   1.3Mb
    proj       4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: add_flags works properly guessing names for rvertnet dataset (@test_multiple_records.R#38) 
  2. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#51) 
  3. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#52) 
  4. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#53) 
  5. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#54) 
  6. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#55) 
  7. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#56) 
  8. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#57) 
  9. Failure: add_flags works properly with a 1-row data.frame (@test_multiple_records.R#58) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    1.1Mb
exprToIgraph: no visible global function definition for 'graph'
exprToIgraph: no visible global function definition for 'V'
exprToIgraph: no visible global function definition for 'V<-'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfExport'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfExport'
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-32~1.5/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
server: no visible global function definition for 'mcparallel'
Found the following significant warnings:
  gdkFuncs.c:1466:3: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast [enabled by default]
  gdkFuncs.c:1510:3: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast [enabled by default]
See 'd:/Rcompile/CRANpkg/local/3.2/RGtk2.Rcheck/00install.out' for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.6Mb
dbConnect,H2Driver : .local: no visible global function definition for
  '.jgetEx'
dbSendQuery,H2Connection-character : .local: no visible global function
  definition for '.jfield'
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.2Mb
    libs   4.3Mb
Package required but not available: 'feather'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rjags.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
getStatsData: no visible global function definition for 'xmlRoot'
getStatsData: no visible global function definition for 'xmlTreeParse'
getStatsData: no visible global function definition for 'xmlValue'
getStatsData: no visible global function definition for 'getNodeSet'
getStatsData: no visible global function definition for 'xmlSApply'
getStatsData: no visible binding for global variable 'xmlGetAttr'
getStatsData: no visible binding for global variable 'xmlValue'
getStatsList: no visible global function definition for 'xmlRoot'
getStatsList: no visible global function definition for 'xmlTreeParse'
getStatsList: no visible global function definition for 'xmlValue'
getStatsList: no visible binding for global variable 'xmlGetAttr'
getStatsList : <anonymous>: no visible global function definition for
  'xmlValue'
getStatsList : <anonymous>: no visible global function definition for
  'xmlGetAttr'
Namespace in Imports field not imported from: 'crul'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
Package required and available but unsuitable version: 'Luminescence'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
parse_grammar : <anonymous>: no visible global function definition for
  'startsWith'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  Generating LALR tables 
  testthat results ================================================================
  OK: 153 SKIPPED: 0 FAILED: 5
  1. Failure: rule (@test.yacc_badrule.R#181) 
  2. Failure: rule (@test.yacc_badrule.R#183) 
  3. Failure: rule (@test.yacc_badrule.R#185) 
  4. Failure: rule (@test.yacc_badrule.R#187) 
  5. Failure: misplaced (@test.yacc_misplaced.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
PD_internal: no visible global function definition for 'qtnorm'
Namespaces in Imports field not imported from:
  'mnormt' 'pwr'
  All declared Imports should be used.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
plot.meta.cum: warning in qnorm((1 - conf.level)/2, s = ses[m]):
  partial argument match of 's' to 'sd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmixmod.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmpi.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
DESeqWrapper: no visible global function definition for
  'newCountDataSet'
DESeqWrapper: no visible global function definition for
  'estimateSizeFactors'
DESeqWrapper: no visible global function definition for 'counts'
DESeqWrapper: no visible global function definition for
  'estimateDispersions'
DESeqWrapper: no visible global function definition for 'nbinomTest'
DESeqWrapper: no visible global function definition for
  'getVarianceStabilizedData'
DESeqWrapper: no visible global function definition for 'pData'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'as.alignment'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'kaks'
nSynNonSites : <anonymous>: no visible global function definition for
  'as.alignment'
nSynNonSites : <anonymous>: no visible global function definition for
  'kaks'
plotDispEsts: no visible global function definition for 'counts'
plotDispEsts: no visible global function definition for 'fitInfo'
runGOAnalysis: no visible binding for global variable 'annFUN.gene2GO'
runGOAnalysis: no visible global function definition for 'runTest'
runGOAnalysis: no visible global function definition for 'score'
runGOAnalysis: no visible global function definition for 'termStat'
runGOAnalysis: no visible global function definition for 'Term'
runGOAnalysis: no visible binding for global variable 'GOTERM'
runGOAnalysis: no visible global function definition for
  'showSigOfNodes'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robcor: no visible global function definition for 'covMcd'
robloxbioc,beadLevelData : .local: warning in
  packageDescription(annoPkg, field = "Version"): partial argument
  match of 'field' to 'fields'
AffySimStudy: no visible global function definition for 'estimate'
IlluminaSimStudy: no visible global function definition for 'estimate'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'arrayNames'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'getArrayData'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'mappedkeys'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'revmap'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'featureData<-'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'phenoData<-'
FaClassic.default: no visible global function definition for 'Cov'
FaClassic.default: no visible global function definition for 'getCov'
FaCov.default: no visible global function definition for
  'CovControlMcd'
FaCov.default: no visible global function definition for 'restimate'
FaCov.default: no visible global function definition for 'Cov'
FaCov.default: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'CovRobust'
compute_cov_cor: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'getCorr'
myplotDD: no visible global function definition for 'getData'
myplotDD: no visible global function definition for 'getCov'
myplotDD: no visible global function definition for 'CovClassic'
myplotDD: no visible global function definition for 'getDistance'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
api: no visible global function definition for 'endsWith'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.1Mb
P: no visible global function definition for 'has.key'
rand_partitions: no visible global function definition for 'hash'
rpart.rules.push: no visible global function definition for 'sqlSave'
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
cell.density.default: no visible binding for global variable
  'universalConstants'
conect.pdb: no visible binding for global variable 'elements'
masses.default: no visible binding for global variable 'elements'
toSymbols.character: no visible binding for global variable 'elements'
toSymbols.integer: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'elements'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
read.multi.dna: no visible binding for global variable 'read.dna'
read.phylip.data: no visible global function definition for 'read.dna'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
Package required but not available: 'wdman'

