installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.1Mb
    libs   1.2Mb
NB: this package is only installed for sub-architecture 'x64'
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  No variables decoded!
  persnr used as id!
  1. Failure: filter (@test-dplyr_methods.R#13) ----------------------------------
  dplyr::filter(testdata, persnr == 198505043334) inherits from `tbl_df/tbl/data.frame` not `incadata`.
  
  
  Using tempfile: D:\temp\RtmpyctwDN\ex_data1f060f4f2751.csv2
  [1] "ex_data1f060f4f2751.csv2"
  file size: 1103 kb
  testthat results ================================================================
  OK: 38 SKIPPED: 1 FAILED: 1
  1. Failure: filter (@test-dplyr_methods.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
File 'iotools/libs/i386/iotools.dll':
  Found non-API call to R: 'getConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API call to R: 'getConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/kerasR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: ensure_db (@test-db.R#12) ------------------------------------------
  ensure_db(db) produced warnings.
  
  
  2. Failure: ensure_queue (@test-queue.R#21) ------------------------------------
  q <- ensure_queue("foo", db = db) produced warnings.
  
  
  testthat results ================================================================
  OK: 506 SKIPPED: 0 FAILED: 2
  1. Failure: ensure_db (@test-db.R#12) 
  2. Failure: ensure_queue (@test-queue.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
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:

======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'macleish-Ex.R' failed
The error most likely occurred in:

> ### Name: etl_extract.etl_macleish
> ### Title: Extract weather data
> ### Aliases: etl_extract.etl_macleish etl_load.etl_macleish
> ###   etl_transform.etl_macleish
> 
> ### ** Examples
> 
> 
> macleish <- etl("macleish")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\RtmpCKWkNy\file9cf429922473.sqlite3
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 251-256 (investigateMatingScene.Rmd) 
Error: processing vignette 'investigateMatingScene.Rmd' failed with diagnostics:
incorrect number of names
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/mcPAFit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/medSTC.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.6Mb
    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/3.4/mmap.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(mnis)
  > 
  > test_check("mnis")
  1. Failure: mnis_joined_between returns expected format (@tests_joined_between.R#11) 
  nrow(xmjb) == 9 isn't true.
  
  
  testthat results ================================================================
  OK: 13 SKIPPED: 3 FAILED: 1
  1. Failure: mnis_joined_between returns expected format (@tests_joined_between.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'Test.R' [8s]
Running the tests in 'tests/Test.R' failed.
Last 13 lines of output:
  +   Dates <- GetDates(SubsetExample$lat, SubsetExample$long, Product)[1:2]
  + 
  +   GetSubset(Lat = SubsetExample$lat, Long = SubsetExample$long, Product = Product, Band = Band,
  +             StartDate = Dates[1], EndDate = Dates[1], KmAboveBelow = 0, KmLeftRight = 0)
  + 
  +   MODISSubsets(LoadDat = SubsetExample, Product = "MCD12Q1", Bands = c("Land_Cover_Type_1"),
  +                Size = c(1,1), StartDate = TRUE)
  + 
  +   MODISSummaries(LoadDat = SubsetExample, Product = "MCD12Q1", Band = "Land_Cover_Type_1",
  +                  ValidRange = c(0,254), NoDataFill = 255, ScaleFactor = 1, StartDate = TRUE)
  + }
  Error in Product == GetProducts() : 
    comparison of these types is not implemented
  Calls: GetBands
  Execution halted
Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 172 SKIPPED: 1 FAILED: 11
  1. Error: we can connect (@test_03_dplyr.R#14) 
  2. Error: dplyr copy_to() (@test_03_dplyr.R#24) 
  3. Error: dplyr tbl( sql() ) (@test_03_dplyr.R#35) 
  4. Error: dplyr select() (@test_03_dplyr.R#43) 
  5. Error: dplyr filter() (@test_03_dplyr.R#51) 
  6. Error: dplyr arrange() (@test_03_dplyr.R#59) 
  7. Error: dplyr mutate() (@test_03_dplyr.R#67) 
  8. Error: dplyr summarise() (@test_03_dplyr.R#75) 
  9. Error: dplyr multiple objects (@test_03_dplyr.R#84) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [58s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 156 SKIPPED: 1 FAILED: 11
  1. Error: we can connect (@test_03_dplyr.R#14) 
  2. Error: dplyr copy_to() (@test_03_dplyr.R#24) 
  3. Error: dplyr tbl( sql() ) (@test_03_dplyr.R#35) 
  4. Error: dplyr select() (@test_03_dplyr.R#43) 
  5. Error: dplyr filter() (@test_03_dplyr.R#51) 
  6. Error: dplyr arrange() (@test_03_dplyr.R#59) 
  7. Error: dplyr mutate() (@test_03_dplyr.R#67) 
  8. Error: dplyr summarise() (@test_03_dplyr.R#75) 
  9. Error: dplyr multiple objects (@test_03_dplyr.R#84) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [88s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  1. Failure: covex-E (@test_covex.R#54) -----------------------------------------
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.989 - 1.02 == -0.0298
  0.9
  
  testthat results ================================================================
  OK: 172 SKIPPED: 0 FAILED: 1
  1. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [94s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  testthat results ================================================================
  OK: 178 SKIPPED: 1 FAILED: 2
  1. Failure: PlotContribution() works properly with PhyloExpressionSet input... (@test-PlotContribution.R#11) 
  2. Failure: PlotContribution() works properly with DivergenceExpressionSet input... (@test-PlotContribution.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [98s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  testthat results ================================================================
  OK: 178 SKIPPED: 1 FAILED: 2
  1. Failure: PlotContribution() works properly with PhyloExpressionSet input... (@test-PlotContribution.R#11) 
  2. Failure: PlotContribution() works properly with DivergenceExpressionSet input... (@test-PlotContribution.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 183-186 (NEArender_vignette.Rmd) 
Error: processing vignette 'NEArender_vignette.Rmd' failed with diagnostics:
undefined columns selected
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-3.4.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.0/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
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:
> ### Title: Weight polls
> ### Aliases: weight_polls
> 
> ### ** Examples
> 
> polldates <- tail(unique(polls$MidDate), 20)
> weight_polls(polldates, method = "curia")
 [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
[20] NaN
> weight_polls(polldates, method = "pundit")
 [1] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
 [8] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
[15] 0.0000000 0.0000000 0.0000000 0.2620402 0.3376533 0.4003065
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  9.83 0.28 10.5 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 ?) ========
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.3Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs     5.8Mb
    models   4.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/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
Warning in gzfile(file, "rb") :
  cannot open compressed file 'd:/RCompile/CRANpkg/lib/3.4/nlme/Meta/Rd.rds', probable reason 'Permission denied'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> lapply -> FUN -> readRDS -> gzfile
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  8: src_sqlite(dbFile(obj), create = F)
  9: check_dbplyr()
  10: check_pkg("dbplyr", "communicate with database backends", install = FALSE)
  11: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with `install.packages(\"{name}\")`")
  12: .abort(text)
  
  testthat results ================================================================
  OK: 109 SKIPPED: 0 FAILED: 4
  1. Error: Database population (@test-poplite.R#452) 
  2. Error: Querying with Database objects (@test-poplite.R#567) 
  3. Error: sample tracking example but with direct keys between dna and samples (@test-poplite.R#801) 
  4. Error: oligoMask queries that break poplite (@test-poplite.R#852) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'run-all.R' [5s]
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  1. Failure: Example 37: SPSS Support with .sav Extension (@test-readers.R#734) -
  spss.reader(data.file, filename, variable.name) showed 0 warnings
  
  
  2. Failure: Example 38: SPSS Support with .sav Extension / Alternative Generation (@test-readers.R#756) 
  spss.reader(data.file, filename, variable.name) showed 0 warnings
  
  
  testthat results ================================================================
  OK: 428 SKIPPED: 0 FAILED: 2
  1. Failure: Example 37: SPSS Support with .sav Extension (@test-readers.R#734) 
  2. Failure: Example 38: SPSS Support with .sav Extension / Alternative Generation (@test-readers.R#756) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 110-111 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    include   4.8Mb
    libs      1.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs      1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/RcppOctave.Rcheck/00install.out' for details.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      21.9Mb
    libs      3.9Mb
Running 'getFuns.R' [2s]
  Comparing 'getFuns.Rout' to 'getFuns.Rout.save' ... OK
  Running 'ijroi-format.R' [4s]
  Comparing 'ijroi-format.Rout' to 'ijroi-format.Rout.save' ... OK
  Running 'reconstruct.R' [4s]
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
    Backwards path
      i = 377 ; sf/Sf = 0.5 ; sf = 368.306937214058
        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 $i
  Calls: retistruct.reconstruct ... ReconstructedOutline -> TriangulatedOutline -> <Anonymous>
  Execution halted
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  1. Failure: default prey (@test-globi.R#6) -------------------------------------
  length(predatorPrey$source_taxon_name) > 10 isn't true.
  
  
  testthat results ================================================================
  OK: 35 SKIPPED: 0 FAILED: 1
  1. Failure: default prey (@test-globi.R#6) 
  
  Error: testthat unit tests failed
  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-34~1.0/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/3.4/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.4/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'Rf_EncodeInteger', 'Rf_EncodeLogical',
    'Rf_EncodeReal', 'Rf_formatInteger', 'Rf_formatLogical',
    'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'Rf_EncodeInteger', 'Rf_EncodeLogical',
    'Rf_EncodeReal', 'Rf_formatInteger', 'Rf_formatLogical',
    'Rf_formatReal'

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:
  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/3.4/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
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.4/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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    rmd   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: src_presto(RPresto::Presto(), schema = "test", catalog = "catalog", host = "http://localhost", 
         port = 8000, user = Sys.getenv("USER"), session.timezone = test.timezone(), parameters = list())
  3: dplyr::src_sql
  4: getExportedValue(pkg, name)
  5: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 219 SKIPPED: 24 FAILED: 3
  1. Error: db_explain works with mock (@test-db_explain.R#25) 
  2. Error: db_query_fields works with mock (@test-db_query_fields.R#42) 
  3. Error: as() works (@test-src_translate_env.R#14) 
  
  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/3.4/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/3.4/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/3.4/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.
Warning in gzfile(file, "rb") :
  cannot open compressed file 'd:/RCompile/CRANpkg/lib/3.4/lattice/Meta/Rd.rds', probable reason 'Permission denied'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> lapply -> FUN -> readRDS -> gzfile
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.5Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Ryacas.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  Phasing...
  
  1
  
  Phasing...
  
  1
  testthat results ================================================================
  OK: 57 SKIPPED: 0 FAILED: 1
  1. Error: can phase ase where one cell has all zero counts (@test-phasing.R#463) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/selectr.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    www   6.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    semantic   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    1.5Mb
    etc    1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/specmine.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.0/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Running 'testthat.R' [81s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  1. Failure: output buffer is flushed (@test-readwrite.R#19) --------------------
  `output` has length 207, not length 1000.
  
  
  testthat results ================================================================
  OK: 52 SKIPPED: 4 FAILED: 1
  1. Failure: output buffer is flushed (@test-readwrite.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  	siaf parameter 3: TRUE 
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  argument "new" is missing, with no default
  1: update(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1)) at testthat/test-tiafs.R:45
  2: update.list(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1))
  
  Error in update.list(model, siaf = NULL, tiaf = NULL, epidemic = ~1, epilink = "log") : 
    argument "new" is missing, with no default
  Calls: test_check ... source_file -> eval -> eval -> update -> update.list
  testthat results ================================================================
  OK: 233 SKIPPED: 1 FAILED: 1
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  	siaf parameter 3: TRUE 
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  argument "new" is missing, with no default
  1: update(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1)) at testthat/test-tiafs.R:45
  2: update.list(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1))
  
  Error in update.list(model, siaf = NULL, tiaf = NULL, epidemic = ~1, epilink = "log") : 
    argument "new" is missing, with no default
  Calls: test_check ... source_file -> eval -> eval -> update -> update.list
  testthat results ================================================================
  OK: 233 SKIPPED: 1 FAILED: 1
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/switchr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/sybilSBML.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  testthat results ================================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: 'cross' works (@test-anchor.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
Warning in gzfile(file, "rb") :
  cannot open compressed file 'd:/RCompile/CRANpkg/lib/3.4/rpart/Meta/Rd.rds', probable reason 'Permission denied'
Error in gzfile(file, "rb") : cannot open the connection
Calls: <Anonymous> -> lapply -> FUN -> readRDS -> gzfile
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘HH’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  rm_accent(umlaut) not equal to `nudeUmlaut`.
  1/1 mismatches
  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
Packages suggested but not available for checking: ‘INLA’ ‘Rgraphviz’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    3.3Mb
Error in re-building vignettes:
  ...
Loading required package: Cairo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'abn_v1.0.2.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.33 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘DESeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘BiocStyle’
Packages required but not available: ‘aroma.affymetrix’ ‘aroma.core’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘actuar’

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

    cm

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'coverage.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10   \usepackage
                  [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rgeos’
Errors in running code in vignettes:
when running code in ‘adehabitatHR.Rnw’
  ...
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").



  When sourcing ‘adehabitatHR.R’:
Error: isTRUE(gpclibPermitStatus()) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Loading required package: adehabitatMA
Loading required package: adehabitatLT
Loading required package: CircStats
Loading required package: MASS
Loading required package: boot
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()

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").



Error: processing vignette 'adehabitatHR.Rnw' failed with diagnostics:
 chunk 173 
Error : isTRUE(gpclibPermitStatus()) is not 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.
Quitting from lines 174-188 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
rgeos required
Execution halted
Package suggested but not available for checking: ‘copula’
Running examples in ‘aftgee-Ex.R’ failed
The error most likely occurred in:

> ### Name: aftgee
> ### Title: Accelerated Failure Time with Generalize Estimating Equation
> ### Aliases: aftgee summary.aftgee
> ### Keywords: aftgee
> 
> ### ** Examples
> 
> library(survival)
> library(copula)
Error in library(copula) : there is no package called ‘copula’
Execution halted
Package required but not available: ‘miscF’

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

> ### Name: plot.AMMI
> ### Title: PLOT AMMI
> ### Aliases: plot.AMMI
> ### Keywords: aplot
> 
> ### ** Examples
> 
> library(agricolae)
> data(plrv)
> model<- with(plrv,AMMI(Locality, Genotype, Rep, Yield))
> # biplot PC2 vs PC1
> plot(model)
> ## plot PC1 vs Yield
> plot(model,0,1,gcol="blue",ecol="green")
> ## triplot PC 2,3,4
> plot(model,first=2,second=3,third=4, type=2,number=TRUE)
> # biplot with influence genotype in pc3 vs pc2
> plot(model,first=2,second=3, type=3,number=TRUE,icol="green")

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


Error in spdep::soi.graph(tri, coords) : rgeos required
Calls: plot ... plot.AMMI -> <Anonymous> -> inherits -> <Anonymous>
Execution halted
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: gomez.nitrogen
> ### Title: Soil nitrogen at three times for eight fertilizer treatments
> ### Aliases: gomez.nitrogen
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(gomez.nitrogen)
> dat <- gomez.nitrogen
> 
> # Note the depletion of nitrogen over time (stage)
> require(HH)
Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘HH’
> interaction2wt(nitro ~ rep/trt + trt*stage, data=dat,
+                main="gomez.nitrogen")
Error in interaction2wt(nitro ~ rep/trt + trt * stage, data = dat, main = "gomez.nitrogen") : 
  could not find function "interaction2wt"
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 79-86 (agridat_examples.Rnw) 
Error: processing vignette 'agridat_examples.Rnw' failed with diagnostics:
there is no package called 'HH'
Execution halted
Error in re-building vignettes:
  ...
Warning in adapt(pT = pT, iD = iD, SF = 1, phi = 0, cp = 0.9, theta = 4,  :
  Power may be lower than planned.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Package suggested but not available for checking: ‘R2jags’
Package required but not available: ‘protiq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algebraichaplo.tex' failed.
LaTeX errors:
! LaTeX Error: File `ngerman.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [square,comma, numbers,sort&compress]{natbib}   % numbers wor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'alleHap.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 \usepackage
                [a4paper]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Error in re-building vignettes:
  ...

Device  2  : alpha =  0.03 
Device  3  : alpha =  0.35 
Device  4  : alpha =  0.5 
Device  9  : alpha =  0.3 
Device  10  : alpha =  0.5 
Device  12  : alpha =  0.3 
Device  13  : alpha =  0.5 
Device  14  : alpha =  0.3 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'alphashape3d.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {upgreek}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.7.4, built: 2015-12-05)
## Copyright (C) 2005-2017 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 

Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
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
Package required but not available: ‘biogram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/psnfss/times.sty)

! LaTeX Error: File `xy.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make: *** [anchors.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/anchors.Rcheck/vign_test/anchors") : 
  running 'make' failed
Execution halted
Package required but not available: ‘gmp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ANOM.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Anthropometry.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.1198 \ifthenelse
                  {\boolean{algocf@slide}}{\RequirePackage{color}}{}%^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘Rgraphviz’

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

> ### Name: ch22Promoters
> ### Title: ch22Promoters Data Set
> ### Aliases: ch22Promoters
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## load Biostrings package
> library(Biostrings)
Error in library(Biostrings) : there is no package called ‘Biostrings’
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 31-44 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
there is no package called 'kebabs'
Execution halted
Packages required but not available:
  ‘genefilter’ ‘edgeR’ ‘DESeq’ ‘aroma.light’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apsimr-basics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: gWidgets
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apt.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [pdftex]{graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=15: zs > maxKappa
Warning in axis(1, at = a, ...) : "axes" is not a graphical parameter
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'archetypes.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘devtools’

Package which this enhances but not available for checking: ‘archivist.github’
Package unavailable to check Rd xrefs: ‘archivist.github’
Running examples in ‘archivist-Ex.R’ failed
The error most likely occurred in:

> ### Name: ahistory
> ### Title: Show Artifact's History
> ### Aliases: ahistory
> 
> ### ** Examples
> 
> 
> createLocalRepo("ahistory_check", default = TRUE)
Directory ahistory_check did not exist. Forced to create a new directory.> library(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

> iris %a%
+ filter(Sepal.Length < 6) %a%
+  lm(Petal.Length~Species, data=.) %a%
+  summary() -> artifact
Error in saveToRepo(env[[nm]], archiveData = FALSE, artifactName = lhs_name) : 
  devtools package required for archiveSessionInfo parameter
Calls: %a% ... eval -> %a% -> eval -> eval -> %a% -> paste0 -> saveToRepo
Execution halted
Running ‘testthat.R’ [6s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  devtools package required for archiveSessionInfo parameter
  1: saveToRepo(d1, userTags = c(":", "", "\n", "\t", "\\", "\\\\"), repoDir = exampleRepoDir) at testthat/test_splitTags.R:13
  2: stop("devtools package required for archiveSessionInfo parameter")
  
  Directory repository did not exist. Forced to create a new directory.Directory repository did not exist. Forced to create a new directory.Directory repository did not exist. Forced to create a new directory.Directory test1234 did not exist. Forced to create a new directory.  adding: test1234/backpack.db (deflated 87%)
    adding: test1234/gallery/ff575c261c949d073b2895b05d1097c3.rda (deflated 71%)
    adding: test1234/gallery/ff575c261c949d073b2895b05d1097c3.txt (deflated 70%)
  testthat results ================================================================
  OK: 36 SKIPPED: 0 FAILED: 3
  1. Error: test aoptions (@test_aoptions.R#8) 
  2. Error: saveToRepo funcion works with regular parameters (@test_jss_artilce.R#56) 
  3. Error: split*Repo does not react on errors as it should and works as it's made to (@test_splitTags.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
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 required but not available: ‘aroma.core’

Packages suggested but not available for checking:
  ‘affxparser’ ‘affyPLM’ ‘aroma.light’ ‘gcrma’ ‘oligo’ ‘oligoClasses’
  ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: ‘aroma.core’ ‘PSCBS’

Packages suggested but not available for checking: ‘aroma.light’ ‘GLAD’

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

Packages suggested but not available for checking:
  ‘EBImage’ ‘aroma.light’ ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Cairo’
Error in re-building vignettes:
  ...
  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

Loading required package: estimability
Loading required package: car

Attaching package: 'car'

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

    recode

Quitting from lines 95-107 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘arules’

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

    abbreviate, write

Warning in apriori(Adult, parameter = list(support = 0.01, confidence = 0.6)) :
  Mining stopped (maxlen reached). Only patterns up to a length of 10 returned!
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'arules.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘graph’ ‘Rgraphviz’
Error in re-building vignettes:
  ...
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 texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'asmapvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.34 \usepackage
                [titles]{tocloft}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ASPBay
Loading required package: hexbin
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ASPBay.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘devtools’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(devtools)
  Error in library(devtools) : there is no package called 'devtools'
  Execution halted
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘partitions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Package required but not available: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘partitions’
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.
Error in re-building vignettes:
  ...