Package suggested but not available for checking: 'Rcompression'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  d:\compiler\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/winsock2.h:15:2: warning: #warning Please include winsock2.h before windows.h [-Wcpp]
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
rsig: no visible binding for global variable 'mclapply'
rsig.all: no visible binding for global variable 'mclapply'
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
RStorm: no visible global function definition for 'alply'
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rtk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/runjags.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
rvgt.ftable : myrdist: no visible global function definition for 'ur'
uerror: no visible global function definition for 'unuran.is.inversion'
uerror : myaqdist: no visible global function definition for 'uq'
unuran.distr.class: no visible global function definition for
  'unuran.details'
xerror: no visible global function definition for 'unuran.is.inversion'
xerror : myaqdist: no visible global function definition for 'uq'
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
Running examples in 'rwty-Ex.R' failed
The error most likely occurred in:

> ### Name: makeplot.splitfreq.matrix
> ### Title: Plots a matrix of split frequency comparisons between multiple
> ###   MCMC chains.
> ### Aliases: makeplot.splitfreq.matrix
> ### Keywords: ASDSF MCMC, clade consensus, convergence, frequency,
> ###   phylogenetics,
> 
> ### ** Examples
> 
> data(salamanders)
> makeplot.splitfreq.matrix(salamanders[1:4], burnin = 20)
[1] "Creating split frequency matrix and ASDSF clustering plots"
$splitfreq.matrix