Attaching package: ‘Brobdingnag’

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

    max, min, prod, range, sum

Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘partitions’
Warning in good(icons) :
  Good's method is for matrices with no NA entries.  Answer supplied is indicative only (but should provide an upper bound)
Error: processing vignette 'fishervig.Rnw' failed with diagnostics:
at fishervig.Rnw:753, could not find function "S"
Execution halted
Package required but not available: ‘edgeR’

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

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

Package suggested but not available for checking: ‘sybilSBML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: BACCO
Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Loading required package: approximator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'both_papers.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Error in re-building vignettes:
  ...

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

    filter, lag

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

    intersect, setdiff, setequal, union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'backtestGraphics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' () global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala (>= 2.10) is not distributed with the rscala package.  Individuals can
install Scala using "rscala::scalaInstall()" which places Scala in "~/.rscala"
in the user's home directory.  System administrators should install Scala
globally as described here: http://www.scala-lang.org/download/install.html.
In short, simply download the archive, unpack it, and add the "scala" script to
the path.  Note that Scala itself requires Java.  The rscala package tries
various techniques to find a suitable Scala installation, including searching
the path.  Details on the search are available using
"rscala::scalaInfo(verbose=TRUE)".

Error in get(n, envir = env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> ... withCallingHandlers -> do.call -> <Anonymous> -> get
Execution halted
Package suggested but not available for checking: ‘rjags’
Package unavailable to check Rd xrefs: ‘rjags’
Packages required but not available: ‘sva’ ‘affyPLM’

Package suggested but not available for checking: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bartMachine.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \graphicspath
                 {{Figures/}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘basicspace.Rnw’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

Execution halted
Package unavailable to check Rd xrefs: ‘Rmpi’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bayesCL.Rcheck/00install.out’ for details.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.4Mb
Packages unavailable to check Rd xrefs: ‘PottsUtils’, ‘mritc’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
 **********   MAMS Version 1.01********** 

Type MAMSNews() to see new features/changes/bug fixes.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BayesFreq.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages required but not available: ‘Rgraphviz’ ‘gRbase’ ‘qtlnet’ ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rstanarm’ ‘shinystan’
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bayesplot)
  This is bayesplot version 1.2.0
  > 
  > Sys.unsetenv("R_TESTS")
  > if (!grepl("^sparc",  R.version$platform))
  +   test_check("bayesplot")
  Error in library(rstanarm) : there is no package called 'rstanarm'
  Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
  testthat results ================================================================
  OK: 173 SKIPPED: 0 FAILED: 0
  Execution halted
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  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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.
Error in re-building vignettes:
  ...
Loading required package: splines
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbefkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbemkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(2.24718525433143,  :
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(0.219940849413555,  :
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(2.76406402172104,  :
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(0.191138285903703,  :
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(2.76406402172104,  :
  NaNs produced
Warning in dbinom(x = c(0, 2, 1, 3, 4, 5, 0, 0, 0, 0, 1, 0, 0, 0, 0), prob = c(0.191138285903703,  :
  NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mle2.tex' failed.
BibTeX errors:
The top-level auxiliary file: mle2.aux
I couldn't open style file chicago.bst
---line 19 of file mle2.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file mle2.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘fabia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘R2jags’ ‘INLA’
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)
Installing package into ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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
Error in re-building vignettes:
  ...
Loading required package: plyr
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcpa.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘BRugs’ ‘rjags’
Package required but not available: ‘beadarray’

Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
plot.asr: no visible global function definition for ‘plot’
plot.casr: no visible global function definition for ‘plot’
plot.del: no visible global function definition for ‘plot’
plot.q: no visible global function definition for ‘plot’
plot.sr: no visible global function definition for ‘plot’
plot.trace1: no visible global function definition for ‘plot’
plot.trace2: no visible global function definition for ‘plot’
plot.trace3: no visible global function definition for ‘plot’
plot.trace4: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb
Package suggested but not available for checking: ‘RcppZiggurat’
Package suggested but not available for checking: ‘Rgraphviz’
Package unavailable to check Rd xrefs: ‘graph’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
For more information on the usage of the BEQI2 tool, type: vignette("BEQI2")
Number of duplicated records: 1
These will be removed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BEQI2.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.74 \allsectionsfont
                     {\sffamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error in re-building vignettes:
  ...
Loading required package: HDInterval
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BEST.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [usenames,dvipsnames,svgnames]{xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘rcdd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BGLR-extdoc.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BHMSMAfMRIvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {latexsym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 123.3Mb
  sub-directories of 1Mb or more:
    include  123.2Mb
Package required but not available: ‘RPostgreSQL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  5.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.0Mb
Packages in Depends field not imported from:
  ‘Matrix’ ‘glmnet’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lasso.stars: no visible global function definition for ‘glmnet’
plot.stars: no visible global function definition for ‘par’
plot.stars: no visible global function definition for ‘plot’
plot.stars: no visible global function definition for ‘lines’
Undefined global functions or variables:
  glmnet lines par plot
Consider adding
  importFrom("graphics", "lines", "par", "plot")
to your NAMESPACE file.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
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’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Overview.tex' failed.
LaTeX errors:
! LaTeX Error: File `accents.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.0Mb
Error in re-building vignettes:
  ...
Loading required package: diptest
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'biogas_quick_start.tex' failed.
LaTeX errors:
! LaTeX Error: File `siunitx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                [version=3]{mhchem} %chemical formulas^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘partitions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [7s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Receiving objects:  16% (1/6),    0 kb
  Receiving objects:  33% (2/6),    0 kb
  Receiving objects:  50% (3/6),    0 kb
  Receiving objects:  66% (4/6),    0 kb
  Receiving objects:  83% (5/6),    0 kb
  Receiving objects: 100% (6/6),    0 kb, done.
  testthat results ================================================================
  OK: 48 SKIPPED: 0 FAILED: 4
  1. Failure: is.biosoftwares.db.active (@test_active.R#10) 
  2. Failure: set.makedir (@test_install_uilts.R#60) 
  3. Failure: set.makedir (@test_install_uilts.R#63) 
  4. Failure: set.makedir (@test_install_uilts.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘biomaRt’ ‘Biostrings’

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

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

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

Packages suggested but not available for checking: ‘GO.db’ ‘org.Hs.eg.db’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Error in re-building vignettes:
  ...

    LdFlags

blockcluster version 4.2.3 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'blockcluster_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BMAmevt.tex' failed.
LaTeX errors:
! LaTeX Error: File `cases.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bms.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \setpapersize
                 {A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘graph’ ‘Rgraphviz’ ‘gRain’
Packages required but not available: ‘gRbase’ ‘gRain’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bnstruct.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `child_crosses_1000-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `alarm_crosses_1000-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `hepar2_crosses_1000-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `andes_crosses-eps-converted-to.pdf' not found
.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘sangerseqR’
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

    dexp, dgamma, dweibull, pexp, pgamma, pweibull, qexp, qgamma,
    qweibull, rexp, rgamma, rweibull

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

    precip

Loading required package: BoolNet
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BoolFilter.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BoolNet_package_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 247.6Mb
  sub-directories of 1Mb or more:
    include    2.7Mb
    lib      244.6Mb
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
Package suggested but not available for checking: ‘dplR’
Package unavailable to check Rd xrefs: ‘dplR’
Packages suggested but not available for checking: ‘BiocStyle’ ‘phyloseq’
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 15-16 (bossa-analysis.Rmd) 
Error: processing vignette 'bossa-analysis.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: scatterplot3d
Loading required package: rgl
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'latex_bpca.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {colortbl}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘gridGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Running examples in ‘breathteststan-Ex.R’ failed
The error most likely occurred in:

> ### Name: stan_fit
> ### Title: Bayesian Stan fit to 13C Breath Data
> ### Aliases: stan_fit
> 
> ### ** Examples
> 
> library(breathtestcore)
> suppressPackageStartupMessages(library(dplyr))
> d = simulate_breathtest_data(n_records = 3) # default 3 records
> data = cleanup_data(d$data)
> # Use more than 100 iterations and 4 chains for serious fits
> # For execution on a local, multicore CPU with excess RAM we recommend
> # calling \code{rstan_options(auto_write = TRUE)}.
> fit = stan_fit(data, chains = 1, iter = 100)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 150, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit.R#24) 
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit.R:24
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = c("m"))$m), beta = as.vector(rstan::extract(fit, permuted = TRUE, 
         pars = c("beta"))$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = c("k"))$k))
  3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  testthat results ================================================================
  OK: 3 SKIPPED: 4 FAILED: 1
  1. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit.R#24) 
  
  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 51-116 (bridgesampling_example.Rmd) 
Error: processing vignette 'bridgesampling_example.Rmd' failed with diagnostics:
there is no package called 'R2jags'
Execution halted
Error in re-building vignettes:
  ...
Creating a new generic function for ‘max’ in the global environment
Creating a new generic function for ‘min’ in the global environment
Creating a new generic function for ‘range’ in the global environment
Creating a new generic function for ‘prod’ in the global environment
Creating a new generic function for ‘sum’ in the global environment
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'brob.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rstanarm’ ‘brms’
Packages unavailable to check Rd xrefs: ‘brms’, ‘rstanarm’
Running ‘test-all.R’ [15s/19s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  Loading required namespace: gam
  Error in library(rstanarm) : there is no package called 'rstanarm'
  Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
  testthat results ================================================================
  OK: 451 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Package suggested but not available for checking: ‘gsl’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cairoDevice.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Cairo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CalibrationGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘ncdf4’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-6, (SVN revision 651)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.2-4 
Warning in engine$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
Packages suggested but not available for checking:
  ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Error in re-building vignettes:
  ...
Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
Loading required package: pheatmap
Loading required package: scatterplot3d
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Canopy_vignettes.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \setmargrb
              {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Removing 14 individuals due to missing phenotypes.


2 marker(s) rejected due to linear non-independence.
 For more information see markers.removed.for.non.independence.txt
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cape.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘DESeq2’ ‘biomaRt’

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

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

> ### Name: cartogram
> ### Title: Calculate cartogram boundaries
> ### Aliases: cartogram
> 
> ### ** Examples
> 
> 
> library(maptools)
Loading required package: sp
Checking rgeos availability: TRUE
> library(cartogram)
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Anx1.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \RequirePackage
                    {fancyvrb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘sva’ ‘leapp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Using_causaldrf.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
Running 'texi2dvi' on 'causaleffect.ltx' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {subcaption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'causalsens.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: parallel
Loading required package: pcaPP
Loading required package: robustbase
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ccaPP-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.126 \usepackage
                 {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘graph’
Package required but not available: ‘VineCopula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Error in re-building vignettes:
  ...
  no non-missing arguments to min; returning Inf
Warning in min(x, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in min(x, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in min(x, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in min(x, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cem.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/
Loading required package: Formula
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'censReg.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘GLAD’
Package suggested but not available for checking: ‘Rmpi’
Package required but not available: ‘Bessel’

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.
Error: processing vignette 'checkpoint.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CheddarQuickstart.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘speaq’
Running examples in ‘ChemoSpec-Ex.R’ failed
The error most likely occurred in:

> ### Name: clupaSpectra
> ### Title: Hierarchical Cluster-Based Peak Alignment on a Spectra Object
> ### Aliases: clupaSpectra
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> data(alignMUD)
> 
> plotSpectra(alignMUD, which = 1:20, lab.pos = 4.5, offset = 0.1,
+   yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
+   main = "Misaligned NMR Spectra (alignMUD)")
> 
> aMUD <- clupaSpectra(alignMUD)
Error in clupaSpectra(alignMUD) : 
  You need to install package speaq to use this function
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChemoSpec.tex' failed.
LaTeX errors:
! LaTeX Error: File `ccaption.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \captionnamefont
                     {\bfseries\large}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘multtest’ ‘gurobi’
Running examples in ‘cherry-Ex.R’ failed
The error most likely occurred in:

> ### Name: Select with shortcuts
> ### Title: Confidence limits for the number of true hypotheses, with
> ###   shortcuts.
> ### Aliases: pickFisher pickSimes pickMeinshausen curveFisher curveSimes
> ###   curveMeinshausen
> ### Keywords: htest
> 
> ### ** Examples
> 
>   # Fisher's method
>   data(NAEP)
>   pickFisher(NAEP, c("NH", "NC", "IA"))
3 hypotheses selected. At confidence level 0.95:
False null-hypotheses >= 2; True null-hypotheses <= 1.
>   pickFisher(NAEP, 1:7)
7 hypotheses selected. At confidence level 0.95:
False null-hypotheses >= 6; True null-hypotheses <= 1.
>   curveFisher(NAEP)
>   curveFisher(NAEP, order=7:1)
> 
> 
>   # Simes method
>   hom <- hommelFast(NAEP)
>   pickSimes(hom, c("NH", "NC", "IA"))
3 hypotheses selected. At confidence level 0.95:
False null-hypotheses >= 2; True null-hypotheses <= 1.
>   pickSimes(hom, 1:7)
7 hypotheses selected. At confidence level 0.95:
False null-hypotheses >= 6; True null-hypotheses <= 1.
>   curveSimes(hom)
>   curveSimes(hom, select=1:7)
>   
>   # Meinshausen's method
>   library(multtest)
Error in library(multtest) : there is no package called ‘multtest’
Execution halted
Error in re-building vignettes:
  ...
16.42065372042111612.6709691596414
The distribution of the curve data indicates noise. The data should be visually 
inspected with a plot (see examples of diffQ).
Approximate and calculated Tm varri. This is an expected behaviour 

			 but the calculation should be confirmed with a plot (see examples of diffQ).
6.533866827983022021.9375753397427
The Tm calculation (fit, adj. R squared ~ 0.849, NRMSE ~ 0.088) is not optimal presumably
due to noisy data. Check raw melting curve (see examples of diffQ).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chipPCR.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
equilibrate: using boltzmann method
subcrt: 3 species at 598.15 K and 120.46 bar (wet)
info.character: found H2O(liq), also available in cr1, cr2, cr3, cr5, cr6, cr7, cr8, cr9, gas, aq
subcrt: 4 species at 598.15 K and 120.46 bar (wet)
subcrt: 2 species at 598.15 K and 120.46 bar
info.character: found H2O(liq), also available in cr1, cr2, cr3, cr5, cr6, cr7, cr8, cr9, gas, aq
subcrt: 4 species at 598.15 K and 120.46 bar (wet)
info.character: found H2O(liq), also available in cr1, cr2, cr3, cr5, cr6, cr7, cr8, cr9, gas, aq
subcrt: 4 species at 598.15 K and 120.46 bar (wet)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'equilibrium.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
median:
  function(x, na.rm, ...)
median.circular:
  function(x, na.rm)

median:
  function(x, na.rm, ...)
median.circular:
  function(x, na.rm)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
R Package to solve regression problems while imposing
	 an L1 constraint on the parameters. Based on S-plus Release 2.1
Copyright (C) 1998, 1999
Justin Lokhorst   <jlokhors@stats.adelaide.edu.au>
Berwin A. Turlach <bturlach@stats.adelaide.edu.au>
Bill Venables     <wvenable@stats.adelaide.edu.au>

Copyright (C) 2002
Martin Maechler <maechler@stat.math.ethz.ch>
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clere.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: attributes are not identical across measure variables; they will be dropped
Warning: attributes are not identical across measure variables; they will be dropped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘ncdf4’ ‘RODBC’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cloudUtil.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/clpAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Iteration: 4 Rho: 1.04103 P: 6.54679e-05
Iteration: 5 Rho: 10.4103 P: 7.05791e-07
Iteration: 6 Rho: 104.103 P: 7.10254e-09
Iteration: 7 Rho: 1041.03 P: 7.07779e-11
Iteration: 8 Rho: 10410.3 P: 7.09584e-13
Iteration: 9 Rho: 104103 P: 7.06903e-15
Iteration: 10 Rho: 1.04103e+06 P: 7.08373e-17
Minimum: 0.000329205
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clue.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘marray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: seriation
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignetteClustered.tex' failed.
LaTeX errors:
! LaTeX Error: File `biblatex.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \bibliography
                 {ClusteredMutationsVignettes.bib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘rggobi’ ‘RGtk2’

Package suggested but not available for checking: ‘kohonen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘moe430a.db’
Package unavailable to check Rd xrefs: ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    sd, sigma

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

    is.primitive

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'complicator.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'CGHbase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Packages suggested but not available for checking:
  ‘CGHcall’ ‘CGHregions’ ‘CNVtools’ ‘Biobase’ ‘CGHbase’
Package unavailable to check Rd xrefs: ‘CGHcall’
Errors in running code in vignettes:
when running code in ‘CNVassoc_vignette.Rnw’
  ...
> data(NeveCalled)

> probs <- getProbs(NeveCalled)
Loading required package: CGHbase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘CGHbase’

  When sourcing ‘CNVassoc_vignette.R’:
Error: unable to find required package ‘CGHbase’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: CNVassocData
Loading required package: mixdist
Loading required package: mclust
Package 'mclust' version 5.2.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: survival
Loading required package: CGHbase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘CGHbase’

Error: processing vignette 'CNVassoc_vignette.Rnw' failed with diagnostics:
 chunk 40 
Error in .requirePackage(package) : 
  unable to find required package ‘CGHbase’
Execution halted
Package suggested but not available for checking: ‘ridge’
Package suggested but not available for checking: ‘limma’
Running examples in ‘CodeDepends-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeCallGraph
> ### Title: Create a graph representing which functions call other functions
> ### Aliases: makeCallGraph makeCallGraph,list-method
> ###   makeCallGraph,character-method
> ### Keywords: hplot programming
> 
> ### ** Examples
> 
> 
>   gg = makeCallGraph("package:CodeDepends")
Loading required package: graph
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘graph’
Error in getClass(Class, where = topenv(parent.frame())) : 
  “graphNEL” is not a defined class
Calls: makeCallGraph ... makeCallGraph -> makeCallGraph -> .local -> new -> getClass
Execution halted
Running ‘draw.R’ [1s/1s]
Running the tests in ‘tests/draw.R’ failed.
Complete output:
  > library(CodeDepends)
  > library(Rgraphviz)
  Error in library(Rgraphviz) : there is no package called 'Rgraphviz'
  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.
Failed with error:  'there is no package called 'graph''
Quitting from lines 144-150 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot make task graph without the graph package (available from the Bioconductor project).
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'codingMatrices.tex' failed.
LaTeX errors:
! LaTeX Error: File `fouriernc.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: coin
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LegoCondInf.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.77 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `Rd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {makeidx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
plot,cold-missing: no visible global function definition for
  ‘extendrange’
Undefined global functions or variables:
  extendrange
Consider adding
  importFrom("grDevices", "extendrange")
to your NAMESPACE file.
Package suggested but not available for checking: ‘snpStats’
Errors in running code in vignettes:
when running code in ‘vignette.Rnw’
  ...
             values.against
values.for    c(-0.1, 1) c(0.9, 1.1)
  c(-0.1, 1)     1.00000  0.05150753
  c(0.9, 1.1)   19.41464  1.00000000

> library(snpStats)

  When sourcing ‘vignette.R’:
Error: there is no package called ‘snpStats’
Execution halted
Error in re-building vignettes:
  ...
Warning in E1ot$app1 - E0ot$app1 :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in E1ot$app1 - E0ot$app1 :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in E1ot$app1 - E0ot$app1 :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in E1ot$app1 - E0ot$app1 :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in E1ot$app1 - E0ot$app1 :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.


Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 7 
Error in library(snpStats) : there is no package called ‘snpStats’
Execution halted
Package suggested but not available for checking: ‘Biobase’
Running examples in ‘colorhcplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: colorhcplot
> ### Title: Colorful Hierarchical Clustering Dendrograms
> ### Aliases: colorhcplot
> ### Keywords: hierarchical cluster color dendrogram plot multivariate
> 
> ### ** Examples
> 
> ## colorhcplot(hc, fac) -- examples
> ##
> ## Example code will generate 2 dendrograms: 
> ## 1) a simple color dendrogram using default parameters; 
> ## 2) a y-axis adjusted dendrogram with thin black lines. 
> ##
> data(geneData, package="Biobase")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Biobase’
Calls: data -> find.package
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
This is colorSpec.  Version: 0.5-3.  Author: Glenn Davis [aut, cre].  Built: R 3.4.0; ; 2017-04-02 06:23:09 UTC; unix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'blueflame.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.84 \usepackage
                {fixltx2e}    % for \textsubscript{} ?^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'R_packages-comf.ltx' failed with diagnostics:
Running 'texi2dvi' on 'R_packages-comf.ltx' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Package suggested but not available for checking: ‘ConsensusClusterPlus’
Errors in running code in vignettes:
when running code in ‘COMMUNAL.Rnw’
  ...

> BRCA.results <- clusterRange(dataMtx = BRCA.100, ks = ks, 
+     varRange = varRange, validation = measures, verbose = F)
Running COMMUNAL over range of variables...	Loading required package: kohonen
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

  When sourcing ‘COMMUNAL.R’:
Error: invalid argument type
Execution halted
Running ‘testthat.R’ [22s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: getParents(X, environment, method = method, alpha = 0.1)
  5: checkDependencies(method)
  6: missingDependenciesMessage("pcalg", method)
  7: stop(paste("The package '", package, "' is needed for ", method, " to \nwork. Please install it.", 
         sep = ""), call. = FALSE)
  
  testthat results ================================================================
  OK: 11 SKIPPED: 0 FAILED: 4
  1. Error: Checks output type for pc (@test_getParents_defaults_all_methods.R#19) 
  2. Error: Checks output type for LINGAM (@test_getParents_defaults_all_methods.R#19) 
  3. Error: Checks output type for ges (@test_getParents_defaults_all_methods.R#19) 
  4. Error: Checks output type for rfci (@test_getParents_defaults_all_methods.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app   2.5Mb
    doc   2.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'compare-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref} % for \url^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GEOquery’

Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘genefilter’ ‘GEOmetadb’ ‘GSVA’
  ‘mogene10sttranscriptcluster.db’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: tcltk

For more information on the usage of the Confidence tool, type:
vignette("confidence")
Examples of input files can be found in:
'/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/confidence.Rcheck/confidence/extdata'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'confidence.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.74 \allsectionsfont
                     {\sffamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'contrast.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algos.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.128 \usepackage
                 {fancyhdr}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘copula’ ‘vines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Rmpfr’ ‘partitions’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   4.7Mb
Package unavailable to check Rd xrefs: ‘Rmpfr’
Errors in running code in vignettes:
when running code in ‘Frank-Rmpfr.Rnw’
  ...
> fnam <- sprintf("mlogL_mpfr_%s.rda", Sys.info()[["machine"]])

> if (!file.exists(fn <- file.path(copDDir, fnam))) {
+     print(system.time(nllMP <- lapply(MPrecBits, function(pBit) {
+         nlM <- thM <- mpfr .... [TRUNCATED] 
Timing stopped at: 0.005 0 0.005

  When sourcing 'Frank-Rmpfr.R':
Error: could not find function "mpfr"
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gsl

Attaching package: 'gsl'

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

    psi, sinc

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: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma

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 36-38 (dNAC.Rmd) 
Error: processing vignette 'dNAC.Rmd' failed with diagnostics:
there is no package called 'partitions'
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘CopyNumber450kCancer.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
Package required but not available: ‘CRF’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Error in re-building vignettes:
  ...
Loading required package: calibrate
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Correlplot.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in (survfit(fit0)$surv)^exp(-colMeans(reg0) %*% coef0) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (survfit(fit_1)$surv)^exp(-colMeans(reg1) %*% coef_1) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: vignette.aux
I couldn't open style file chicago.bst
---line 45 of file vignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Error in re-building vignettes:
  ...
Loading required package: nlme
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'covBM_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {bm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rmgarch’
Error in re-building vignettes:
  ...
Attaching package: 'fit.models'

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

    mahalanobis

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

Loading required package: foreach
Loading required package: PerformanceAnalytics

Attaching package: 'PerformanceAnalytics'

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

    legend

Quitting from lines 35-44 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
there is no package called 'rmgarch'
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘qvalue’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgdal’ ‘sf’
Error in re-building vignettes:
  ...

    
ISDA(R) is a registered mark of the International Swaps and
    Derivatives 
Association, Inc.
 
Please type **yes** to assent to
    the aforementioned terms.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'creditr.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: TH.data

Attaching package: 'TH.data'

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Crossover.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 \usepackage
                {algorithm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with zeroes
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CrossScreening-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {cleveref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Error in re-building vignettes:
  ...
Categorical Regression Splines (version 0.15-27)
[vignette("crs_faq") provides answers to frequently asked questions]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'crs.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘rJPSGCS’ ‘chopsticks’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BayesCslogistic: no visible global function definition for
  ‘model.response’
BayesCslogistic: no visible global function definition for
  ‘model.matrix’
MleCslogistic: no visible global function definition for
  ‘model.response’
MleCslogistic: no visible global function definition for ‘model.matrix’
MleCslogistic: no visible global function definition for ‘optim’
plot.BayesCslogistic: no visible global function definition for ‘is’
plot.BayesCslogistic: no visible global function definition for ‘par’
plot.BayesCslogistic: no visible global function definition for
  ‘density’
print.BayesCslogistic: no visible global function definition for ‘coef’
print.MleCslogistic: no visible global function definition for ‘coef’
summary.BayesCslogistic: no visible global function definition for
  ‘var’
summary.BayesCslogistic: no visible global function definition for
  ‘median’
summary.MleCslogistic: no visible global function definition for
  ‘pnorm’
summary.MleCslogistic: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  coef density is median model.matrix model.response optim par pnorm
  qnorm var
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("stats", "coef", "density", "median", "model.matrix",
             "model.response", "optim", "pnorm", "qnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package which this enhances but not available for checking: ‘pbdMPI’
Error in re-building vignettes:
  ...
Loading required package: lattice
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cubist.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘CuCubes-Ex.R’ failed
The error most likely occurred in:

> ### Name: ComputeMaxInfoGains
> ### Title: Max information gains
> ### Aliases: ComputeMaxInfoGains
> 
> ### ** Examples
> 
>   ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,
+     discretizations = 1, range = 0, divisions = 22, dimensions = 1)

 *** caught illegal operation ***
address 0x103eaccb1, cause 'illegal opcode'

Traceback:
 1: .C(CuCubes, as.integer(acceleration.type.int), as.integer(0),     as.integer(n), as.integer(k), as.integer(dimensions), as.integer(divisions),     as.integer(discretizations), as.integer(seed), as.double(range),     as.double(pseudo.count), as.integer(reduce.method.int), as.double(0),     integer(length = 0), as.integer(0), as.double(data), as.integer(decision),     out = double(length = k))
 2: ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,     discretizations = 1, range = 0, divisions = 22, dimensions = 1)
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cudaBayesreg.Rcheck/00install.out’ for details.
Packages unavailable to check Rd xrefs: ‘DNAcopy’, ‘tilingArray’
Package which this enhances but not available for checking: ‘RGtk2’
Package required but not available: ‘PMA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cwhmisc.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `russian'. Either you misspelled it
(babel)                or the language definition file russian.ldf was not foun
d.

See the babel package documentation for explanation.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'presentazioneCladagMinottiSpedicato.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
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l.8 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Sparseness = 75.7 %
  Sorting covariates by covariateId and rowId
  1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R#212) 
  error$message does not match "1 - 1".
  Actual value: "c++ exception (unknown reason)"
  
  
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  testthat results ================================================================
  OK: 177 SKIPPED: 9 FAILED: 1
  1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R#212) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘gRbase’ ‘RBGL’ ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(d3r)
  > 
  > test_check("d3r")
  1. Failure: d3_igraph works (@test_igraph.R#36) --------------------------------
  d3_igraph(bull_node_attr, json = FALSE) not equal to list(...).
  Component "links": Component "weight": Modes: character, numeric
  Component "links": Component "weight": target is character, current is numeric
  
  
  testthat results ================================================================
  OK: 9 SKIPPED: 4 FAILED: 1
  1. Failure: d3_igraph works (@test_igraph.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error: processing vignette 'marray-notes.Rnw' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simulate-regdiags.tex' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

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

! Emergency stop.
<read *> 
         
l.1 ...ohyper,justified]{tufte-handout}\usepackage
                                                  []{graphicx}\usepackage[]{...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot9a827e5ee17d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot9a827e5ee17d.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning: parse error in file '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/datasus.Rcheck/datasus/doc/Introduction_to_datasus.R':
invalid multibyte character in parser at line 50
Package suggested but not available for checking: ‘GenomicRanges’
Error in re-building vignettes:
  ...
  Consider 'structure(list(), *)' instead.
Warning in structure(res, label = node$name, members = 1, height = height,  :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(res, label = node$name, members = 1, height = height,  :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(res, label = node$name, members = 1, height = height,  :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(res, label = node$name, members = 1, height = height,  :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(res, label = node$name, members = 1, height = height,  :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
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]="./webshot176e46179b7f8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot176e46179b7f8.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
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dbhydroR.tex' failed.
LaTeX errors:
! LaTeX Error: File `mdframed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
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: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object 'force_v1'
Error: processing vignette 'test.Rmd' failed with diagnostics:
unable to load shared object '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/stringi/libs/stringi.so':
  dlopen(/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/stringi/libs/stringi.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libc++.1.dylib
  Referenced from: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/stringi/libs/stringi.so
  Reason: image not found
Execution halted
Package required and available but unsuitable version: ‘dplyr’

Package suggested but not available for checking: ‘RPostgreSQL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   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.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dbscan.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘RedeR’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

    as.Date, as.Date.numeric

Loading required package: lattice

Attaching package: 'lattice'

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

    melanoma

Classes and Methods for R developed in the

Political Science Computational Laboratory

Department of Political Science

Stanford University

Simon Jackman

hurdle and zeroinfl functions by Achim Zeileis


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 29-31 (chytrid_dede_example.Rmd) 
Error: processing vignette 'chytrid_dede_example.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’ ‘GenomeInfoDb’

Package suggested but not available for checking: ‘VariantAnnotation’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘moduleColor’
Error in re-building vignettes:
  ...

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 [2/8]
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
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
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: 'desctable'

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

    datatable

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

    IQR, chisq.test, fisher.test

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]="./webshot1cc02dd9cfa6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1cc02dd9cfa6.png': No such file or directory
Quitting from lines 66-73 (desctable.Rmd) 
Error: processing vignette 'desctable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package unavailable to check Rd xrefs: ‘gmp’
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'desirability.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

Type X to quit or <RETURN> to proceed,
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! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘RBGL’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dclone’ ‘dcmle’
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
Packages required but not available: ‘MLInterfaces’ ‘genefilter’ ‘ALL’

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

Packages suggested but not available for checking:
  ‘impute’ ‘GOstats’ ‘org.Hs.eg.db’ ‘AnnotationDbi’

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            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Rvignette_DiagTest3Grp.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Error in re-building vignettes:
  ...
  not all rows sum up to 1 => normalization forced
Warning in DR_data(Bld[31:36, 1:4]) :
  not all rows sum up to 1 => normalization forced
Warning in DR_data(Bld[31:36, 1:4]) :
  not all rows sum up to 1 => normalization forced
Warning in DR_data(BloodSamples[, c(1, 2, 4)]) :
  not all rows sum up to 1 => normalization forced
only one variable in [0, 1] supplied - beta-distribution assumed.
check this assumption.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DirichletReg-vig.tex' failed.
LaTeX errors:
! LaTeX Error: File `blkarray.sty' not found.

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

! Emergency stop.
<read *> 
         
l.50 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dirmcmc_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Package unavailable to check Rd xrefs: ‘diversitree’
Error in re-building vignettes:
  ...
Cross tabulating interactions for gbm model with 11 predictors
1 2 3 4 5 6 7 8 9 10 
maximum value = 0.58

Loading required package: survival
Loading required package: lattice
Loading required package: splines
Loading required package: parallel
Loaded gbm 2.1.3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'brt.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/t1enc.def))

! LaTeX Error: File `paralist.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.66 \usepackage
                {relsize}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on diveMove.log.
make: *** [diveMove.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/diveMove.Rcheck/vign_test/diveMove") : 
  running 'make' failed
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'diveRsity.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    include  19.2Mb
Packages required but not available: ‘graph’ ‘gRbase’ ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DNAtools.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘supraHex’ ‘graph’ ‘Rgraphviz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: numDeriv
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BD_EM.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LSmeans.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    -  Login failed
  1: domino.login(Sys.getenv("TESTUSER"), Sys.getenv("TESTUSERPASS"), FALSE, "https://app.dominodatalab.com") at testthat/test-login.R:5
  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
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doRedis.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.22 \usepackage
                {upquote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘doMPI’ ‘devtools’
Package unavailable to check Rd xrefs: ‘doMPI’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doRNG-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘gmp’
Packages suggested but not available for checking: ‘dbplyr’ ‘RPostgreSQL’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Packages unavailable to check Rd xrefs: ‘dbplyr’, ‘RPostgreSQL’
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  
  testthat results ================================================================
  OK: 2623 SKIPPED: 9 FAILED: 8
  1. Failure: row_number(), ntile(), min_rank(), percent_rank(), dense_rank(), and cume_dist() work (@test-hybrid.R#413) 
  2. Failure: desc is correctly handled by window functions (@test-mutate-windowed.R#9) 
  3. Failure: desc is correctly handled by window functions (@test-mutate-windowed.R#10) 
  4. Failure: row_number gives correct results (@test-mutate-windowed.R#17) 
  5. Failure: rank functions deal correctly with NA (#774) (@test-mutate-windowed.R#113) 
  6. Failure: rank functions deal correctly with NA (#774) (@test-mutate-windowed.R#120) 
  7. Failure: rank functions deal correctly with NA (#774) (@test-mutate-windowed.R#141) 
  8. Failure: rank functions deal correctly with NA (#774) (@test-mutate-windowed.R#148) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Package suggested but not available for checking: ‘git2r’
Package unavailable to check Rd xrefs: ‘git2r’
Error in re-building vignettes:
  ...
                        sleep dataset
presidential            Terms of 11 presidents from Eisenhower to Obama
seals                   Vector field of seal movements
txhousing               Housing sales in TX


Use ‘data(package = .packages(all.available = TRUE))’
to list the data sets in all *available* packages.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dslice.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘sva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: TSclust
Loading required package: wmtsa
Loading required package: pdc
Loading required package: cluster
Loading required package: TSdist
Loaded TSdist v3.4. See ?TSdist for help, citation("TSdist") for use in publication.