$asdsf.tree
Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : 
  invalid graphics state
Calls: print -> print.ggplot -> grid.newpage -> <Anonymous>
Execution halted
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
RXlarlso: no visible global function definition for 'lars'
RXuclars: no visible global function definition for 'lars'
Found the following significant warnings:
  Warning: S3 methods 'anova.merMod', 'as.data.frame.boot', 'as.data.frame.thpr', 'as.data.frame.VarCorr.merMod', 'as.function.merMod', 'coef.lmList4', 'coef.merMod', 'confint.lmList4', 'confint.merMod', 'confint.thpr', 'densityplot.thpr', 'deviance.merMod', 'df.residual.merMod', 'dotplot.coef.mer', 'dotplot.ranef.mer', 'drop1.merMod', 'extractAIC.merMod', 'family.glmResp', 'family.lmResp', 'family.merMod', 'family.nlsResp', 'fitted.merMod', 'fixef.merMod', 'formula.lmList4', 'formula.merMod', 'getME.merMod', 'hatvalues.merMod', 'isGLMM.merMod', 'isLMM.merMod', 'isNLMM.merMod', 'isREML.merMod', 'log.thpr', 'logLik.merMod', 'model.frame.merMod', 'model.matrix.merMod', 'ngrps.factor', 'ngrps.merMod', 'nobs.merMod', 'plot.coef.mer', 'plot.lmList4.confint', 'plot.merMod', 'plot.ranef.mer', 'predict.merMod', 'print.merMod', 'print.ranef.mer', 'print.summary.merMod', 'print.VarCorr.merMod', 'profile.merMod', 'qqmath.merMod', 'qqmath.ranef.mer', 'ranef.merMod', 'refit.merMod', 'refitML.merMod', 'residua [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.2/Rz.Rcheck/00install.out' for details.
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
summary.CrossTable: no visible global function definition for
  'assocstats'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/s2.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
Plot.ll: warning in axis(1, chpt - n * 2.5/100, tick = F, lab =
  expression(hat(k)), cex.axis = 1, col.axis = "red"): partial argument
  match of 'lab' to 'labels'
plot,SaemixSimData : .local: no visible binding for global variable
  'name.group'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
distanceLimitedPDSIZ,downLog-perpendicularDistance-dlsNumeric : .local:
  warning in matrix(c(os.len, 0, 1), nr = 1): partial argument match of
  'nr' to 'nrow'
downLogs,numeric-missing : .local: warning in matrix(c(xlim, ylim), nr
  = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min", "max"))):
  partial argument match of 'nr' to 'nrow'
standingTrees,numeric-missing : .local: warning in matrix(c(xlim,
  ylim), nr = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min",
  "max"))): partial argument match of 'nr' to 'nrow'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersects'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersection'
izGrid,matrix-Tract : .local: no visible global function definition for
  'intersectExtent'
izGridMirage,InclusionZone-mirageTract : .local: no visible global
  function definition for 'gIntersects'
izGridMirage,InclusionZone-mirageTract : .local : mirageSection: no
  visible global function definition for 'gIntersection'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
foldchange.seq.twoclass.paired: no visible global function definition
  for 'rowMedians'
foldchange.seq.twoclass.unpaired: no visible global function definition
  for 'rowMedians'
samr: no visible global function definition for 'impute.knn'
samr.xl.impute.data: no visible global function definition for
  'impute.knn'
samr.xl.impute.data: no visible binding for global variable
  'samr.xl.var.knn.neighbors'
my.SOnePro: missing arguments not allowed in calls to 'c'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
convert.infusion: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'transpose'
dde.model: no visible global function definition for 'size'
dde.model: no visible global function definition for 'transpose'
de.output: no visible global function definition for 'size'
explicit.model: no visible global function definition for 'size'
finalize.report: no visible global function definition for 'transpose'
finalize.report: no visible global function definition for 'size'
fitmle : obj.fun: no visible global function definition for 'size'
fitmle.cov: no visible global function definition for 'transpose'
get.cov.matrix: no visible global function definition for 'size'
get.parms.data: no visible global function definition for 'size'
get.secondary: no visible global function definition for 'transpose'
init.cond: no visible global function definition for 'size'
init.update: no visible global function definition for 'size'
input.scaling: no visible global function definition for 'size'
make.dosing: no visible global function definition for 'size'
ode.model: no visible global function definition for 'size'
ode.model: no visible global function definition for 'transpose'
problem.eval: no visible global function definition for 'size'
residual.report: no visible global function definition for 'size'
scarabee.check.model: no visible global function definition for 'size'
scarabee.gridsearch : grid.obj.fun: no visible global function
  definition for 'size'
scarabee.read.data: no visible global function definition for 'size'
scarabee.read.parms: no visible global function definition for 'size'
simulation.report: no visible global function definition for 'size'
weighting: no visible global function definition for 'size'
prime.factor: no visible binding for global variable 'primlist'
c,scidbdf : .local: warning in build_dim_schema(x, newname = j):
  partial argument match of 'newname' to 'newnames'
scio.refit: no visible global function definition for 'QUIC'
CreatePssm: no visible binding for global variable 'training'
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
buildSNPannotation: no visible global function definition for 'db'
buildSNPannotation: no visible global function definition for
  'dbListFields'
buildSNPannotation: no visible global function definition for
  'dbGetQuery'
fblr: no visible global function definition for 'mvrnorm'
fblr.weight: no visible global function definition for 'mvrnorm'
Namespaces in Imports field not imported from:
  'gbm' 'graphics' 'ncdf4' 'rgdal' 'sp'
  All declared Imports should be used.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> 
> ## Not run: 
> ##D # if m is a sdmModels object (output of sdm function) then:
> ##D 
> ##D getVarImp(m,id=1,wtest='training') # variable importance based on training dataset
> ##D 
> ##D vi <- getVarImp(m,id=1,wtest='test.dep') 
> ##D 
> ##D plot(vi,'auc')
> ##D 
> ##D plot(vi,'cor')
> ##D 
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.47 0.14 3.44 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
ConnCompLabel: no visible global function definition for 'setValues'
SigDiff: no visible global function definition for 'setValues'
asc.from.raster: no visible global function definition for 'getValues'
aspect: no visible global function definition for 'setValues'
grid.area: no visible global function definition for 'setValues'
grid.perimeter: no visible global function definition for 'setValues'
lcmw: no visible global function definition for 'setValues'
raster.from.asc: no visible global function definition for 'raster'
raster.from.asc: no visible global function definition for
  'projection<-'
raster.from.asc: no visible global function definition for 'setValues'