Loading required package: doParallel
Loading required package: iterators
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dtwclust.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.78 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getEQD2.default(D = D$dvh[, "dose"], fd = fd, ab = ab) :
  'D' must be > 0
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DVHmetrics.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.92 \usepackage
                {apacite}                     % after hyperref^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   8.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs     2.8Mb
    models   4.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'InstallationForUsers.tex' failed.
LaTeX errors:
! LaTeX Error: File `menukeys.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svminternals.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: EasyMx-package
> ### Title: EasyMx: Easy modeling in OpenMx
> ### Aliases: EasyMx-package EasyMx
> 
> ### ** Examples
> 
> 
> # Make and run a one factor model
> require(EasyMx)
> 
> data(demoOneFactor)
> fmod <- list(G=names(demoOneFactor))
> fit1 <- emxFactorModel(fmod, demoOneFactor, run=TRUE)
Running Model with 15 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: emxFactorModel -> mxRun -> runHelper -> .Call
Execution halted
Package required but not available: ‘sdcTable’

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

Package suggested but not available for checking: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'eDMA_1.4-0.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
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: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EGRET.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.66 \usepackage
                {subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Some columns contain no data and are omitted.
Some numeric columns contain only 0 values and are omitted.
Some numeric fields contain 0 values:
Please check if these are really meant as 0 or if they are erroneously assigned because of DBase restrictions.
If so, use something like:
site$Column_name[site$Column_name==0] <- NA

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'eHOF.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: eiPack
Loading required package: MASS
Loading required package: coda
Loading required package: msm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ei.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.22 \usepackage
                {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ElastH.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.6Mb
Error in re-building vignettes:
  ...
    sd, sigma

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

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘iCheck’ ‘samr’ ‘GSEAlm’ ‘globaltest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tutorial.tex' failed.
BibTeX errors:
The top-level auxiliary file: tutorial.aux
I couldn't open style file agsm.bst
---line 3 of file tutorial.aux
 : \bibstyle{agsm
 :               }
I'm skipping whatever remains of this command
I found no style file---while reading file tutorial.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
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:
  ...
Loading required package: ElstonStewart
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: parallel
Loading required package: digest
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Elston-Stewart.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘siggenes’ ‘gcrma’ ‘biomaRt’ ‘AnnotationDbi’

Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘lumi’ ‘GOstats’ ‘Category’ ‘vsn’ ‘GO.db’ ‘GSEABase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘move’
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 328-331 (EMbC_qckref.Rmd) 
Error: processing vignette 'EMbC_qckref.Rmd' failed with diagnostics:
there is no package called 'move'
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.5Mb
Running ‘testthat.R’ [57s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  testthat results ================================================================
  OK: 62 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: Person Carl Boettiger <cboettig@gmail.com> was not given any role. 
  2: Person Matthew B. Jones was not given any role. 
  Execution halted
wire.init.fit : wire.init.km: no visible global function definition for
  ‘kmeans’
wire.init.reg: no visible global function definition for ‘lm’
wire.init.reg: no visible global function definition for ‘coef’
wire.init.reg: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef kmeans lm resid
Consider adding
  importFrom("stats", "coef", "kmeans", "lm", "resid")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggtree’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Packages required but not available: ‘DESeq2’ ‘GenomicRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘spocc’ ‘rgeos’
Error in re-building vignettes:
  ...
ERROR: dependency ‘rgeos’ is not available for package ‘geoaxe’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/geoaxe’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'geoaxe' had non-zero exit status
ERROR: dependency ‘geoaxe’ is not available for package ‘rgbif’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/rgbif’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'rgbif' had non-zero exit status
ERROR: dependency ‘rgbif’ is not available for package ‘spocc’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/spocc’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'spocc' had non-zero exit status

The downloaded source packages are in
	'/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmpf3RLJr/downloaded_packages'
Loading required package: ENMeval
Loading required package: dismo
Loading required package: raster
Loading required package: sp
Loading required package: rJava
Loading required package: parallel
Quitting from lines 38-52 (ENMeval-vignette.Rmd) 
Error: processing vignette 'ENMeval-vignette.Rmd' failed with diagnostics:
there is no package called 'spocc'
Execution halted
Running examples in ‘envDocument-Ex.R’ failed
The error most likely occurred in:

> ### Name: env_doc
> ### Title: Report the working environment in which an analysis was
> ###   performed.
> ### Aliases: env_doc
> 
> ### ** Examples
> 
>  env_doc("print") # print information to stdout
Warning in getScriptPath() :
  Obtained value for path <print> does not end with .R, .Rmd or .Rnw: print
Error: Package git2r needed for this function to work. Please install it or call env_doc(git = FALSE).
Execution halted
Running ‘test_envDocument.R’ [1s/1s]
Running the tests in ‘tests/test_envDocument.R’ failed.
Last 13 lines of output:
  > # 
  > # Note: I'm not sure how to run a true regression test on this package since its
  > # purpose is to print out a lot of machine-specific info.  For now just make
  > # sure it outupts the appropriate sections (system, Rversion and included package envDocument)
  > 
  > library(envDocument)
  > 
  > # Calling env_doc with defaults returns a single data frame of information
  > # about the environment
  > info <- env_doc()
  Error: Package git2r needed for this function to work. Please install it or call env_doc(git = FALSE).
  In addition: Warning message:
  In getScriptPath() :
    Obtained value for path <NA> does not end with .R, .Rmd or .Rnw: NA
  Execution halted
Running examples in ‘envirem-Ex.R’ failed
The error most likely occurred in:

> ### Name: PETseasonality
> ### Title: PET seasonality
> ### Aliases: PETseasonality
> 
> ### ** Examples
> 
> # Find example rasters
> rasterFiles <- list.files(system.file('extdata', package='envirem'), full.names=TRUE)
> env <- stack(rasterFiles)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: stack ... raster -> raster -> .local -> .rasterObjectFromFile
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: survival
Package epiR 0.9-79 is loaded
Type help(epi.about) for summary information


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EpiBayes2Level.tex' failed.
LaTeX errors:
! LaTeX Error: File `titling.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {datetime}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
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]="./webshot84772aa4655e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot84772aa4655e.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Errors in running code in vignettes:
when running code in ‘simLexis.rnw’
  ...

> box(lwd = 3)

> source("../R/simLexis.R", keep.source = TRUE)
Warning in file(filename, "r", encoding = encoding) :
  cannot open file '../R/simLexis.R': No such file or directory

  When sourcing ‘simLexis.R’:
Error: cannot open the connection
Execution halted
when running code in ‘yll.rnw’
  ...

> plyll("Sus")

> source("../R/erl.R", keep.source = TRUE)
Warning in file(filename, "r", encoding = encoding) :
  cannot open file '../R/erl.R': No such file or directory

  When sourcing ‘yll.R’:
Error: cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from ‘package:base’:

    merge.data.frame

Warning in Lexis(entry = list(Per = dodm, Age = dodm - dobth, DMdur = 0),  :
  Dropping 4 rows with duration of follow up < tol

Warning in coxph(Surv(DMdur, DMdur + lex.dur, lex.Xst %in% c("Dead(Ins)",  :
  a variable appears on both the left and right sides of the formula
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simLexis.tex' failed.
LaTeX errors:
! LaTeX Error: File `nth.sty' not found.

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

! Emergency stop.
<read *> 
         
l.34 \usepackage
                {makeidx,Sweave,floatflt,amsmath,amsfonts,amsbsy,enumitem,dc...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘Rgraphviz’

Package suggested but not available for checking: ‘RCytoscape’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'equatevignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `upgreek.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
samplk2 (samplk)      Longitudinal networks of positive affection
                      within a monastery as a "network" object
samplk3 (samplk)      Longitudinal networks of positive affection
                      within a monastery as a "network" object

Error in ergm.MCMLE(init, nw, model, initialfit = (initialfit <- NULL),  : 
  Number of edges in a simulated network exceeds that in the observed by a factor of more than 20. This is a strong indicator of model degeneracy or a very poor starting parameter configuration. If you are reasonably certain that neither of these is the case, increase the MCMLE.density.guard control.ergm() parameter.
Loading required namespace: latticeExtra
Warning in formals(fun) : argument is not a function
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ergm.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'eRm.tex' failed.
LaTeX errors:
! LaTeX Error: File `kpfonts.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘ESEA.Rnw’
  ...

> PathwayNetwork <- Results[[2]][[1]]

> SavePathway2File(PathwayNetwork, layout = layout.circle, 
+     file = "Graph")
[1] "...writing to file"

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

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: parmigene

Error: processing vignette 'ESEA.Rnw' failed with diagnostics:
 chunk 11 
Error in loadNamespace(name) : there is no package called ‘graph’
Execution halted
Package suggested but not available for checking: ‘RPostgreSQL’
Package unavailable to check Rd xrefs: ‘RODBC’
Package required but not available: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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

trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13529 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmphhBoTr/eurostat/ten00081_date_code_TF.rds
trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 5933 bytes
==================================================
downloaded 5933 bytes

Quitting from lines 341-357 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Namespaces in Imports field not imported from:
  ‘ggalt’ ‘pander’ ‘psych’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'events.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {inconsolata}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: xts
Loading required package: boot
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ees.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [colorlinks,linkcolor=blue,citecolor=red]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘exams-Ex.R’ failed
The error most likely occurred in:

> ### Name: exams
> ### Title: Generation of Simple Exams
> ### Aliases: exams print.exams_metainfo
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## define an exams (= list of exercises)
> myexam <- list(
+   "boxplots",
+   c("tstat", "ttest", "confint"),
+   c("regression", "anova"),
+   "scatterplot",
+   "relfreq"
+ )
> 
> if(interactive()) {
+ ## compile a single random exam (displayed on screen)
+ sol <- exams(myexam)
+ sol
+ }
> 
> ## generate multiple exams (stored in output directory)
> odir <- tempfile()
> sol <- exams(myexam, n = 3, dir = odir, template = c("exam", "solution"))
Warning in exams(myexam, n = 3, dir = odir, template = c("exam", "solution")) :
  The template exam.tex has been adapted to exams2pdf() and is not fully
  compatible with exams() anymore. Template oexam.tex used instead.
Warning in exams(myexam, n = 3, dir = odir, template = c("exam", "solution")) :
  The template solution.tex has been adapted to exams2pdf() and is not
  fully compatible with exams() anymore. Template osolution.tex used
  instead.
Error in texi2dvi(out_tex[j], pdf = TRUE, clean = TRUE, quiet = quiet) : 
  Running 'texi2dvi' on 'exam1.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: exams -> texi2dvi
Execution halted
Running ‘encodings.R’ [2s/2s]
Running the tests in ‘tests/encodings.R’ failed.
Last 13 lines of output:
    Running 'texi2dvi' on 'plain81.tex' failed.
  LaTeX errors:
  ! LaTeX Error: File `a4wide.sty' not found.
  
  Type X to quit or <RETURN> to proceed,
  or enter new name. (Default extension: sty)
  
  ! Emergency stop.
  <read *> 
           
  l.5 \newenvironment
                     {question}{\item \textbf{Problem}\newline}{}^^M
  !  ==> Fatal error occurred, no output PDF file produced!
  Calls: exams2pdf -> xexams -> <Anonymous> -> texi2dvi
  Execution halted
Errors in running code in vignettes:
when running code in ‘exams.Rnw’
  ...
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \newenvironment
                   {question}{\item \textbf{Problem}\newline}{}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
when running code in ‘exams2.Rnw’
  ...
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'exams.Rnw' failed with diagnostics:
 chunk 7 (label = tstat-non-interacive) 
Error in texi2dvi(out_tex[j], pdf = TRUE, clean = TRUE, quiet = quiet) : 
  Running 'texi2dvi' on 'plain1.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \newenvironment
                   {question}{\item \textbf{Problem}\newline}{}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Packages suggested but not available for checking: ‘INLA’ ‘rgeos’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    exiftool  10.2Mb
Packages required but not available:
  ‘Biostrings’ ‘Rsamtools’ ‘GenomicRanges’ ‘GenomicAlignments’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
The following objects are masked from ‘package:foreign’:

    read.dbf, write.dbf

Note: Function plotsurf depends on akima which has
 a restricted licence that explicitly forbids commercial use.
 akima is therefore disabled by default and may be enabled by
 akimaPermit(). Calling this function includes your agreement to
 akima`s licence restrictions.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'expectreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Rmpfr’
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/expoRkit.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘GEOquery’ ‘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
Error in re-building vignettes:
  ...
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘Rgraphviz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FAOSTAT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {draftwatermark}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
cv.cocktail: no visible global function definition for ‘predict’
cv.survpath: no visible global function definition for ‘predict’
cv.survpath: no visible binding for global variable ‘weighted.mean’
error.bars: no visible global function definition for ‘segments’
getoutput: no visible global function definition for ‘new’
lambda.interp: no visible global function definition for ‘approx’
plot.cocktail: no visible global function definition for ‘matplot’
plot.cocktail: no visible global function definition for ‘gray.colors’
plot.cocktail: no visible global function definition for ‘text’
plot.cv.cocktail: no visible global function definition for ‘points’
plot.cv.cocktail: no visible global function definition for ‘axis’
plot.cv.cocktail: no visible global function definition for ‘abline’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  abline approx axis gray.colors matplot new points predict segments
  text weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "matplot", "points",
             "segments", "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  12.8Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Error in re-building vignettes:
  ...


Attaching package: 'fastR'

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

    panel.smooth

Loading required package: knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Updates.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘glpkAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in fitted.FPCA(FPCAsparse, derOptns = list(p = 1, kernelType = "epan")) :
  Potentially you use too many components to estimate derivatives. 
  Consider using SelectK() to find a more informed estimate for 'K'.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fdapaceVignetteKnitr.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.36 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs   4.8Mb
Error in re-building vignettes:
  ...

Loading required package: maps
Note: method with signature 'matrix#Matrix' chosen for function 'crossprod',
 target signature 'matrix#dgTMatrix'.
 "ANY#TsparseMatrix" would also be valid
Note: method with signature 'ddenseMatrix#dsparseMatrix' chosen for function 'crossprod',
 target signature 'dtrMatrix#dgTMatrix'.
 "Matrix#TsparseMatrix" would also be valid
Loading required package: mapdata
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FLAM_canada.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                [left=25mm, right=25mm, top=20mm, bottom=20mm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘fdth’

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

    sd, var

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'latex_fdt.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test-as-dgCMatrix.R’ [3s/4s]
  Running ‘test-empty_array.R’ [4s/5s]
  Running ‘test-existence_collision.R’ [2s/4s]
  Running ‘test-hash.mapping.R’ [3s/4s]
  Running ‘test-hashing.R’ [3s/4s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'testTimeAndSimpleUse.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro-fgpt.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \makeatletter
                  ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: fifer
Loading required package: MASS
Loading required package: xtable
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fifer_package.tex' failed.
LaTeX errors:
! LaTeX Error: File `apa.cls' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {hyperref}  %this allows us to cite URLs in the text^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gb2016_complement.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
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.
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 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘examples/fitcoach-usage.Rmd’, ‘examples/fitcoach-usage.html’,
    ‘summary.Rmd’, ‘summary.html’
Package has no Sweave vignette sources and no VignetteBuilder field.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Packages suggested but not available for checking:
  ‘devtools’ ‘multipanelfigure’
Packages required but not available: ‘flowWorkspace’ ‘flowCore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
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 in forecasting_ga(evalFunc = f, chsize = 2, minv = rep(-10, 2),  : 
  only replacement of elements is allowed
Calls: forecasting_ga -> .Call
Execution halted
Packages required but not available: ‘Rglpk’ ‘Rsymphony’

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

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

    filter, lag

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

    intersect, setdiff, setequal, union

Note: show_basis assumes spherical distance functions when plotting
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FRK_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                [margin=1in]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘partitions’ ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2
Loading required package: gsubfn
Loading required package: proto
Loading required package: hmeasure
Loading required package: parallel
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fscaret.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.3Mb
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > 
  > test_check("FSelectorRcpp")
Error in re-building vignettes:
  ...
Iacus, Springer NY, (2008)
To check the errata corrige of the book, type vignette("sde.errata")

Attaching package: ‘ftsa’

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

    sd, var

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ftsa.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Package required but not available: ‘breastCancerVDX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.adfPlot: no visible global function definition for ‘persp’
adfTest: no visible global function definition for ‘embed’
adfTest: no visible global function definition for ‘lm’
adfTest: no visible global function definition for ‘approx’
padf: no visible global function definition for ‘approx’
qadf: no visible global function definition for ‘approx’
unitrootTest: no visible global function definition for ‘embed’
unitrootTest: no visible global function definition for ‘lm’
urdfTest: no visible global function definition for ‘capture.output’
urersTest: no visible global function definition for ‘capture.output’
urkpssTest: no visible global function definition for ‘capture.output’
urppTest: no visible global function definition for ‘capture.output’
urspTest: no visible global function definition for ‘capture.output’
urzaTest: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  approx capture.output embed lm persp
Consider adding
  importFrom("graphics", "persp")
  importFrom("stats", "approx", "embed", "lm")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package suggested but not available for checking: ‘WGCNA’
Package unavailable to check Rd xrefs: ‘WGCNA’
Running examples in ‘fuzzyforest-Ex.R’ failed
The error most likely occurred in:

> ### Name: wff
> ### Title: WGCNA based fuzzy forest algorithm
> ### Aliases: wff wff.default wff
> 
> ### ** Examples
> 
> library(WGCNA)
Error in library(WGCNA) : there is no package called ‘WGCNA’
Execution halted
Package required but not available: ‘ROI.plugin.glpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FuzzyNumbersTutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

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

! Emergency stop.
<read *> 
         
l.80 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘cffdrs’
Error in re-building vignettes:
  ...

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

    as.Date, as.Date.numeric

Loading required package: strucchange
Loading required package: sandwich
Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) :
  argument 'replacement' has length > 1 and only the first element will be used
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ArrayBin’
Error in re-building vignettes:
  ...


Attaching package: 'gamboostLSS'

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

    model.weights

Loading required namespace: BayesX
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘DAAGbio’
Error in re-building vignettes:
  ...
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.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'InflatedDistributioninR.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \usepackage
                {Rd}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in panel(x[id], y[id], col = col[id], pch = pch[id], ...) :
  Some points are missed out 
increase the y limits using ylim.worm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GAMLSS_GMRF.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {Rd}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.8Mb
Error in re-building vignettes:
  ...
Loading required package: HaploSim
Loading required package: reshape

Attaching package: ‘reshape’

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

    expand

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.6Mb
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     43.2Mb
Error in re-building vignettes:
  ...

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

    sigma

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

    cbind, rbind

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gaston.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  12.8Mb
Package suggested but not available for checking: ‘paleofire’
Error in re-building vignettes:
  ...
Loading required package: g.data
Warning in g.data.attach(ddp) :
  New DDP: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpTHh796/newdir154642e4489b6
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'g.data.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {indentfirst}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: geepack
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'geepack-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gems.tex' failed.
LaTeX errors:
! LaTeX Error: File `pict2e.sty' not found.

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

! Emergency stop.
<read *> 
         
l.81 \usepackage
                {tikz}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
Package unavailable to check Rd xrefs: ‘snpStats’
Error in .requirePackage(package) : 
    unable to find required package 'snpStats'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Running examples in ‘GenCAT-Ex.R’ failed
The error most likely occurred in:

> ### Name: GenCAT
> ### Title: Running GenCAT
> ### Aliases: GenCAT
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> ###############
> #Running GenCAT
> ###############
> data("CardioMapped")
> 
> #Subset CardioMapped to decrease CPU time
> CardioMappedSub<-CardioMapped[CardioMapped$chr < 15,]
> set.seed(1)
> CardioMappedSub<-CardioMappedSub[sample(1:nrow(CardioMappedSub), 100),]
> 
> print(head(CardioMappedSub))
            SNP effect_allele other_allele   testStat chr position class
17232 rs9572807             C            T -0.3014771  13 72423959 DACH1
24151 rs4389009             G            A -1.4443860  13 99193519 STK24
37178 rs7151730             T            A  0.1387317  14 33531585 NPAS3
58941 rs1076958             G            A  2.0597766  14 91131857 TTC7B
13089 rs7987481             G            A -1.0024210  13 47318950 LRCH1
58302  rs411064             G            A  0.2132412  14 90008860 FOXN3
> 
> library(snpStats)
Error in library(snpStats) : there is no package called ‘snpStats’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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: 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: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
Quitting from lines 62-69 (GenCAT-vignette.Rmd) 
Error: processing vignette 'GenCAT-vignette.Rmd' failed with diagnostics:
unable to find required package 'snpStats'
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Geneland-Doc.pdf’, ‘Geneland-Doc.tex’, ‘dag-final.pdf’, ‘dag3.pdf’,
    ‘fig/MCMC.jpg’, ‘fig/MyMap_zoom10.jpeg’, ‘fig/MyMap_zoom7.jpeg’,
    ‘fig/choosefiles.jpg’, ‘fig/choosesep.jpg’, ‘fig/dag-final.pdf_t’,
    ‘fig/dag3.pdf_t’, ‘fig/example_spatial2_bis.jpeg’,
    ‘fig/example_spatial3_bis.jpeg’, ‘fig/example_spatial3_ter.jpeg’,
    ‘fig/example_spatial_bis.jpeg’, ‘fig/exp_q_quart.jpeg’,
    ‘fig/initial.jpg’, ‘fig/map.jpeg’, ‘fig/multip_run.jpg’,
    ‘fig/multip_run2.jpg’, ‘fig/npop.jpeg’, ‘fig/output.jpg’,
    ‘fig/parallel.jpg’, ‘fig/postproc.jpg’, ‘fig/power.jpeg’,
    ‘fig/vor1.jpeg’, ‘fig/vor2.jpeg’, ‘fig/wdl1.jpeg’
Package has no Sweave vignette sources and no VignetteBuilder field.
Packages required but not available: ‘Rgraphviz’ ‘graph’ ‘gRain’

Package suggested but not available for checking: ‘RHugin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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.
Error in re-building vignettes:
  ...

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

    decompose, spectrum

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

    union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Packages suggested but not available for checking:
  ‘KEGG.db’ ‘reactome.db’ ‘AnnotationDbi’
Package required but not available: ‘snpStats’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object 'force_v1'
Error: processing vignette 'geoaxe_vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.9Mb
Package suggested but not available for checking: ‘sf’
Error in re-building vignettes:
  ...
A Package for Generalised Linear Spatial Models


geoRglm version 0.9-8 (2015-04-23) is now loaded

-----------------------------------------------------------



Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'geoRglmintro.tex' failed.
LaTeX errors:
! LaTeX Error: File `texnames.sty' not found.

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

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required namespace: raster
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'geosphere.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rgdal’

Package which this enhances but not available for checking: ‘INLA’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 31-41 (lgcp.Rnw) 
Error: processing vignette 'lgcp.Rnw' failed with diagnostics:
package rgdal is required for spTransform methods
Execution halted
Package suggested but not available for checking: ‘RGtk2’
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 95-96 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
  conversion failure on 'Barbara Choroś-Tomczyk' in 'mbcsToSbcs': dot substituted for <9b>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <c5>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <99>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <c5>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <99>
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ggenealogy.tex' failed.
LaTeX errors:
! LaTeX Error: File `media9.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘EBImage’ ‘gridGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1243b62c4d438.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1243b62c4d438.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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]="./webshot147836ea0d337.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot147836ea0d337.png': No such file or directory
Quitting from lines 16-30 (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 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: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_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
Error in re-building vignettes:
  ...
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.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Notice.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘ggsn-Ex.R’ failed
The error most likely occurred in:

> ### Name: blank
> ### Title: Blank theme
> ### Aliases: blank
> 
> ### ** Examples
> 
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
Execution halted
Package suggested but not available for checking: ‘vdiffr’
Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 15 SKIPPED: 0 FAILED: 13
  1. Error: geom_linerangeh() flips (@test-geoms.R#7) 
  2. Error: geom_pointangeh() flips (@test-geoms.R#13) 
  3. Error: geom_crossbarh() flips (@test-geoms.R#31) 
  4. Error: geom_errorbarh() flips (@test-geoms.R#37) 
  5. Error: geom_barh() flips (@test-geoms.R#45) 
  6. Error: geom_histogramh() flips (@test-geoms.R#57) 
  7. Error: geom_violinh() flips (@test-geoms.R#71) 
  8. Error: geom_boxploth() flips (@test-geoms.R#81) 
  9. Error: facet_grid() with free scales flips (@test-geoms.R#95) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘git2r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Warning in (psi + skewness.norm) * (chi + Q) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in log.const.top + log.top :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Generalized_Hyperbolic_Distribution.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GlobalAncova’ ‘globaltest’ ‘limma’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘GlobalAncova’, ‘globaltest’, ‘DESeq’, ‘limma’
Running examples in ‘GiANT-Ex.R’ failed
The error most likely occurred in:

> ### Name: GiANT-package
> ### Title: Enrichment analysis
> ### Aliases: GiANT
> 
> ### ** Examples
> 
> # load data
> require(GlobalAncova)
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GlobalAncova’
> data(vantVeer)
Warning in data(vantVeer) : data set ‘vantVeer’ not found
> data(phenodata)
Warning in data(phenodata) : data set ‘phenodata’ not found
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found
> 
> ##################################
> # Example 1: gene set analysis   #
> ##################################
> res <- geneSetAnalysis(  
+   # parameters for geneSetAnalysis
+   dat = vantVeer,
+   geneSets = pathways[1:3],
+   analysis = analysis.averageCorrelation(),
+   adjustmentMethod = "fdr",
+   # additional parameters for analysis.averageCorrelation
+   labs = phenodata$metastases,
+   method = "pearson",
+   numSamples = 100)
Error in vector(mode = "list", length = length(geneSets)) : 
  object 'pathways' not found
Calls: geneSetAnalysis -> vector
Execution halted
Errors in running code in vignettes:
when running code in ‘giant_package_vignette.Snw’
  ...
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found

> resGsea <- geneSetAnalysis(labs = phenodata$metastases, 
+     method = "pearson", numSamples = 1000, dat = vantVeer, geneSets = pathways, 
+     an .... [TRUNCATED] 

  When sourcing ‘giant_package_vignette.R’:
Error: object 'pathways' not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GlobalAncova’
Warning in data(vantVeer) : data set ‘vantVeer’ not found
Warning in data(phenodata) : data set ‘phenodata’ not found
Warning in data(pathways) : data set ‘pathways’ not found

Error: processing vignette 'giant_package_vignette.Snw' failed with diagnostics:
 chunk 5 
Error in vector(mode = "list", length = length(geneSets)) : 
  object 'pathways' not found
Execution halted
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GiRaF_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Packages required but not available:
  ‘Biostrings’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘rtracklayer’

Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
fitgl: no visible global function definition for ‘na.omit’
fitgl: no visible global function definition for ‘median’
fitgl: no visible global function definition for ‘IQR’
fitgl: no visible binding for global variable ‘hist’
fitgl: no visible global function definition for ‘ppoints’
fitgl: no visible global function definition for ‘quantile’
fitgl: no visible global function definition for ‘nlminb’
glshapeplot: no visible global function definition for ‘plot’
glshapeplot: no visible global function definition for ‘title’
glshapeplot : momentLine: no visible global function definition for
  ‘lines’
glshapeplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  IQR hist lines median na.omit nlminb plot points ppoints quantile
  title
Consider adding
  importFrom("graphics", "hist", "lines", "plot", "points", "title")
  importFrom("stats", "IQR", "median", "na.omit", "nlminb", "ppoints",
             "quantile")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘BRugs’ ‘R2jags’ ‘rjags’
Running ‘bym.R’ [4s/6s]
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + checkChain(kParams, c("intercept", "SDCountySpatial"))
  + dev.off()
  + 
  + 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
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/ae/t1aer.fd))))
No file jags.aux.
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/ts1cmr.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: xetex
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/ae/t1aett.fd)
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/ts1cmtt.fd) [1]Syntax Error: Invalid page count 0
Syntax Error: Cannot allocate page cache
make: *** [jags.pdf] Segmentation fault: 11
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/glmmBUGS.Rcheck/vign_test/glmmBUGS") : 
  running 'make' failed
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.79 \title
           {An Introduction to Model-Fitting with the R package \texttt{glmm...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  51.8Mb
Error in re-building vignettes:
  ...
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning in f(x, order = 1) : value out of range in 'lgamma'
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: stats4
Warning in qt((1 - level)/2, df) : NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'glmmTMB.tex' failed.
BibTeX errors:
The top-level auxiliary file: glmmTMB.aux
I couldn't open style file chicago.bst
---line 19 of file glmmTMB.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file glmmTMB.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Warning: from glmnet Fortran code (error code -26); Convergence for 26th lambda value not reached after maxit=100 iterations; solutions for larger lambdas returned
Warning: from glmnet Fortran code (error code -26); Convergence for 26th lambda value not reached after maxit=100 iterations; solutions for larger lambdas returned
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'glmnetcr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.30 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: glmpath
Loading required package: survival
Loading required package: mvtnorm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'glmpathcr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.30 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/glpkAPI.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘preprocessCore’
Running examples in ‘glycanr-Ex.R’ failed
The error most likely occurred in:

> ### Name: quantilenorm
> ### Title: Quantile Normalization of glycan data
> ### Aliases: quantilenorm
> 
> ### ** Examples
> 
> data(mpiu)
> mpiun <- quantilenorm(mpiu)
Error in quantilenorm(mpiu) : 
  Unable to proceed since package preprocessCore from
        BioConductor is not available on this system. This
        package is a prerequisite to use the quantilenorm function!
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Error in quantilenorm(mpiu, transpose = TRUE) : 
    Unable to proceed since package preprocessCore from
          BioConductor is not available on this system. This
          package is a prerequisite to use the quantilenorm function!
  Calls: test_check ... force -> source_file -> eval -> eval -> quantilenorm
  testthat results ================================================================
  OK: 5 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gmatrix.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

trying URL 'http://i.space.com/images/i/000/010/634/original/shuttle-atlantis-lifts-off.jpg?1309297321'
Content type 'image/jpeg' length 776635 bytes (758 KB)
==================================================
downloaded 758 KB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GMCM-JStatSoft.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.117 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘graph’ ‘mutoss’
Error in re-building vignettes:
  ...
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \usepackage
                {algorithm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In wilcox.test.default(x, y, alternative = "less", correct = TRUE) :
  cannot compute exact p-value with ties
2: In wilcox.test.default(x, y, alternative = "less", correct = TRUE) :
  cannot compute exact p-value with ties
3: In wilcox.test.default(x, y, alternative = "less", correct = TRUE) :
  cannot compute exact p-value with ties
4: In wilcox.test.default(x, y, alternative = "less", correct = TRUE) :
  cannot compute exact p-value with ties
5: In wilcox.test.default(x, y, alternative = "less", correct = TRUE) :
  cannot compute exact p-value with ties
Execution halted
Error in re-building vignettes:
  ...
that memeber histograms have the same order of the bins.

Warning in as.mhist(tmp.x) :
  `bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.

Warning in as.mhist(tmp.x) :
  `bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GMD-data-processing.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 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
Error in re-building vignettes:
  ...
Loading required package: sandwich
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning: The provided gradv is not used when smooth=TRUE
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gmm_with_R.tex' failed.
LaTeX errors:
! LaTeX Error: File `srcltx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gmp.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘imudata’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Error in re-building vignettes:
  ...

Warning in Delta1_xk * mystep :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in Delta1_xk * mystep :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GNE-howto.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.43 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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:
  ...

Warning in setCoefs - ref %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in setCoefs - scaleRef %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in setCoefs - ref %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gnmOverview.tex' failed.
BibTeX errors:
The top-level auxiliary file: gnmOverview.aux
I couldn't open style file chicago.bst
---line 181 of file gnmOverview.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file gnmOverview.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘copula’ ‘VineCopula’

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

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
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")'.

Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gPCA.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {bm} % allows for bold math symbols^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gplm-examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 \usepackage
                [colorlinks,bookmarks,bookmarksopen=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in glm(as.formula(paste(Y.name, "~ ", paste(indicators_tree[-nber_indicators],  :
  fitting to calculate the null deviance did not converge -- increase 'maxit'?
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `chicago.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [colorlinks = true, linkcolor = blue, breaklinks, citecolor =...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Warning: parse error in file '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/GPoM.Rcheck/GPoM/doc/II_PreProcessing.R':
invalid multibyte character in parser at line 59
Warning: parse error in file '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/GPoM.Rcheck/GPoM/doc/IV_VisualizeOutputs.R':
invalid multibyte character in parser at line 30
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  32.1Mb
Running ‘testthat.R’ [37s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  testthat results ================================================================
  OK: 1532 SKIPPED: 531 FAILED: 9
  1. Error: CPU gpuMatrix Symmetric Single Precision Matrix Eigen Decomposition (@test_cpu_gpuMatrix_eigen.R#28) 
  2. Error: CPU gpuMatrix Symmetric Double Precision Matrix Eigen Decomposition (@test_cpu_gpuMatrix_eigen.R#48) 
  3. Error: CPU gpuMatrix Single Precision Matrix SVD Decomposition (@test_cpu_gpuMatrix_svd.R#26) 
  4. Error: CPU gpuMatrix Double Precision Matrix SVD Decomposition (@test_cpu_gpuMatrix_svd.R#55) 
  5. Error: vclMatrix Symmetric Single Precision Matrix Eigen Decomposition (@test_cpu_vclMatrix_eigen.R#28) 
  6. Error: vclMatrix Symmetric Double Precision Matrix Eigen Decomposition (@test_cpu_vclMatrix_eigen.R#48) 
  7. Error: CPU vclMatrix Single Precision Matrix SVD Decomposition (@test_cpu_vclMatrix_svd.R#26) 
  8. Error: CPU vclMatrix Double Precision Matrix SVD Decomposition (@test_cpu_vclMatrix_svd.R#55) 
  9. Failure: CPU vclMatrix Double Precision Matrix Element-Wise Logs (@test_cpu_vclMatrtix_math.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gputools.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Packages required but not available: ‘gRbase’ ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ge-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘GRAN-Overview.Rnw’
  ...

> BiocStyle::latex()

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

Error: processing vignette 'GRAN-Overview.Rnw' failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called ‘BiocStyle’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'manual_de.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `greek'. Either you misspelled it
(babel)                or the language definition file greek.ldf was not found.


See the babel package documentation for explanation.
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Packages suggested but not available for checking: ‘devtools’ ‘rgdal’
Running examples in ‘graticule-Ex.R’ failed
The error most likely occurred in:

> ### Name: graticule_labels
> ### Title: Create graticule labels.
> ### Aliases: graticule_labels
> 
> ### ** Examples
> 
> xx <- c(100, 120, 160, 180)
> yy <- c(-80,-70,-60, -50,-45, -30)
> prj <- "+proj=lcc +lon_0=150 +lat_0=-80 +lat_1=-85 +lat_2=-75 +ellps=WGS84"
> plot(graticule(lons = xx, lats = yy,  proj = prj))
Error in sp::spTransform(l, sp::CRS(proj)) : 
  package rgdal is required for spTransform methods
Calls: plot -> graticule -> <Anonymous> -> <Anonymous>
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 38-75 (graticule.Rmd) 
Error: processing vignette 'graticule.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Packages required but not available: ‘graph’ ‘RBGL’

Package suggested but not available for checking: ‘Rgraphviz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GreedyExperimentalDesign.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithmicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘gridGraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gridGraphics.Rcheck/00install.out’ for details.
Running ‘testpage.R’ [1s/1s]
Running the tests in ‘tests/testpage.R’ failed.
Last 13 lines of output:
  > 
  > 
  > #######################################
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  sh: gs: command not found
  Error in PostScriptTrace("testpage.ps", "testpage.xml") : 
    sorry, 'gs' cannot be found
  Execution halted
Errors in running code in vignettes:
when running code in ‘import.Rnw’
  ...

> library("grImport")
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")
sh: gs: command not found

  When sourcing 'import.R':
Error: sorry, 'gs' cannot be found
Execution halted
when running code in ‘importText.Rnw’
  ...

> library(grImport)
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")
sh: gs: command not found

  When sourcing 'importText.R':
Error: sorry, 'gs' cannot be found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

sh: gs: command not found

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in PostScriptTrace("chess_game_01.fromInkscape.eps") : 
  sorry, 'gs' cannot be found
Execution halted
Packages required but not available: ‘gRbase’ ‘graph’ ‘gRain’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Package suggested but not available for checking: ‘impute’
Package required but not available: ‘illuminaio’

Package suggested but not available for checking: ‘brassicaData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgdal’ ‘rgeos’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spatio-temporal-kriging.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gsw.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘interval’
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ashg2012.tex' failed.
LaTeX errors:
! LaTeX Error: File `a0poster.cls' not found.

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

! Emergency stop.
<read *> 
         
l.2 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘Rgraphviz’ ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gumbel.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.45 \setmarginsrb
                  {2.9cm}{1.5cm}{2.9cm}{1cm}{\headheight}{\headsep}{\foothei...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [8s/14s]
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
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Package which this enhances but not available for checking: ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 64.1Mb
  sub-directories of 1Mb or more:
    java  62.9Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/h5.Rcheck/00install.out’ for details.
Package required but not available: ‘ggtree’

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 67-70 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
HTTP error 403.
Execution halted
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: iterators
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
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 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hdm_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `soul.sty' not found.

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

! Emergency stop.
<read *> 
         
l.69 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Error in re-building vignettes:
  ...