slope: no visible global function definition for 'setValues'
sp.from.asc: no visible global function definition for 'CRS'
sp.from.asc: no visible global function definition for 'GridTopology'
sp.from.asc: no visible global function definition for
  'SpatialGridDataFrame'
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
dathomog: no visible global function definition for 'kde2d'
fitMod: no visible global function definition for 'survreg'
fitswavecav: no visible global function definition for 'year'
prepData: no visible global function definition for 'year'
prepData: no visible global function definition for 'month'
prepData: no visible global function definition for 'day'
rosBoxPlot: no visible global function definition for 'ros'
GKhat.env: no visible global function definition for 'Gest'
GKhat.env: no visible global function definition for 'rpoispp'
GKhat.env: no visible global function definition for 'Kest'
GKhat.env: no visible global function definition for 'runifpoint'
Okriging: no visible global function definition for 'point'
Okriging: no visible global function definition for 'krige'
eda6: no visible global function definition for 'qqPlot'
makeppp: no visible global function definition for 'ppp'
nnGK.ppp: no visible global function definition for 'Gest'
nnGK.ppp: no visible global function definition for 'Kest'
nnGKenv.ppp: no visible global function definition for 'Gest'
nnGKenv.ppp: no visible global function definition for 'Kest'
plotkriged: no visible global function definition for 'point'
quad.chisq.ppp: no visible global function definition for 'ppp'
quad.poisson.ppp: no visible global function definition for 'ppp'
vario: no visible global function definition for 'point'
vario: no visible global function definition for 'pair'
vario: no visible global function definition for 'est.variogram'
vario: no visible global function definition for 'plot.point'
vario: no visible global function definition for 'spacecloud'
vario: no visible global function definition for 'spacebox'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
semdiag: no visible global function definition for 'sem'
semdiag.robfit.r: no visible global function definition for 'sem'
semdiag.robfit1.r: no visible global function definition for 'sem'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
semPlotModel.mplus.model: no visible global function definition for
  'readModels'
plot.sempls: no visible global function definition for
  'trellis.par.get'
plot.sempls: no visible global function definition for
  'trellis.par.set'
plot.sempls: no visible global function definition for 'xyplot'
plsm2sem.plsm: no visible global function definition for 'specifyModel'
plsm2sem.plsm: no visible global function definition for
  'specify.model'
read.splsm: no visible global function definition for
  'xmlInternalTreeParse'
read.splsm: no visible global function definition for 'xpathApply'
read.splsm: no visible binding for global variable 'xmlGetAttr'
summary.bootsempls: no visible global function definition for 'boot.ci'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/semver.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/SeqFeatR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/seqminer.Rcheck/00install.out' for details.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'betareg'
A package should be listed in only one of these fields.
Namespaces in Imports field not imported from:
  'betareg' 'lattice'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'betareg' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
indirectCalibration: no visible global function definition for
  'betareg'
xy.plot.lat: no visible global function definition for 'xyplot'
xy.plot.lat: no visible global function definition for 'strip.custom'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.abline'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.xyplot'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.text'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sf.Rcheck/00install.out' for details.
plotBoundary: no visible global function definition for
  'scale_y_continuous'
distLaplacian: no visible global function definition for 'sparseMatrix'
laplacian: no visible global function definition for 'sparseMatrix'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sharx.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'DT' 'gridExtra' 'latticeExtra' 'msm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shinyBS' 'shinythemes'
  All declared Imports should be used.
Package required and available but unsuitable version: 'CompQuadForm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
footpoint.nodes: no visible global function definition for
  'coordinates'
nt.connect: no visible global function definition for 'bbox'
nt.connect: no visible global function definition for
  'as.SpatialLines.SLDF'
nt.connect: no visible global function definition for
  'SpatialLinesDataFrame'
ptsinnt.view: no visible global function definition for 'bbox'
readshpnw: no visible global function definition for 'coordinates'
Undocumented S4 methods:
  generic '[' and siglist 'Prob0,ANY,missing,ANY'
  generic '[' and siglist 'bFdr,ANY,missing,ANY'
  generic '[' and siglist 'basicFdr,ANY,missing,ANY'
  generic '[' and siglist 'eFdr,ANY,missing,ANY'
  generic '[' and siglist 'estimate,ANY,missing,ANY'
  generic '[' and siglist 'loss,ANY,missing,ANY'
  generic '[' and siglist 'pseudoFdr,ANY,missing,ANY'
  generic '[' and siglist 'sFdr,ANY,missing,ANY'
  generic '[' and siglist 'sortableEstimate,ANY,missing,ANY'
  generic '[' and siglist 'unsortableEstimate,ANY,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
bayesMVN: no visible global function definition for 'rmultireg'
bayestwoNorm: no visible global function definition for 'runireg'
overlap: no visible global function definition for 'overlap.xypolygon'
panelcontour: no visible global function definition for 'kde2d'
siardensityplot: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'geweke.diag'
siarproportionbygroupplot: no visible global function definition for
  'hdr'
siarproportionbysourceplot: no visible global function definition for
  'hdr'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: fitEllipse
> ### Title: Fit a multivariate normal distribution to x and y data using
> ###   jags
> ### Aliases: fitEllipse
> 
> ### ** Examples
> 
> x <- stats::rnorm(50)
> y <- stats::rnorm(50)
> parms <- list()
> parms$n.iter <- 2 * 10^3
> parms$n.burnin <- 500
> parms$n.thin <- 2     
> parms$n.chains <- 2    
> priors <- list()
> priors$R <- 1 * diag(2)
> priors$k <- 2
> priors$tau.mu <- 1.0E-3
> fitEllipse(x, y, parms, priors)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 116-150 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for
  'cov.shrink'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
clusterSetup,ANY-data.frame-SampleControl : .local: no visible binding
  for global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl : .local: no visible
  binding for global variable 'cnam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/simmr.Rcheck/00install.out' for details.
Simpsons: no visible global function definition for 'Mclust'
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
Running examples in 'sisus-Ex.R' failed
The error most likely occurred in:

> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> # set working directory for many output files with setwd()
> # see http://statacumen.com/sisus for workbook
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Warning in download.file(xls, tf, mode = "wb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... <Anonymous> -> xls2sep -> download.file -> file.exists
Execution halted
Namespace in Imports field not imported from: 'mcmc'
  All declared Imports should be used.
prop : <anonymous>: no visible global function definition for
  'startsWith'
Running examples in 'sjstats-Ex.R' failed
The error most likely occurred in:

> ### Name: prop
> ### Title: Proportion of values in a vector
> ### Aliases: prop
> 
> ### ** Examples
> 
> data(efc)
> 
> # proportion of value 1 in e42dep
> prop(efc, e42dep == 1)
Error in FUN(X[[i]], ...) : could not find function "startsWith"
Calls: prop -> lapply -> FUN
Execution halted
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
qskewhyp: multiple local function definitions for 'zeroFn' with
  different formal arguments
Namespaces in Imports field not imported from:
  'rgdal' 'utils'
  All declared Imports should be used.
fitted.sma: no visible global function definition for 'join'
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
File 'SMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.
em: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
getRoughnessMatrix: no visible global function definition for 'ns'
plotSmeRaw: no visible global function definition for 'xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.lines'
sme.default: no visible global function definition for 'ns'
sme.list: no visible binding for global variable 'ns'
sme.list : <anonymous>: no visible global function definition for 'ns'
vcov.sme: no visible global function definition for 'ns'
coxph.disparity: no visible global function definition for 'basehaz'
disparity.glm : <anonymous>: no visible global function definition for
  'gamma.shape'
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'nlme' 'survival'
  All declared Imports should be used.
sfApply: no visible global function definition for 'parApply'
sfClusterApply: no visible global function definition for
  'clusterApply'
sfClusterApplyLB: no visible global function definition for
  'clusterApplyLB'
sfClusterCall: no visible global function definition for 'clusterCall'
sfClusterSetupRNG: no visible global function definition for
  'clusterSetupRNG'
sfClusterSetupRNGstream: no visible global function definition for
  'clusterSetupRNGstream'
sfClusterSetupSPRNG: no visible global function definition for
  'clusterSetupSPRNG'
sfClusterSplit: no visible global function definition for
  'clusterSplit'
sfInit: no visible global function definition for
  'setDefaultClusterOptions'
sfInit: no visible global function definition for 'makeCluster'
sfInit: no visible global function definition for 'makeNWScluster'
sfInit: no visible global function definition for 'makeMPIcluster'
sfLapply: no visible global function definition for 'parLapply'
sfMM: no visible global function definition for 'parMM'
sfSapply: no visible global function definition for 'parSapply'
sfStop: no visible global function definition for 'stopCluster'
WGassociation: no visible global function definition for 'mclapply'
interleave: no visible global function definition for 'mclapply'
setupSNP: no visible global function definition for 'mclapply'
summary.setupSNP: no visible global function definition for 'mclapply'
tableHWE: no visible global function definition for 'mclapply'
convert.genes.to.GRanges: no visible global function definition for
  'GRanges'
convert.genes.to.GRanges: no visible global function definition for
  'IRanges'
convert.genes.to.GRanges: no visible global function definition for
  'metadata<-'
convert.pos.to.GRanges: no visible global function definition for
  'GRanges'
convert.pos.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'GRanges'
convert.variants.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'metadata<-'
find.overlapping.genes: no visible global function definition for
  'findOverlaps'
find.overlapping.genes: no visible global function definition for
  'subjectHits'
get.mgi.features: no visible global function definition for 'TabixFile'
get.mgi.features: no visible global function definition for
  'headerTabix'
get.mgi.features: no visible global function definition for 'scanTabix'
get.strains: no visible global function definition for 'TabixFile'
get.strains: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'TabixFile'
get.variants: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'scanTabix'
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
my.normdata.gen: no visible global function definition for 'mvrnorm'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
eplot: no visible global function definition for 'trellis.par.get'
eplot: no visible global function definition for 'trellis.par.set'
eplot: no visible global function definition for 'xyplot'
munsell_to_rgb: no visible global function definition for 'munsell2rgb'
roots: no visible global function definition for 'areapl'
roots: no visible global function definition for 'point.in.polygon'
skeletal: no visible global function definition for 'areapl'
skeletal: no visible global function definition for 'point.in.polygon'
turnoverFit: no visible binding for global variable 'IntCal13'
turnoverFit: no visible binding for global variable 'Hua2013'
initialize,NlModel : .local: no visible global function definition for
  'TransportDecompositionOperator.new'
plot3d: no visible global function definition for 'persp3d'
SOS: no visible global function definition for 'getCurlHandle'
Namespaces in Imports field not imported from:
  'gtools' 'hashmap' 'uuid'
  All declared Imports should be used.
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
SJ: no visible binding for global variable 'bs'
SJ: no visible global function definition for 'get.adjacency'
SJ : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ: no visible binding for global variable 'ecount'
SJ.dag: no visible binding for global variable 'bs'
SJ.dag : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ.dag: no visible binding for global variable 'ecount'
SJpath: no visible global function definition for 'get.adjacency'
SJpath : <anonymous>: no visible global function definition for
  'graph.adjacency'
generate.dag.data: no visible global function definition for 'vcount'
generate.dag.data: no visible global function definition for
  'topological.sort'
generate.dag.data: no visible global function definition for
  'neighbors'
grpsel: no visible global function definition for 'Matrix'
moralize: no visible global function definition for 'vcount'
moralize: no visible global function definition for 'as.undirected'
moralize: no visible global function definition for 'get.adjacency'
moralize: no visible global function definition for 'add.edges'
moralize: no visible global function definition for 'simplify'
plot.SJ: no visible global function definition for
  'layout.fruchterman.reingold'
plot.SJ.dag: no visible global function definition for
  'layout.fruchterman.reingold'
print.SJ: no visible binding for global variable 'ecount'
print.SJ: no visible global function definition for 'ecount'
print.SJ.dag: no visible binding for global variable 'ecount'
print.SJ.dag: no visible global function definition for 'ecount'
rdag: no visible global function definition for 'graph.adjacency'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
  'Ntip'
phy.deresolve: no visible global function definition for
  'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
  'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
  'branching.times'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.treeplot: no visible global function definition for
  'diverge_hcl'
spacodi.treeplot: no visible global function definition for
  'nodelabels'
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
livy_statement_parse_response : scalaTypeOfArray: possible error in
  regexec("^\\[L(.*);", scalaType, perl = TRUE): unused argument (perl
  = TRUE)
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
getcoef_list: no visible global function definition for 'drop0'
sparsepredict: no visible global function definition for
  'lambda.interp'
sparsepredict: no visible global function definition for 'nonzeroCoef'
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    data   3.4Mb
    doc    5.0Mb
    help   4.8Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'Matrix::expm' by 'expm::expm' when loading 'spdep'
See 'd:/Rcompile/CRANpkg/local/3.2/spdep.Rcheck/00install.out' for details.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
err.default: no visible global function definition for 'prediction'
err.default: no visible global function definition for 'performance'
rgl.sphMW: no visible global function definition for 'plot3d'
rgl.sphcirc: no visible global function definition for 'rotate3d'
rgl.sphcirc: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'open3d'
rgl.sphgrid: no visible global function definition for 'plot3d'
rgl.sphgrid: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'text3d'
rgl.sphpoints: no visible global function definition for 'points3d'
rgl.sphsun: no visible global function definition for 'plot3d'
rgl.sphtext: no visible global function definition for 'text3d'
monophyly: no visible global function definition for 'prop.part'
monophylyBoot: no visible global function definition for 'nj'
monophylyBoot: no visible global function definition for 'boot.phylo'
monophylyBoot : <anonymous>: no visible global function definition for
  'root'
monophylyBoot : <anonymous>: no visible global function definition for
  'nj'
monophylyBoot: no visible global function definition for 'prop.part'
polyBalance: no visible global function definition for 'node.depth'
read.BOLD: no visible global function definition for 'as.DNAbin'
read.GB: no visible global function definition for 'as.DNAbin'
slideAnalyses: no visible global function definition for 'nj'
slideAnalyses: no visible global function definition for 'node.depth'
slideAnalyses: no visible binding for global variable 'nj'
tree.comp: no visible global function definition for 'unroot'
tree.comp: no visible global function definition for 'prop.part'
tree.comp: no visible global function definition for 'node.depth'
cv.spikeslab: no visible global function definition for 'mclapply'
gnet.get: no visible global function definition for 'lars'
gnet.get: no visible global function definition for 'predict.lars'
plot.spikeslab: no visible global function definition for 'plot.lars'
sparsePC.spikeslab : get.pc : <anonymous>: no visible global function
  definition for 'randomForest'
sparsePC.spikeslab: no visible global function definition for
  'randomForest'
spikeslab: no visible global function definition for 'randomForest'
SPIn: no visible global function definition for 'solve.QP'
Ell.Theta: no visible global function definition for 'ell.theta'
Namespace in Imports field not imported from: 'geoR'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'
  ...
+     Ap <- pvec * tA
+     pnew <- colMeans(t(Ap)/colSums(Ap))
+     pnew * (pnew > 0)
+ }