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

---------------------
Welcome to heatmaply version 0.10.1
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 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘RNetCDF’ ‘ncdf4’
Package suggested but not available for checking: ‘synbreed’
Packages required but not available: ‘DESeq2’ ‘SummarizedExperiment’

Package suggested but not available for checking: ‘glmmADMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘marray’
Errors in running code in vignettes:
when running code in ‘hexagon_binning.Rnw’
  ...
+     shape = shape)

> hdiffplot(erode(hbF, cdfcut = 0.25), erode(hbM, cdfcut = 0.25), 
+     unzoom = 1.3)

> library("marray")

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

Error: processing vignette 'hexagon_binning.Rnw' failed with diagnostics:
 chunk 10 (label = marray1) 
Error in library("marray") : there is no package called ‘marray’
Execution halted
Packages required but not available: ‘ggimage’ ‘gridGraphics’

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

Package suggested but not available for checking: ‘RcmdrPlugin.HH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘GenomeInfoDb’ ‘GenomicRanges’ ‘rtracklayer’ ‘HiTC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HiCseg.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘XMLRPC’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/HierO.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.4Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/HiPLARM.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘multtest’ ‘qvalue’ ‘pi0’
Package unavailable to check Rd xrefs: ‘pi0’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HiveR.tex' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

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

! Emergency stop.
<read *> 
         
l.9 \documentclass{tufte-handout}\usepackage
                                            []{graphicx}\usepackage[]{color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (case,noncase) to (1,0)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hmeasure.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘Biostrings’ ‘GenomicRanges’ ‘bamsignals’ ‘Rsamtools’ ‘GenomicTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘MenuCollection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mice
Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  52 observations with no observed data.  These observations were removed

Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  45 of 4661 imputations with # donors < 5, consider increasing sdCutoff or using method='p.draw'

* miceadds 2.3-0 (2017-02-21 15:02:53)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Using_Hot_Deck_Data.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {graphicx, subfigure, float} % graphics commands^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rgraphviz’

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

> ### Name: Beijingdistricts
> ### Title: Boundaries of districts (SpatialPolygonsDataFrame) in Beijing
> ### Aliases: Beijingdistricts
> ### Keywords: hierarchical spatial data
> 
> ### ** Examples
> 
> data(Beijingdistricts)
> 
> library(spdep)
Loading required package: sp
Loading required package: Matrix
> plot(Beijingdistricts,border="light grey")
> # extract the area of each district
> library(rgeos)
Error in library(rgeos) : there is no package called ‘rgeos’
Execution halted
Error in re-building vignettes:
  ...
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()
Quitting from lines 15-18 (hsar.Rmd) 
Error: processing vignette 'hsar.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch_analysing_longitudinal_dataI.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    geyser

The following object is masked from 'package:HSAUR3':

    birds

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch_analysing_longitudinal_dataI.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: HSAUR
Loading required package: tools
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch_analysing_longitudinal_dataI.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

    nbands

Warning in points2grid(points, tolerance, round) :
  cell size from constant coordinate 3 possibly taken from other coordinate
Warning in checkhull(sh_cline, 1) :
  Mismatch of continuum line at wavelength = 1060 
  Maximum distance between continuum line & spectrum at
  Wavelength = 1060
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Hsdar-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 \usepackage
                [ansinew]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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: S3 methods ‘parse_all.function’, ‘parse_all.character’, ‘parse_all.connection’, ‘parse_all.default’, ‘replay.character’, ‘replay.default’, ‘replay.error’, ‘replay.list’, ‘replay.message’, ‘replay.recordedplot’, ‘replay.source’, ‘replay.value’, ‘replay.warning’ were declared in NAMESPACE but not found
Warning: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object 'force_v1'
Quitting from lines 40-41 (develop_advanced.Rmd) 
Error: processing vignette 'develop_advanced.Rmd' failed with diagnostics:
could not find function "parse_all"
Execution halted
Package required but not available: ‘edgeR’

Package suggested but not available for checking: ‘HTSFilter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DESeq2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
    doc    1.4Mb
Packages required but not available:
  ‘GenomicRanges’ ‘GenomicFeatures’ ‘GenomeInfoDb’ ‘rtracklayer’
  ‘biomaRt’ ‘genoset’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hwde.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \newcommand
               {\keywords}[1]{\addvspace{\baselineskip}\noindent{{\bf Keywor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HWEBayes-Guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \renewcommand
                 {\baselinestretch}{1}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘gRbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘rgdal’
Error in re-building vignettes:
  ...

Attaching package: ‘Brobdingnag’

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

    max, min, prod, range, sum

Loading required package: hyperdirichlet
Loading required package: abind
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'correspondence.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    sd, sigma

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

    is.primitive

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hypergeometric.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Consider 'structure(list(), *)' instead.
Warning in structure(x, class = unique(c("AsIs", oldClass(x)))) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Tracing function "spc.fit.poly.below" in package "hyperSpec"
Tracing function "spc.fit.poly.below" in package "hyperSpec"
Tracing function "spc.fit.poly.below" in package "hyperSpec"
Tracing function "spc.fit.poly.below" in package "hyperSpec"
Untracing function "spc.fit.poly.below" in package "hyperSpec"
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'baseline.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                []{helvet}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IalsaSynthesis)
  > 
  > test_check("IalsaSynthesis")
  Error in loadNamespace(name) : there is no package called 'devtools'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Package required but not available: ‘nem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.1Mb
Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `apa6.cls' not found.

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

! Emergency stop.
<read *> 
         
l.2 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Rglpk’
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  testthat results ================================================================
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.3Mb
    doc    2.1Mb
    libs   8.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Rcpp
Loading required package: coda
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'icenReg.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.6Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pritikin-schmidt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  14.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ilc.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     17.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Packages suggested but not available for checking: ‘Rmpfr’ ‘gmp’
Running examples in ‘IMIFA-Ex.R’ failed
The error most likely occurred in:

> ### Name: G_expected
> ### Title: 1st Moment of the Dirichlet / Pitman-Yor processes
> ### Aliases: G_expected
> 
> ### ** Examples
> 
> G_expected(N=50, alpha=19.23356)
Error in (function (N, alpha, discount = 0L)  : 
  object 'mpfrind' not found
Calls: G_expected -> do.call -> mapply -> <Anonymous>
Execution halted
Package required but not available: ‘imputeLCMD’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'imputeTS-Time-Series-Missing-Value-Imputation-in-R.tex' failed.
LaTeX errors:
! LaTeX Error: File `environ.sty' not found.

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

! Emergency stop.
<read *> 
         
l.317 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Error in re-building vignettes:
  ...
Loading required package: permute
Warning in wilcox.test.default(indvar.barcelona$B, indvar.moia$B) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(Spec.ind.barcelona, Spec.ind.moia) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(O.barcelona.ind, O.moia.ind) :
  cannot compute exact p-value with ties
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PigeonExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘minfi’
Error in re-building vignettes:
  ...
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: survival

Attaching package: 'InformativeCensoring'

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

    cox.zph

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gamma_imputation_Jackson_2014.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘rcdd’ ‘blackbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘easypackages’ ‘pacman’
Packages unavailable to check Rd xrefs: ‘easypackages’, ‘pacman’
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.
Package which this enhances but not available for checking: ‘psgp’
Package required but not available: ‘a4Core’

Packages suggested but not available for checking:
  ‘MLP’ ‘biomaRt’ ‘org.Hs.eg.db’ ‘a4Base’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Interatrix.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Package required but not available: ‘Rdisop’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘Biostrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘iotools/libs/iotools.so’:
  Found non-API call to R: ‘getConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'IPMpack_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘HH’
Errors in running code in vignettes:
when running code in ‘IPSUR.Rnw’
  ...
> library(TeachingDemos)

> plot(z.test(PlantGrowth$weight, stdev = 0.7), "Conf")
Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

  When sourcing 'IPSUR.R':
Error: could not find function "normal.and.t.dist"
Execution halted
Error in re-building vignettes:
  ...

    mnorm

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

    cm

Warning in sqrt(sigma2) : NaNs produced
Warning in sqrt(sigma2) : NaNs produced

Attaching package: 'TeachingDemos'

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

    faces, slider

Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

Error: processing vignette 'IPSUR.Rnw' failed with diagnostics:
 chunk 250 
Error in normal.and.t.dist(mu.H0 = mu, obs.mean = obs.mean, std.dev = std.dev,  : 
  could not find function "normal.and.t.dist"
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'iqLearn.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'irace-package.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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
Packages required but not available: ‘graph’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10  \usepackage
                 [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isotone.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > setwd(tempdir())
  > 
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Package required but not available: ‘partitions’

Depends: includes the non-default packages:
  ‘partitions’ ‘VGAM’ ‘MASS’ ‘ape’ ‘apTreeshape’ ‘geiger’ ‘gtools’
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.
Package required but not available: ‘lfa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'JADE-BSSasymp.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {authblk}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
10: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
11: eval(expr, p)
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 = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Jdmbs.Rcheck/vign_test/Jdmbs")
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: ‘org.Hs.eg.db’ ‘AnnotationDbi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("jiebaR")
  Loading required package: jiebaR
  Loading required package: jiebaRD
  Error in library(devtools) : there is no package called 'devtools'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.3Mb
Package required and available but unsuitable version: ‘psych’

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.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'technical.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
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.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'json-opencpu.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘KEGGgraph’ ‘biomaRt’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kcirt.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ade4
Loading required package: lattice
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simulation.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \title
          {KDETrees Simulations}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titling.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘org.Hs.eg.db’
Package suggested but not available for checking: ‘stsm’
Package unavailable to check Rd xrefs: ‘stsm’
Running examples in ‘KFKSDS-Ex.R’ failed
The error most likely occurred in:

> ### Name: DS
> ### Title: Disturbance Smoother for State Space Models
> ### Aliases: DS DS.deriv
> ### Keywords: ts, model
> 
> ### ** Examples
> 
> # local level plus seasonal model with arbitrary parameter values
> # for the 'JohnsonJohnson' time series
> m <- stsm::stsm.model(model = "llm+seas", y = JohnsonJohnson, 
+   pars = c("var1" = 2, "var2" = 15, "var3" = 30))
Error in loadNamespace(name) : there is no package called ‘stsm’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \input
          {header}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘illustration.png’, ‘kinn.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
Package required but not available: ‘kelvin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/kmcudaR.Rcheck/00install.out’ for details.
Warning: parse error in file '02_fromLongitudinalData.r':
invalid multibyte character in parser at line 1
'library' or 'require' call not declared from: ‘codetools’
Running ‘01_testDistance3d.r’ [0s/1s]
Running the tests in ‘tests/01_testDistance3d.r’ failed.
Complete output:
  > source("../R/distance3d.r")
  Error in file(filename, "r", encoding = encoding) : 
    cannot open the connection
  Calls: source -> file
  In addition: Warning message:
  In file(filename, "r", encoding = encoding) :
    cannot open file '../R/distance3d.r': No such file or directory
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: knotR
Warning in plot.window(...) : "box" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in box(...) : "box" is not a graphical parameter
Warning in title(...) : "box" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'knot.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    rename, round_any

Warning: Removed 27 rows containing missing values (geom_path).
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kobe.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'koRpus_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘pcalg’ ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Loading required package: relations
Loading required package: sets
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsfonts,hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'variablekey.tex' failed.
LaTeX errors:
! LaTeX Error: File `cancel.sty' not found.

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

! Emergency stop.
<read *> 
         
l.33 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: boot
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'laeken-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `soul.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Package unavailable to check Rd xrefs: ‘R2jags’
Packages required but not available: ‘GOstats’ ‘GOSemSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs           9.9Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.8Mb
    libs      3.4Mb
Packages suggested but not available for checking: ‘Rgraphviz’ ‘graph’
Running ‘test-all.R’ [45s/65s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  testthat results ================================================================
  OK: 300 SKIPPED: 0 FAILED: 2
  1. Error: Effects (@test-inference.R#27) 
  2. Error: Graph attributes (@test-model.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘geojsonio’
Running ‘test-all.R’ [10s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Actual value: "c++ exception (unknown reason)"
  
  
  2. Failure: lawn_centroid fails correctly (@test-centroid.R#50) ----------------
  error$message does not match "Unexpected number".
  Actual value: "c++ exception (unknown reason)"
  
  
  testthat results ================================================================
  OK: 805 SKIPPED: 0 FAILED: 2
  1. Failure: lawn_centroid fails correctly (@test-centroid.R#47) 
  2. Failure: lawn_centroid fails correctly (@test-centroid.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.19 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘iterpc’ ‘gmp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘topicmodels’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'details.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘chopsticks’

Packages suggested but not available for checking:
  ‘rtracklayer’ ‘GenomicRanges’ ‘GenomeInfoDb’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘sf’ ‘rgdal’ ‘rgeos’
Running examples in ‘leaflet-Ex.R’ failed
The error most likely occurred in:

> ### Name: addRasterImage
> ### Title: Add a raster image as a layer
> ### Aliases: addRasterImage projectRasterForLeaflet
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
> 
> r <- raster(xmn=-2.8, xmx=-2.79, ymn=54.04, ymx=54.05, nrows=30, ncols=30)
> values(r) <- matrix(1:900, nrow(r), ncol(r), byrow = TRUE)
> crs(r) <- CRS("+init=epsg:4326")
> 
> leaflet() %>% addTiles() %>%
+   addRasterImage(r, colors = "Spectral", opacity = 0.8)
Error in .requireRgdal() : package 'rgdal' is not available
Calls: %>% ... projectRasterForLeaflet -> <Anonymous> -> .requireRgdal
Execution halted
Running ‘test-all.R’ [3s/4s]
  Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 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
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:
  ...
Loading required package: lhs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'augmentLHS_Example.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {graphicx}                  % for figure inclusion^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/libstableR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [69s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [using inverse distance weighting]
  [using Delaunay triangulation]
  [using universal kriging]
  2284747 bytes written
  1. Failure: Test if I/O are equal (@test-writeLAS.R#15) ------------------------
  i@data not equal to o@data.
  Column 'Z': Mean relative difference: 0.001260578
  
  
  testthat results ================================================================
  OK: 148 SKIPPED: 0 FAILED: 1
  1. Failure: Test if I/O are equal (@test-writeLAS.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘Rmpfr’

Depends: includes the non-default packages:
  ‘sn’ ‘moments’ ‘BB’ ‘Bolstad2’ ‘optimx’ ‘Rmpfr’
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.
Error in re-building vignettes:
  ...
Loading required package: parallel

DEoptim package
Differential Evolution algorithm in R
Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich

Loading required package: ggplot2
Loading required package: gtools
Loading required package: rtf
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usage.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'linkcomm.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LinRegInteractive.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      18.2Mb
    testdata   1.5Mb
Package required but not available: ‘LDheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmm-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: lmodel2
RMA was not requested: it will not be computed.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mod2user.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘samr’

Package suggested but not available for checking: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  ...
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
Error in re-building vignettes:
  ...
Loading required package: LogConcDEAD
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: logcondens
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LogConcDEAD.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \renewcommand
                 {\textfraction}{0.05}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plotGlm.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
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
Packages suggested but not available for checking: ‘rjags’ ‘devtools’
Packages unavailable to check Rd xrefs: ‘rjags’, ‘devtools’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bdt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                [margin=1.0in]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘rgdal’ ‘rgeos’
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    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.
Quitting from lines 418-422 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Error in re-building vignettes:
  ...
Loading required package: magree
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'landis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘Biostrings’ ‘pdInfoBuilder’ ‘convert’ ‘marray’ ‘GEOquery’
  ‘GEOmetadb’ ‘annotate’ ‘GO.db’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘RBGL’
  ‘genefilter’ ‘simpleaffy’ ‘impute’ ‘oligo’ ‘beadarray’ ‘lumi’
  ‘GOstats’ ‘globaltest’ ‘WGCNA’ ‘Rgraphviz’ ‘ssize’ ‘KEGGREST’
  ‘KEGGgraph’ ‘graph’ ‘Category’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Package suggested but not available for checking: ‘RNetCDF’
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: quadprog
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Mangrove.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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]="./webshot875a24484c01.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot875a24484c01.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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotca4c591575d8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotca4c591575d8.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 196-197 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Packages unavailable to check Rd xrefs: ‘rgdal’, ‘OpenStreetMap’
Running examples in ‘mapmisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: netherlands
> ### Title: Data from the Netherlands
> ### Aliases: netherlands nldElev nldTiles nldCities world
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> # soil data
> library("sp")
> data("meuse")
> coordinates(meuse) <- ~x+y
> 
> if(require('rgdal', quietly=TRUE)) {
+ 	 proj4string(meuse) <- CRS("+init=epsg:28992")
+ } else {
+  proj4string(meuse) <- CRS(
+   paste("+proj=sterea +lat_0=52.15616055555555 +lon_0=5.38763888888889",
+     "+k=0.9999079 +x_0=155000 +y_0=463000 +ellps=bessel +units=m +no_defs"
+   )
+  )
+ }
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgdal’
> 
> meuse$soilFac = factor(meuse$soil, levels=c(1,2,3), 
+ 	labels=c("Calcareous","Non-Calc's","Red Brick"))
> soilCol = colourScale(meuse$soilFac)
> 	
> data("netherlands")
> 
> map.new(meuse)
> plot(nldTiles,add=TRUE)
> points(nldCities)
> text(nldCities,label=nldCities$name, pos=2)
> points(meuse, pch=16, col=soilCol$plot)
> legend('topleft', fill=soilCol$col,legend=soilCol$legend)
> insetMap(meuse, "bottomright",map=world)
Error in .requireRgdal() : package 'rgdal' is not available
Calls: insetMap -> projectExtent -> .requireRgdal
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: raster
Quitting from lines 510-529 (mapmisc.rnw) 
Error: processing vignette 'mapmisc.rnw' failed with diagnostics:
object 'nldCitiesRot' not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Checking rgeos availability: TRUE
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: non-unique values when setting 'row.names': ‘37055’, ‘37095’

Error: processing vignette 'combine_maptools.Rnw' failed with diagnostics:
 chunk 18 
Error in unionSpatialPolygons(nc90, IDs = paste(nc90$ST, nc90$CO, sep = "")) : 
  package rgeos required for unionSpatialPolygons
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Chunk margins3a:
  lm(formula = mpg ~ wt * I(wt^2) * hp * I(hp^2), data = mtcars) 

m <- lm(mpg ~ wt * I(wt^2) * hp * I(hp^2), data = mtcars)
margins(m)

Number of messages:
message 
      6 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TechnicalDetails.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AsymptoticMarkowitz.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.92 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EMDerivation.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ASGSCA’
Package which this enhances but not available for checking: ‘graph’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘MaxentVariableSelection.Rmd’, ‘MaxentVariableSelection.html’,
    ‘auto/library.el’, ‘library.bib’
Error in re-building vignettes:
  ...
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Number of samples considered (number of samples found): 100(0) 
Finished

Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MBHdesign.tex' failed.
LaTeX errors:
! LaTeX Error: File `nicefrac.sty' not found.