> library(interval)

  When sourcing 'SQUAREM.R':
Error: there is no package called 'interval'
Execution halted
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section 'Good practice' in '?.onAttach'.
fit.model: no visible global function definition for 'hadamard'
station: no visible binding for global variable 'WTdiff'
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
as.spikeTrain: no visible global function definition for 'spikeTimes'
gamObj.gampsth: no visible binding for global variable 'PoissonF'
gammaMLE: multiple local function definitions for 'rFct' with different
  formal arguments
gssObj.gsspsth: no visible binding for global variable 'gfit'
gssObj.gsspsth0: no visible binding for global variable 'gfit'
gsslockedTrain: no visible global function definition for 'gssanova'
gsslockedTrain0: no visible global function definition for 'gssanova0'
gsspsth: no visible global function definition for 'gssanova'
gsspsth0: no visible global function definition for 'gssanova0'
invgaussMLE: multiple local function definitions for 'rFct' with
  different formal arguments
lines.CountingProcessSamplePath: no visible binding for global variable
  'st'
mkAR: no visible binding for global variable 'lN.1'
mkM2U: no visible global function definition for 'ssden'
mkM2U : <anonymous>: no visible global function definition for 'dssden'
mkM2U : dFct: no visible global function definition for 'dssden'
mkPostSimAnalysis: no visible global function definition for
  'findGlobals'
qqDuration: no visible binding for global variable 'yi'
qqDuration: no visible binding for global variable 'si'
thinProcess: no visible binding for global variable 'targetFct'
thinProcess: no visible binding for global variable 'posMax'
rg.robmva: no visible global function definition for 'cov.mve'
Namespaces in Imports field not imported from:
  'magrittr' 'rpart'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/StatMethRank.Rcheck/00install.out' for details.
getHb: no visible binding for global variable 'masshb'
getHbgrid: no visible binding for global variable 'masshbgrid'
showComposition: no visible binding for global variable 'compositions'
testComposition: no visible binding for global variable 'compositions'
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
.rp.stan3d: no visible global function definition for 'rp.control'
.rp.stan3d: no visible global function definition for 'rp.slider'
.rp.stan3d: no visible global function definition for 'rp.button'
.rp.stan3d : <anonymous>: no visible global function definition for
  'par3d'
.rp.stan3d : <anonymous>: no visible global function definition for
  'rotationMatrix'
.rp.stan3d: no visible global function definition for 'rp.do'
.rp.stan3d: no visible global function definition for 'rp.block'
.setBG: no visible global function definition for 'surface3d'
.setPlot: no visible global function definition for 'plot3d'
.setPlot: no visible global function definition for 'axis3d'
.setPlot: no visible global function definition for 'par3d'
.setPlot: no visible global function definition for 'aspect3d'
.setPlot: no visible global function definition for 'rotationMatrix'
.stan3d.redraw: no visible global function definition for 'par3d'
.stan3d.redraw: no visible global function definition for 'rgl.pop'
.stan3d.redraw: no visible binding for global variable 'spheres3d'
rlgcp: no visible global function definition for 'bbox'
stan: no visible global function definition for 'lines3d'
stan: no visible global function definition for 'segments3d'
stan: no visible global function definition for 'points3d'
bin.info.cubature : compute.fun: no visible global function definition
  for 'adaptIntegrate'
tess.info : new.points: no visible global function definition for
  'as.points'
tess.info : new.points: no visible global function definition for 'csr'
tess.info.MISER : int.fun: no visible global function definition for
  'as.points'
tess.info.MISER : int.fun: no visible global function definition for
  'inpip'
tessdev: no visible global function definition for 'deldir'
tessdev: no visible global function definition for 'tile.list'
tessdev : sum.l: no visible global function definition for 'as.points'
tessdev : sum.l: no visible global function definition for 'inpip'
tessdev.info : all: no visible global function definition for
  'as.points'
tessdev.info : all: no visible global function definition for 'inpip'
tessresid: no visible global function definition for 'deldir'
tessresid: no visible global function definition for 'tile.list'
tessresid : num: no visible global function definition for 'as.points'
tessresid : num: no visible global function definition for 'inpip'
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'broom' 'car' 'lmerTest' 'pbkrtest'
  All declared Imports should be used.
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
plot,GBH-ANY : .local: no visible binding for global variable
  'sorted.hyp'
plot,GBH-ANY : .local: no visible binding for global variable 'pval'
plot,GBH-ANY : .local: no visible binding for global variable 'group'
plot,GBH-ANY : .local: no visible binding for global variable 'type'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/subprocess.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'ISwR' 'MASS' 'corpcor'
  All declared Imports should be used.
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
gen.y.mat2: no visible global function definition for 'survfit'
superpc.cv: no visible global function definition for 'coxph'
superpc.cv: no visible global function definition for 'coxph.control'
superpc.fit.to.outcome: no visible global function definition for
  'coxph'
superpc.fit.to.outcome: no visible global function definition for
  'coxph.control'
superpc.lrtest.curv: no visible global function definition for 'coxph'
superpc.predictionplot: no visible binding for global variable
  'shrinkages'
superpc.predictionplot: no visible global function definition for
  'survfit'
surv.to.class2: no visible global function definition for 'survfit'
pbc.sample: no visible binding for global variable 'pbc'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

schemper: no visible global function definition for 'survfit'
Est.PH: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'coxph'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'survexp'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'survexp'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'survexp'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
Running examples in 'survminer-Ex.R' failed
The error most likely occurred in:

> ### Name: ggcoxdiagnostics
> ### Title: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2
> ### Aliases: ggcoxdiagnostics
> 
> ### ** Examples
> 
> 
> if(require(RTCGA.clinical)){
+ # TCGA data exmaple (http://cancergenome.nih.gov/)
+ # source("https://bioconductor.org/biocLite.R")
+ # biocLite("RTCGA.clinical") # data for examples
+ # library(RTCGA.clinical) # also loads 'RTCGA' package
+ survivalTCGA(BRCA.clinical, OV.clinical,
+             extract.cols = c("admin.disease_code", "patient.days_to_birth")) -> BRCAOV.survInfo
+ BRCAOV.survInfo$age  <- round((-as.numeric(BRCAOV.survInfo$patient.days_to_birth))/365,2)
+ 
+ library(survival)
+ coxph.fit <- coxph(Surv(times, patient.vital_status) ~ admin.disease_code + age,
+               data = BRCAOV.survInfo)
+ 
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_dark(), point.col = "white", point.aplha = 0.3)
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_RTCGA(), # library(RTCGA.clinical)
+  type = "deviance") + ylab('Deviance Residuals')
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_light(), linear.predictions = FALSE)
+ # ggcoxdiagnostics(coxph.fit, ggtheme = theme_void(), type = "deviance", linear.predictions = FALSE)
+ }
Loading required package: RTCGA.clinical
Loading required package: RTCGA
Loading required package: knitr
Welcome to the RTCGA (version: 1.0.2).
Error: could not find function "survivalTCGA"
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: RTCGA
Welcome to the RTCGA (version: 1.0.2).
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
could not find function "survivalTCGA"
Execution halted
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Namespaces in Imports field not imported from:
  'MASS' 'graphics' 'methods' 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'kernlab'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
roccurve: warning in formatC(sum(c1 * cumsum(c2)), digit = 4): partial
  argument match of 'digit' to 'digits'
svmmajtuning: warning in .svmmaj(Z[groups != i, ], y[groups != i],
  lambda = lambda[l], w = w[groups != i], increase.step =
  increase.step, hinge = newHinge, theta = theta, check.positive =
  FALSE, convergence = convergence, ...): partial argument match of
  'hinge' to 'hingef'
auc: no visible global function definition for 'error'
getUpdate: no visible global function definition for 'vanilladot'
getUpdate: no visible global function definition for 'kernelMatrix'
qhat.theta: no visible global function definition for 'kernelMatrix'
roccurve: no visible global function definition for 'error'
svmmaj.default: no visible binding for global variable 'vanilladot'
svmmaj.default: no visible global function definition for 'kpar'
svmmaj2.default: no visible binding for global variable 'vanilladot'
svmmaj2.default: no visible global function definition for 'kpar'
svmmajtuning: no visible binding for global variable 'vanilladot'
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
adjust.linearmodel: no visible global function definition for 'rlm'
confounding: no visible global function definition for 'heatmap.2'
hca.plot: no visible global function definition for 'colorpanel'
hca.plot: no visible global function definition for 'hcluster'
hca.test: no visible global function definition for 'hcluster'
kill.pc: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'impute.knn'
prince.plot: no visible global function definition for 'heatmap.2'
prince.var.plot: no visible global function definition for 'impute.knn'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sybilSBML.Rcheck/00install.out' for details.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'parallel'
  All declared Imports should be used.
cleavogram : savecleavogram : savefic: warning in jpeg(file =
  filename): partial argument match of 'file' to 'filename'
fn.V: no visible global function definition for 'LowRankQP'
synth: no visible global function definition for 'LowRankQP'
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.3Mb
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TDA.Rcheck/00install.out' for details.
ConvDiffCoef: no visible global function definition for 'pascal'
DeconTrace: no visible global function definition for 'as.Zpg'
DeconTrace: no visible global function definition for 'butter'
MakeDPZ: no visible global function definition for 'bilinear'
MatchCoefDPZ: no visible global function definition for 'Zpg'
PZ2Coef: no visible global function definition for 'Poly'
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs      13.0Mb
    tessdata  30.9Mb
test_pkg : <anonymous>: no visible global function definition for
  '.traceback'
Dif.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Event.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'q.search'
Print.Summary: no visible global function definition for 'survfitr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
Namespace in Imports field not imported from: 'irlba'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/textTinyR.Rcheck/00install.out' for details.
determine_replications: no visible global function definition for
  'microbenchmark'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
boot_autocov: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'tsboot'
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dmvt'
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.8Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: eval(code, new_test_environment)
  3: eval(expr, envir, enclos)
  4: expect_is(trakt.user.watchlist(user = sample_user, type = "movies", extended = "min"), 
         "data.frame") at test_user.R:25
  5: expect_that(object, is_a(class), info, label)
  6: condition(object)
  7: paste0(class(x), collapse = ", ")
  8: trakt.user.watchlist(user = sample_user, type = "movies", extended = "min")
  9: convert_datetime(response)
  10: stop("Object type not supported")
  
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TreeBUGS.Rcheck/00install.out' for details.
mytree.asymmetric.age: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.age: no visible global function definition for
  'drop.fossil'
mytree.asymmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.taxa: no visible global function definition for
  'drop.fossil'
mytree.symmetric.age: no visible global function definition for
  'collapse.singles'
mytree.symmetric.age: no visible global function definition for
  'drop.fossil'
mytree.symmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.symmetric.taxa: no visible global function definition for
  'drop.fossil'
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'discrcoord'
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'gam'
sim.cont: no visible global function definition for 'lsoda'
TSget,character-TSfameLocalConnection : .local: no visible global
  function definition for 'zoo'
TSget,character-TSfameServerConnection : .local: no visible global
  function definition for 'zoo'
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
plotDominationGraph: no visible global function definition for
  'graph.adjacency'
plotDominationGraph: no visible global function definition for
  'layout.norm'
sampleCombinations: no visible global function definition for
  'qrng_alloc'
sampleCombinations: no visible global function definition for
  'qrng_get'
tunePareto: no visible global function definition for 'sfLibrary'
tunePareto : <anonymous>: no visible global function definition for
  'sfLibrary'
tunePareto: no visible global function definition for 'sfExport'
tunePareto: no visible global function definition for 'sfLapply'
tunePareto.NaiveBayes: no visible binding for global variable
  'NaiveBayes'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uaparserjs.Rcheck/00install.out' for details.
uniCoxCV: no visible global function definition for 'coxph'
Namespace in Imports field not imported from: 'mcmcplots'
  All declared Imports should be used.
Running examples in 'upmfit-Ex.R' failed
The error most likely occurred in:

> ### Name: upmrun
> ### Title: Bayesian Markov Chain Monte Carlo model building for
> ###   household-community tuberculosis transmission models
> ### Aliases: upmrun
> 
> ### ** Examples
> 
> upmrun(design.matrix=upmdata, n.iter=100, prior.alpha = c(-2.2, 1/sqrt(3)))
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 119-122 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uroot.Rcheck/00install.out' for details.
File 'UScensus2010/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage(paste("Package ", dscr$Package, ": ", dscr$Title,     "\n", "Version ", dscr$Version, " created on ", dscr$Date,     ".\n", sep = ""))
    packageStartupMessage(paste("Zack Almquist, University of California-Irvine\nne\n",     sep = ""))
    packageStartupMessage("For citation information, type citation(\"UScensus2010\").")
    packageStartupMessage("Type help(package=UScensus2010) to get started.")

See section 'Good practice' in '?.onAttach'.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
mcmc.estimate: no visible global function definition for '%dopar%'
mcmc.estimate: no visible global function definition for 'foreach'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/valr.Rcheck/00install.out' for details.
SVEC: no visible global function definition for 'Null'
causality: no visible global function definition for 'ginv'
stability: no visible global function definition for 'efp'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.3Mb
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
vioplot: warning in axis(1, at = at, label = label): partial argument
  match of 'label' to 'labels'
vioplot: warning in axis(2, at = at, label = label): partial argument
  match of 'label' to 'labels'
raster.proj: no visible global function definition for 'rasterFromXYZ'
.vdensecalc: no visible global function definition for 'contour3d'
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 65-67 (vtreatRareLevels.Rmd) 
Error: processing vignette 'vtreatRareLevels.Rmd' failed with diagnostics:
unused argument (left.open = TRUE)
Execution halted
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Namespaces in Imports field not imported from:
  'DT' 'ENMeval' 'RColorBrewer' 'devtools' 'dismo' 'dplyr' 'maptools'
  'raster' 'rgdal' 'rgeos' 'rmarkdown' 'shinyBS' 'shinyjs'
  'shinythemes' 'spThin' 'spocc'
  All declared Imports should be used.
color.factor: warning in rgb(red = t.rgb[1, ], green = t.rgb[2, ], blue
  = t.rgb[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
p.flow_comp: warning in line_sumrain(xdata = xdata, cum_sum =
  cumsum(data[crain, ])/10, theMax = rain.max, col = "grey"): partial
  argument match of 'cum_sum' to 'cum_sum_rain'
Errors in running code in vignettes:
when running code in 'vignette.Rnw'
  ...

> library(waterData)

> q05054000 <- importDVs("05054000", code = "00060", 
+     stat = "00003", sdate = "2000-01-01", edate = "2010-12-31")
Unknown IO errorfailed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

  When sourcing 'vignette.R':
Error: 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error : 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

Execution halted
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
Packages required but not available: 'subprocess' 'semver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

[1] "Welcome to the webvis pacakge."
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
Running examples in 'wiqid-Ex.R' failed
The error most likely occurred in:

> ### Name: dippers
> ### Title: Capture-recapture data for European dippers
> ### Aliases: dippers
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dippers)
> 
> DH <- dippers[1:7]  # Extract the detection histories
> survCJS(DH)  # the phi(.) p(.) model
Call: survCJS(DH = DH)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.5602 0.5105 0.6088
p1   0.9026 0.8305 0.9460

AIC: 670.8377 
> survCJS(DH, phi ~ .time)  # the phi(t) p(.) model
Call: survCJS(DH = DH, model = phi ~ .time)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6258 0.3965 0.8098
phi2 0.4542 0.3295 0.5849
phi3 0.4784 0.3669 0.5921
phi4 0.6244 0.5079 0.7281
phi5 0.6079 0.4970 0.7088
phi6 0.5833 0.4688 0.6895
p1   0.9021 0.8286 0.9461

AIC: 673.7301 
> 
> # Floods affected the 2nd and 3rd intervals
> df <- data.frame(flood = c(FALSE, TRUE, TRUE, FALSE, FALSE, FALSE))
> survCJS(DH, phi ~ flood, data=df)
Call: survCJS(DH = DH, model = phi ~ flood, data = df)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6071 0.5451 0.6658
phi2 0.4688 0.3858 0.5537
p1   0.8998 0.8262 0.9443

AIC: 666.1028 
> 
> # Including a grouping factor:
> survCJS(DH, phi ~ flood * group, data=df, group=dippers$sex)
Call: survCJS(DH = DH, model = phi ~ flood * group, data = df, group = dippers$sex)

Real values (duplicates omitted):
          est  lowCI  uppCI
F:phi1 0.6033 0.5163 0.6842
F:phi2 0.4568 0.3468 0.5712
M:phi1 0.6108 0.5246 0.6906
M:phi2 0.4833 0.3612 0.6073
F:p1   0.8999 0.8263 0.9444

AIC: 669.9911 
> 
> # Bayesian estimation:
> 
> Bdip <- BsurvCJS(DH, parallel=FALSE)
Error: The 'rjags' package and the JAGS program are needed to run this function.
Execution halted