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

! Emergency stop.
<read *> 
         
l.93 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
Error in re-building vignettes:
  ...

Loading required package: sandwich

Attaching package: ‘party’

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

    varimp

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SurvivalEnsembles.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘Rglpk’ ‘glpkAPI’

Packages suggested but not available for checking: ‘Rgraphviz’ ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CourseNotes.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {makeidx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mcmcse_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.78 \title
           {An Introduction to Estimating Monte Carlo Standard Errors with R...
!  ==> Fatal error occurred, no output PDF file produced!
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.
Quitting from lines 228-229 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.4Mb
Error in re-building vignettes:
  ...
Loading required package: meteoland
Loading required package: sp
Loading required package: qmap
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: spdep
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FireBehaviour.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Effect decomposition on the scale of the linear predictor
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on exp(scale of the linear predictor)
conditional on: gender, educ, age 
with x* = 0, x = 1

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'medflex.tex' failed.
LaTeX errors:
! LaTeX Error: File `nccmath.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mediation-old.tex' failed.
LaTeX errors:
! LaTeX Error: File `arydshln.sty' not found.

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

! Emergency stop.
<read *> 
         
l.47 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Packages required but not available: ‘pcaMethods’ ‘seqLogo’

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
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.
Package unavailable to check Rd xrefs: ‘untb’
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'memgeneTutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘aws.s3’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'memuse-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.189 \usepackage
                 {fancyhdr}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘RGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstanarm’
Error in re-building vignettes:
  ...

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

Working directory is /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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

Quitting from lines 320-333 (Using_predictInterval.Rmd) 
Error: processing vignette 'Using_predictInterval.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.4Mb
Package required but not available: ‘crmn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [53s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("metafor")
  1. Error: escalc() works correctly for measure='COR/UCOR/ZCOR' (@test_misc_escalc.r#127) 
  Please install the 'gsl' package to use measure='UCOR'.
  1: escalc(measure = "UCOR", ri = ri, ni = ni, data = dat, subset = c(1, 13, 33, 102)) at testthat/test_misc_escalc.r:127
  2: escalc.default(measure = "UCOR", ri = ri, ni = ni, data = dat, subset = c(1, 13, 
         33, 102))
  3: .Fcalc(1/2, 1/2, (ni - 2)/2, 1 - ri^2)
  4: stop("Please install the 'gsl' package to use measure='UCOR'.")
  
  testthat results ================================================================
  OK: 777 SKIPPED: 30 FAILED: 1
  1. Error: escalc() works correctly for measure='COR/UCOR/ZCOR' (@test_misc_escalc.r#127) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘EBImage’ ‘gWidgetsRGtk2’

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

Package suggested but not available for checking: ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘GEOquery’ ‘org.Hs.eg.db’ ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’
  ‘hgu95av2.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'metaMA.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘runjags’ ‘rjags’
Packages required but not available: ‘GSEABase’ ‘genefilter’ ‘impute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Packages suggested but not available for checking:
  ‘HTSFilter’ ‘DESeq’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: indirectEffect
> ### Title: Estimate the asymptotic covariance matrix of standardized or
> ###   unstandardized indirect and direct effects
> ### Aliases: indirectEffect
> ### Keywords: compute effect sizes
> 
> ### ** Examples
> 
> ## A correlation matrix as input
> x <- matrix(c(1, 0.4, 0.2, 0.4, 1, 0.3, 0.2, 0.3, 1), ncol=3)
> dimnames(x) <- list( c("y", "m", "x"), c("y", "m", "x") )
> indirectEffect(x, n=300)
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: indirectEffect -> mxRun -> runHelper
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 38-39 (metaviz.Rmd) 
Error: processing vignette 'metaviz.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: qmap
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Meteorology.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  10.5Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'basic-dutils.ltx' failed with diagnostics:
Running 'texi2dvi' on 'basic-dutils.ltx' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {etex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mev-vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: mev-vignette.aux
I couldn't open style file apalike2.bst
---line 44 of file mev-vignette.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file mev-vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: MGLM
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘biomaRt’

Package suggested but not available for checking: ‘grasp2db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabulary.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette1.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \IfFileExists
                  {upquote.sty}{\usepackage{upquote}}{}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: survival
Loading required package: texreg
Version:  1.36.23
Date:     2017-03-03
Author:   Philip Leifeld (University of Glasgow)

Please cite the JSS article in your publications -- see citation("texreg").
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhurdle.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {amssymb, amsfonts}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘sjlabelled’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `blindtext.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [bf]{caption2}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘sybilSBML’ ‘glpkAPI’
Error in re-building vignettes:
  ...
     # Call miRNAss with default parameters
     p = miRNAss(x,y)
     
     # Calculate some performance measures
     SE = mean(p[ celegans$CLASS & y==0] > 0)
     SP = mean(p[!celegans$CLASS & y==0] < 0)
     cat("Sensitivity: ", SE, "\nSpecificity: ", SP, "\n")
     

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'miRNAss.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \renewcommand
                 \Affilfont{\itshape\small}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘globaltest’ ‘GlobalAncova’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Package required but not available: ‘RcppGSL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mixor.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Error in re-building vignettes:
  ...
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  1 y value <= 0 omitted from logarithmic plot
species, w\\_inf, w\\_mat, beta, sigma, r\\_max, k\\_vbError in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mizer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.45 \numberwithin
                  {equation}{section}	% Equation numbers relative to section...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in file(con, "r") : cannot open the connection
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FOCUS_Z.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \input
           {header}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages unavailable to check Rd xrefs: ‘genefilter’, ‘limma’
Package required but not available: ‘rsgcc’

Packages suggested but not available for checking:
  ‘GeneSelector’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mldr.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in lmList(normexam ~ standLRT + sex | school, Exam, subset = type ==  :
  Fitting failed for 1 group(s), probably because a factor only had one level
refitting model(s) with ML (instead of REML)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StarData.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Exercises.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘Rfast’ ‘rknn’
Running ‘run-base.R’ [387s/543s]
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
         test.i = test.i, measures = measures, weights = weights, rdesc = rin$desc, model = model, 
         extract = extract, show.info = show.info)
  7: train(learner, task, subset = train.i, weights = weights[train.i])
  8: requireLearnerPackages(learner)
  9: requirePackages(learner$package, why = stri_paste("learner", learner$id, sep = " "), 
         default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  testthat results ================================================================
  OK: 2711 SKIPPED: 2 FAILED: 2
  1. Error: NoFeaturesModel works with FilterWrapper (@test_base_NoFeaturesModel.R#30) 
  2. Error: predict.threshold (@test_base_predict.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Re-fitting to get Hessian


Re-fitting to get Hessian


Re-fitting to get Hessian

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mlt.tex' failed.
LaTeX errors:
! LaTeX Error: File `accents.sty' not found.

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

! Emergency stop.
<read *> 
         
l.27 \usepackage
                {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MNP.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.2-6, (SVN revision 651)
 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: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.2-4 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ExploreModelMap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \setlength
              {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modelObj.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘rstanarm’
Running ‘Test.R’ [2s/10s]
Running the tests in ‘tests/Test.R’ failed.
Last 13 lines of output:
  +   Dates <- GetDates(SubsetExample$lat, SubsetExample$long, Product)[1:2]
  + 
  +   GetSubset(Lat = SubsetExample$lat, Long = SubsetExample$long, Product = Product, Band = Band,
  +             StartDate = Dates[1], EndDate = Dates[1], KmAboveBelow = 0, KmLeftRight = 0)
  + 
  +   MODISSubsets(LoadDat = SubsetExample, Product = "MCD12Q1", Bands = c("Land_Cover_Type_1"),
  +                Size = c(1,1), StartDate = TRUE)
  + 
  +   MODISSummaries(LoadDat = SubsetExample, Product = "MCD12Q1", Band = "Land_Cover_Type_1",
  +                  ValidRange = c(0,254), NoDataFill = 255, ScaleFactor = 1, StartDate = TRUE)
  + }
  Error in Product == GetProducts() : 
    comparison of these types is not implemented
  Calls: GetBands
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingMODISTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
Loading required package: splines
Warning: max number of iterations attained
Warning: max number of iterations attained
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    cm

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
Warning in matrix(l, nrow = 1) %*% solve(V1) %*% matrix(l, ncol = 1)/sigma2 :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mombf.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {lscape}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.0Mb
    libs   2.3Mb
Packages suggested but not available for checking: ‘fftw’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
Error in re-building vignettes:
  ...
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

Attaching package: 'monitoR'

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

    readMP3

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'monitoR_QuickStart.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.4Mb
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.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modelling.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MortHump.Rnw’
Error in re-building vignettes:
  ...
Loading required package: parallel
Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

Using parallel package.
  * Set seed with set.rseed().
  * Disable this message with options(`mosaic:parallelMessage` = FALSE)

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Resampling.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! LaTeX Error: File `pst-node.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mountainplot.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \setlist
             {nolistsep}  % Reduce spacing between list items^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘CGHcall’ ‘aroma.affymetrix’ ‘aroma.cn’ ‘aroma.core’ ‘aroma.light’
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.
Packages suggested but not available for checking:
  ‘asreml’ ‘happy.hbrem’ ‘Heatplus’ ‘VPdtw’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mptinr_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgdal’ ‘devtools’
Running examples in ‘mptools-Ex.R’ failed
The error most likely occurred in:

> ### Name: mp2sp
> ### Title: Create a SpatialPointsDataFrame describing Metapop population
> ###   centroids
> ### Aliases: mp2sp
> ### Keywords: spatial
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> r <- system.file('example_001.tif', package='mptools')
> coords <- mp2xy(mp, r, 9.975)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: mp2xy ... <Anonymous> -> <Anonymous> -> .local -> .rasterObjectFromFile
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.
Extracting simulation results from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Extracting population metadata from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Quitting from lines 136-140 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Found the following significant warnings:
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target [-Wtarget-lifetime]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mra.Rcheck/00install.out’ for details.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Bromaghin_etal_2013_OJE.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MRCV-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.100 \usepackage
                 {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘geojsonio’ ‘rgdal’ ‘rgeos’ ‘rmapshaper’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2Extras’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

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

    decompose, spectrum

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

    union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mRMRe.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 required but not available: ‘AnnotationDbi’

Packages suggested but not available for checking:
  ‘GO.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘Biostrings’
Packages required but not available: ‘mzR’ ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
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.
Package required but not available: ‘MSeasy’

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
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.
sh: xgettext: command not found
sh: msgmerge: command not found
sh: msgmerge: command not found
sh: msgfmt: command not found
sh: msgconv: command not found
Quitting from lines 136-138 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
running msgconv on 'R-en@quot' UTF-8 localization failed
Execution halted
Package required but not available: ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in coxph(Surv(time, status) ~ ccr5 * factor(trans) + strata(trans),  :
  X matrix deemed to be singular; variable 2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {fullpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘cartography’
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 43-53 (MTA_Scenario.Rmd) 
Error: processing vignette 'MTA_Scenario.Rmd' failed with diagnostics:
there is no package called 'cartography'
Execution halted
Error in re-building vignettes:
  ...
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chfls1.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pgirmess’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   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.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SIRtrans.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \usepackage
                {mathtools}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘pcaMethods’ ‘gridGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Error in re-building vignettes:
  ...
Loading required package: abind

Attaching package: ‘multipol’

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

    single

Loading required package: polynom
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multisensi-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `epic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘kohonen’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: glmnet
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MultiVarSel.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Attaching package: ‘multivator’

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

    levels, rbind

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cias.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘mutoss’

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

> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'article.ltx' failed with diagnostics:
Running 'texi2dvi' on 'article.ltx' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [noend]{algpseudocode}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Packages required but not available:
  ‘autothresholdr’ ‘BiocParallel’ ‘EBImage’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Running ‘doRUnit.R’ [14s/21s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Number of failures: 1 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 2 errors, 1 failure
  ERROR in test.5PL: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
  FAILURE in test.bcrm: Error in checkEqualsNumeric(mean(fits$median.coef), 4.01789, tolerance = tolerance.jags) : 
    'is.NA' value mismatch: 0 in current 1 in target
  
  ERROR in test.ncal: Error in 0:(ncol(single.fit$coefficients) - 1) : argument of length 0
  Error: 
  
  unit testing failed (#test failures: 1, #R errors: 2)
  
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in loadNamespace(name) : there is no package called 'rjags'
Error in loadNamespace(name) : there is no package called 'rjags'
Error in loadNamespace(name) : there is no package called 'rjags'
Quitting from lines 100-102 (nCal-vignette.Rnw) 
Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
argument of length 0
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Package suggested but not available for checking: ‘BiocInstaller’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quick-start.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [colorlinks=true, urlcolor=blue, pdfborder={0 0 0}]{hyperref...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  computing positions for slice 4
  computing positions for slice 5
  computing positions for slice 6
  computing positions for slice 7
  computing positions for slice 8
  computing positions for slice 9
  computing positions for slice 10
  computing positions for slice 11
rendering splines for each vertex ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ndtv.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Error in re-building vignettes:
  ...
Loading required package: neldermead
Loading required package: optimbase
Loading required package: Matrix
Loading required package: optimsimplex
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'neldermead_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Warning in coxdetails$hazard/exp(apply(coxdetails$x, 2, mean) %*% beta) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in ((C[exposureindex, ] - C[nexposures + 1, ]) %*% covariatesurvs) *  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NestedCohort.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {psfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘AnnotationDbi’ ‘graph’ ‘samr’

Package suggested but not available for checking: ‘KEGG.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   2.9Mb
Package suggested but not available for checking: ‘hasseDiagram’
Package unavailable to check Rd xrefs: ‘hasseDiagram’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.0Mb
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.
Packages required but not available: ‘WGCNA’ ‘minet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/Sampson.zip'
Content type 'application/zip' length 2182 bytes
==================================================
downloaded 2182 bytes

Warning in get.vertex.attribute.active(net, "happiness", onset = 2.5, terminus = 4.5) :
  Multiple attribute values matched query spell for attribute happiness.active on some vertices. Only earliest value used

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'networkDynamic.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘KEGGgraph’

Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ngram-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.217 \usepackage
                 {fancyhdr}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    CppCode       12.0Mb
    R              3.0Mb
    classic-bugs   1.5Mb
    include        3.8Mb
    libs           8.3Mb
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Running ‘test-all.R’ [26s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  Error in library(devtools) : there is no package called 'devtools'
  Calls: <Anonymous> ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 198 SKIPPED: 0 FAILED: 2
  1. Error: Nlsy79Gen2 (@test-column-utilities.R#89) 
  2. Error: RenameNlsyColumn (@test-column-utilities.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
plot.isp: no visible global function definition for ‘median’
plot.isp: no visible global function definition for ‘plot’
plot.isp: no visible global function definition for ‘lines’
plot.nmcd: no visible global function definition for ‘median’
plot.nmcd: no visible global function definition for ‘plot’
plot.nmcd: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines median plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘RcppOctave’ ‘doMPI’ ‘devtools’ ‘Biobase’
.wrapResult: no visible global function definition for ‘exprs’
algorithm,NMFStrategyOctave: no visible global function definition for
  ‘fstop’
evar,ANY: no visible binding for global variable ‘Biobase’
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable ‘n’
nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global
  variable ‘RNGobj’
nmfModel,formula-ANY : merge_pdata: no visible global function
  definition for ‘pData’
nmfModel,formula-ANY: no visible global function definition for ‘exprs’
rss,matrix: no visible binding for global variable ‘Biobase’
Undefined global functions or variables:
  Biobase RNGobj exprs fstop n pData
Packages unavailable to check Rd xrefs: ‘RcppOctave’, ‘Biobase’
Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NMF-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: NMOF
found several files...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DEnss.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NoiseFiltersR.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  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)

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nopaco.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

 You can now run (pdf)latex on ‘noweb.tex’ 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'noweb.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nplr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \setlength
               {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
2: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
3: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
4: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
Execution halted
Error in re-building vignettes:
  ...
Nonparametric Kernel Methods for Mixed Datatypes (version 0.60-3)
[vignette("np_faq",package="np") provides answers to frequently asked questions]
[vignette("np",package="np") an overview]
[vignette("entropy_np",package="np") an overview of entropy-based methods]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'entropy_np.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘aroma.core’ ‘aroma.affymetrix’

Depends: includes the non-default packages:
  ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
  ‘aroma.affymetrix’ ‘DNAcopy’
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.
Package suggested but not available for checking: ‘PMA’
Running examples in ‘nscancor-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcancor
> ### Title: Non-Negative and Sparse Multi-Domain CCA
> ### Aliases: mcancor
> 
> ### ** Examples
> 
> library(glmnet)
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

> data(breastdata, package="PMA")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘PMA’
Calls: data -> find.package
Execution halted
Packages required but not available: ‘EBImage’ ‘bioimagetools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'NUCOMBog.ltx' failed with diagnostics:
Running 'texi2dvi' on 'NUCOMBog.ltx' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'oaih.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
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.
Unexported object imported by a ':::' call: ‘tree:::tree.matrix’
  See the note in ?`:::` about the use of this operator.
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.
Packages suggested but not available for checking: ‘ncdf4’ ‘rgdal’ ‘marmap’
Packages unavailable to check Rd xrefs: ‘rgdal’, ‘marmap’, ‘ncdf4’
Error in re-building vignettes:
  ...
Loading required package: lattice
Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'odfWeave.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 64.4Mb
  sub-directories of 1Mb or more:
    libs  64.0Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Actual value: "c++ exception (unknown reason)"
  
  
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  error$message does not match "The length value".
  Actual value: "c++ exception (unknown reason)"
  
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running examples in ‘ompr.roi-Ex.R’ failed
The error most likely occurred in:

> ### Name: with_ROI
> ### Title: Configures a solver based on 'ROI'
> ### Aliases: with_ROI
> 
> ### ** Examples
> 
> library(magrittr)
> library(ompr)
> library(ROI)
ROI: R Optimization Infrastructure
Registered solver plugins: nlminb, ecos, ipop, lpsolve, nloptr, quadprog, scs.
Default solver: auto.
> library(ROI.plugin.glpk)
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI: R Optimization Infrastructure
  Registered solver plugins: nlminb, ecos, ipop, lpsolve, nloptr, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
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:
  ...
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: File `varwidth.sty' not found.

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

! Emergency stop.
<read *> 
         
l.69 \RequirePackage{varwidth}[2009/03/30]
                                          ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  "phi" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "box" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "r" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "theta" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "phi" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onionpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: minpack.lm
Waiting for profiling to be done...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onls.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ontologyPlot’
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 80-92 (intro-to-ontologyX.Rmd) 
Error: processing vignette 'intro-to-ontologyX.Rmd' failed with diagnostics:
there is no package called 'ontologyPlot'
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/OpenCL.Rcheck/00install.out’ for details.
installed size is 110.1Mb
  sub-directories of 1Mb or more:
    libs    101.9Mb
    models    4.6Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: OpenMx
> ### Title: OpenMx: An package for Structural Equation Modeling and Matrix
> ###   Algebra Optimization
> ### Aliases: OpenMx OpenMx-package
> 
> ### ** Examples
> 
> library(OpenMx)
> data(demoOneFactor)
> # ===============================
> # = Make and run a 1-factor CFA =
> # ===============================
> 
> latents  = c("G") # the latent factor
> manifests = names(demoOneFactor) # manifest variables to be modeled
> # ====================
> # = Make the MxModel =
> # ====================
> 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)
+ )
> 
> # ===============================
> # = mxRun it and get a summary! =
> # ===============================
> 
> m1 = mxRun(m1)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: mxRun -> runHelper -> .Call
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘org.At.tair.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'optimbase_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: optimsimplex
Loading required package: optimbase
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'optimsimplex_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: clinfun
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OptInterim.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Error in .requirePackage(package) : 
  unable to find required package ‘Biobase’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Errors in running code in vignettes:
when running code in ‘ordinalgmifs.Rnw’
  ...
Loading required package: survival

> data(hccframe)

> cumulative.logit <- ordinal.gmifs(group ~ 1, x = hccframe[, 
+     -1], data = hccframe)

Execution halted

... incomplete output.  Crash?
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clm_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [amsmath,thmmarks,standard,thref]{ntheorem}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘IsoGene’ ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: orgutils
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'orgutils_examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `libertine.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘genefilter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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 ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.5Mb
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: sp
Checking rgeos availability: TRUE
Quitting from lines 63-66 (basic-maps.Rmd) 
Error: processing vignette 'basic-maps.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'overlap.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [usenames,dvipsnames,svgnames]{xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Error in re-building vignettes:
  ...
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: Removed 370 rows containing missing values (geom_point).
Warning: Removed 370 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'P2C2M_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DEU_PISA2012_description.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: GCD
This is paleofire v1.1.9 | GCD v3.0.5
trying URL 'http://blarquez.com/public/data/data_cageo.zip'
Content type 'application/zip' length 14857 bytes (14 KB)
==================================================
downloaded 14 KB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'paleofire-paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pan-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Factors are dropped from the summary
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Non-factors are dropped from the summary
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'papeR_with_latex.tex' failed.
LaTeX errors:
! LaTeX Error: File `capt-of.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: highlight
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'parallelDist.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.383 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘pcalg’ ‘Rgraphviz’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'parfm.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

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

Downloading MP data
Downloading constituency data
Warning in left_join_impl(x, y, by$x, by$y, suffix$x, suffix$y) :
  joining factor and character vector, coercing into character vector
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]="./webshoteaacee2eefe.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshoteaacee2eefe.png': No such file or directory
Quitting from lines 19-64 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partDSAvig.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partsm.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.47 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Vignette 'Japanese.Rnw' requires 'uplatex' and 'dvipdfmx'
Error: processing vignette 'Japanese.Rnw' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘patchDVI::JSweave’) for vignette with name ‘Japanese’. The following files exist in directory ‘.’: ‘Japanese.Rnw’, ‘patchDVI.Rnw’, ‘patchDVI.bib’, ‘sample.Rnw.txt’
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
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'patternplot-intro.Rmd'
Quitting from lines 11-14 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
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 ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Error in re-building vignettes:
  ...
Loading required package: pbkrtest
Loading required package: lme4
Loading required package: Matrix
refitting model(s) with ML (instead of REML)
refitting model(s) with ML (instead of REML)
   [[ suppressing 10 column names '1', '2', '3' ... ]]
   [[ suppressing 10 column names '1', '2', '3' ... ]]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbkrtest-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pcaL1.Rcheck/00install.out’ for details.
Packages required but not available: ‘graph’ ‘RBGL’ ‘gmp’

Package suggested but not available for checking: ‘Rgraphviz’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
large z may result in inaccurate quantiles
Loading required package: polynom
Loading required package: reshape2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PDQutils.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘gsl’
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])
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Package suggested but not available for checking: ‘globaltest’
Errors in running code in vignettes:
when running code in ‘penalized.Rnw’
  ...

> fit <- penalized(response, X, lambda1 = 2, lambda2 = 2, 
+     fusedl = chr)


> library(globaltest)

  When sourcing ‘penalized.R’:
Error: there is no package called ‘globaltest’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").

Error: processing vignette 'penalized.Rnw' failed with diagnostics:
 chunk 31 (label = globaltest) 
Error in library(globaltest) : there is no package called ‘globaltest’
Execution halted
Error in re-building vignettes:
  ...
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Definition.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘biomaRt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Paper_Analysis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {tikz}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in z + c(-1, 1) * sigma * qnorm((1 + conf.level)/2) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PerformanceAnalyticsChartsPresentation-Meielisalp-2007.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Error in re-building vignettes:
  ...
Loading required package: gsl
Loading required package: R2Cuba
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pgs_user.tex' failed.
LaTeX errors:
! LaTeX Error: File `path.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘seqLogo’ ‘Biostrings’
Error in re-building vignettes:
  ...
Loading required package: ape
Loading required package: seqLogo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘seqLogo’
Loading required package: seqLogo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘seqLogo’
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ancestral.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./Ancestral-figLOGO.pdf): PDF inclusion: required
 page does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
File ‘phmm/libs/phmm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘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.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: lattice
Loading required package: Matrix
Warning in lmer(m ~ -1 + t + z1 + z2 + (z1 + z2 | cluster) + offset(log(N)),  :
  calling lmer with 'family' is deprecated; please use glmer() instead
Warning in (function (fn, par, lower = rep.int(-Inf, n), upper = rep.int(Inf,  :
  failure to converge in 10000 evaluations
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0102246 (tol = 0.001, component 1)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'phmm_poisson_df.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘pavo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘R.oo’

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

Loading required package: ape
Loading required package: compoisson
Loading required package: MASS
Loading required package: ggplot2
Warning in setEquDist.GeneralSubstitution(this, value, force = TRUE) :
  The provided probabilities have been rescaled in order to sum to one!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!


Execution halted
Package required but not available: ‘qvalue’

Package suggested but not available for checking: ‘OCplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RPostgreSQL’ ‘topicmodels’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pivotalr.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
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.
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]="./webshotc6164697968e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc6164697968e.png': No such file or directory
Quitting from lines 61-64 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘devtools’ ‘ReportingTools’
Package unavailable to check Rd xrefs: ‘devtools’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pkgmaker-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘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.
Package which this enhances but not available for checking: ‘gmp’
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
Error in re-building vignettes:
  ...
Warning in rug(subTics) : some values will be clipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plan.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {boxedminipage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicRanges’ ‘VariantAnnotation’ ‘Rsamtools’ ‘rtracklayer’
  ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

Package suggested but not available for checking: ‘latticist’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq’
Error in re-building vignettes:
  ...
Saving an object of class 'gstatModel'...
Subsetting observations to fit the prediction domain in 2D...
Generating predictions using the trend model (RK method)...
Running 5-fold cross validation using 'krige.cv'...
Creating an object of class "SpatialPredictions"
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...
Writing to KML...
Closing  fmd_ST.kml
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss1079.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘mvabund’
Error in re-building vignettes:
  ...

Attaching package: ‘pls’

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

    loadings

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pls-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘survcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: value[[3L]](cond)
  6: errorHandler(req, res, e)
  7: .makeMessage(..., domain = domain)
  8: lapply(list(...), as.character)
  9: FUN(X[[i]], ...)
  10: as.character.default(X[[i]], ...)
  
  Error in test %||% "(unknown)" : 
    no function to return from, jumping to top level
  testthat results ================================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: htmlwidgets serialize properly (@test-serializer-htmlwidgets.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...


Attaching package: 'gridExtra'

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

    combine

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

Execution halted
Package required but not available: ‘gWidgetsRGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘polmineR.Rcpp’ ‘europarl.en’ ‘rcqp’
as.popgraph: no visible global function definition for ‘is’
centroid_distance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘cov’
decorate_graph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘lines’
overlay_popgraph: no visible global function definition for ‘points’
overlay_popgraph: no visible global function definition for ‘text’
permute_popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘qchisq’
popgraph: no visible global function definition for ‘prcomp’
popgraph: no visible global function definition for ‘var’
read.popgraph: no visible global function definition for ‘read.table’
test_congruence: no visible global function definition for ‘cor.test’
to_data.frame: no visible global function definition for ‘is’
to_pgraph: no visible global function definition for ‘is’
write_popgraph: no visible global function definition for ‘is’
write_popgraph : <anonymous>: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  cor.test cov is lines points prcomp qchisq read.table text var
  write.csv
Consider adding
  importFrom("graphics", "lines", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor.test", "cov", "prcomp", "qchisq", "var")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Popgraph.tex’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Loading required package: boot
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'popKorn.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
8             8         8    18      0  1.6844357  0.53539884          2     F
9             9         9    20      1  0.9113913 -0.55527835          2     F
10           10        10    12      1  0.2374303  1.77950291          1     M
# ... with more rows

> library(VariantAnnotation)

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

    select

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

    filter

Error in makeSchemaFromData(dna, "dna") : 
  ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
Starting clinical
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Starting samples
Starting dna
Error in filter_.Database(.data, .dots = lazyeval::lazy_dots(...)) : 
  ERROR: Cannot uniquely map columns to table, try using: tableX.columnY
Starting gender
Starting clinical
Starting samples
Starting dna

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Error in re-building vignettes:
  ...
Warning in replayPlot(x) : "border" is not a graphical parameter
Warning in replayPlot(x) : "fill" is not a graphical parameter
Warning in replayPlot(x) : "border" is not a graphical parameter
Warning in replayPlot(x) : "fill" is not a graphical parameter
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algo.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \usepackage
                {mathtools}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    object.size

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

    startsWith

Calculating life expectancy at birth ...
... done
Calculating net number of migrants ...
... done
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'burkina-faso-females.tex' failed.
BibTeX errors:
The top-level auxiliary file: burkina-faso-females.aux
I couldn't open style file apa.bst
---line 19 of file burkina-faso-females.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file burkina-faso-females.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

> suppressMessages(library(ROI.plugin.quadprog))

> suppressMessages(library(ROI.plugin.glpk))

  When sourcing ‘ROI_vignette.R’:
Error: there is no package called ‘ROI.plugin.glpk’
Execution halted
when running code in ‘custom_moments_objectives.Rnw’
  ...
+     r .... [TRUNCATED] 

> opt.sd <- optimize.portfolio(R, SD.portf, optimize_method = "ROI", 
+     momentFUN = "sigma.robust")
Loading required package: MASS

  When sourcing ‘custom_moments_objectives.R’:
Error: No solution found: Error in UseMethod("as.constraint") : 
  no applicable method for 'as.constraint' applied to an object of class "c('matrix', 'list')"
Execution halted
when running code in ‘portfolio_vignette.Rnw’
  ...

> maxret <- add.objective(portfolio = init, type = "return", 
+     name = "mean")

> opt_maxret <- optimize.portfolio(R = R, portfolio = maxret, 
+     optimize_method = "ROI", trace = TRUE)

  When sourcing ‘portfolio_vignette.R’:
Error: paste0("package:", plugin) %in% search() || requireNamespace(plugin,  .... is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DesignThoughts.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {ctable}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectEstim.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectHFT.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
  the condition has length > 1 and only the first element will be used
Warning in if (alpha == 0) { :
  the condition has length > 1 and only the first element will be used
Warning in window.mcmc(mc$mcmc, start = start, end = end, thin = thinMCMC) :
  end value not changed
Warning in if (alpha == 0) { :
  the condition has length > 1 and only the first element will be used
Warning in if (alpha == 0) { :
  the condition has length > 1 and only the first element will be used
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Quitting from lines 412-423 (UserGuide.Rmd) 
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
package 'Rmpfr' not found
Execution halted
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 ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Packages required but not available: ‘AnnotationDbi’ ‘GOSemSim’ ‘GO.db’

Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Hs.eg.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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PerfMeas’
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Packages suggested but not available for checking: ‘rosm’ ‘rgdal’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'charfunc.tex' failed.
LaTeX errors:
! LaTeX Error: File `esint.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'profdpm.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \newcommand
                {\bz}{\boldsymbol{z}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.0Mb
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
Execution halted
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Packages suggested but not available for checking: ‘RODBC’ ‘RPostgreSQL’
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
Error in re-building vignettes:
  ...
  In `d' `NA' elements were replaced with string "NA"
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in location(g3, species = c("human"), vertex.size = 3, vertex.label.cex = 0.5,  :
  There are some 'NA' values in graph attribute 'category'!
Warning in if (layout %in% c("reingold.tilford", "circle", "random", "fruchterman.reingold",  :
  the condition has length > 1 and only the first element will be used
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ALDEx2’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: RcppArmadillo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'prospectr-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [cm, headings]{fullpage} % for larger margins^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Biostrings’ ‘GOSemSim’ ‘org.Hs.eg.db’
Package suggested but not available for checking: ‘aroma.light’
Package unavailable to check Rd xrefs: ‘aroma.light’
Running ‘PairedPSCBS,boot.R’ [3s/4s]
Running the tests in ‘tests/PairedPSCBS,boot.R’ failed.
Last 13 lines of output:
    at #02. segmentByPairedPSCBS.data.frame(dataS, knownSegments = knownSegments, 
                avgDH = "median", seed = 48879)
            - segmentByPairedPSCBS.data.frame() is in environment 'PSCBS'
  
    at #01. segmentByPairedPSCBS(dataS, knownSegments = knownSegments, avgDH = "median", 
                seed = 48879)
            - segmentByPairedPSCBS() is in environment 'PSCBS'
  
  Error: Package 'aroma.light' is not available from any of the repositories: 'http://cran.r-project.org'
  In addition: Warning messages:
  1: In segmentByPairedPSCBS.default(CT = data$CT, thetaT = data$thetaT,  :
    Argument 'preserveScale' for segmentByPairedPSCBS() now defaults to FALSE. Prior to PSCBS v0.50.0 (October 2015) the default was TRUE.  To avoid this warning, explicitly specify this argument when calling segmentByPairedPSCBS() or make sure to set option 'PSCBS/preserveScale' to either TRUE or FALSE.  This warning will be removed in a future version.
  2: In parseRepos(sets = repos, where = where, fallback = fallback,  :
    Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: '@CRAN@' -> 'http://cran.r-project.org'
  Execution halted
Errors in running code in vignettes:
when running code in ‘PairedPSCBS.tex.rsp’
  ...
 Calling genotypes from normal allele B fractions...
   num [1:73346] 0.827 0.875 0.887 0.884 0.103 ...
Warning in parseRepos(sets = repos, where = where, fallback = fallback,  :
  Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
 Calling genotypes from normal allele B fractions...done
Segmenting paired tumor-normal signals using Paired PSCBS...done

  When sourcing ‘PairedPSCBS.R’:
Error: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
Execution halted
Error in re-building vignettes:
  ...
  Cluster #4 of 5...done
  Cluster #5 of 5...
   Segments in cluster:
    int 8
   Left indices of neighboring segments:
    int(0) 
  Cluster #5 of 5...done
  Left indices of segments to be merged:
   int 6
 Merging neighboring segments within each cluster...done
 Merging segments...
 Merging segments...done
 Updating segment means...
 Updating segment means...done
Prune segments by hierarchical clustering...done
Segmenting paired tumor-normal signals using Paired PSCBS...
 Calling genotypes from normal allele B fractions...
   num [1:73346] 0.827 0.875 0.887 0.884 0.103 ...
Warning in parseRepos(sets = repos, where = where, fallback = fallback,  :
  Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
 Calling genotypes from normal allele B fractions...done
Segmenting paired tumor-normal signals using Paired PSCBS...done
Error: processing vignette 'PairedPSCBS.tex.rsp' failed with diagnostics:
Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
Execution halted
Package suggested but not available for checking: ‘fftw’
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, round.POSIXt, trunc.POSIXt, units

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multiple.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \definecolor
                {shadecolor}{rgb}{0.9, 0.9, 0.9}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘printr’
Errors in running code in vignettes:
when running code in ‘overview.Rnw’
  ...

> if (!require("GPArotation")) {
+     stop("GPArotation must be installed to do rotations")
+ } else {
+     f3t <- fa(Thurstone, 3, n.obs = 213)
+   .... [TRUNCATED] 

  When sourcing ‘overview.R’:
Error: could not find function "fa"
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `siunitx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
PwrGSD 2.000
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GrpSeqBnds-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `harvard.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cleaning_and_debugging.tex' failed.
LaTeX errors:
! LaTeX Error: File `animate.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QGglmmHowTo.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {fancyhdr}		%En-tête personnalisés (voir \fancyhead)^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/qtbase.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: qtl
Loading required package: lattice
Loading required package: corpcor
Loading required package: mnormt
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cmst.tex' failed.
LaTeX errors:
! LaTeX Error: File `epsf.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.2Mb
Error in re-building vignettes:
  ...
Warning in fixXgeno.f2(cross, alleles) :
   --Assuming that all individuals are female.

Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
  Dropping 4 individuals with missing phenotypes.

Warning in checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,  :
  Dropping 4 individuals with missing phenotypes.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcsft.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \marginparwidth
                    0pt^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘qtbase’

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

Package suggested but not available for checking: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error in re-building vignettes:
  ...
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qualityTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.23 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.9Mb
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: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 146-147 (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.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Quipu_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.31 \sectionfont
                 {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
conf.statement: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta
Consider adding
  importFrom("stats", "pbeta")
to your NAMESPACE file.
Running ‘loadlibs.r’ [0s/1s]
  Running ‘test.r’ [1s/1s]
Running the tests in ‘tests/test.r’ failed.
Last 13 lines of output:
  > source('loadlibs.r')
  > loadlibs(forcelocal=TRUE)
  
  Attaching package: 'combinat'
  
  The following object is masked from 'package:utils':
  
      combn
  
  make: *** No rule to make target `../src/core.o', needed by `../src/Quor.so'.  Stop.
  Error in dyn.load(file.path(package.loc, "src", "Quor.so")) : 
    unable to load shared object '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so':
    dlopen(/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so, 6): image not found
  Calls: loadlibs -> dyn.load
  Execution halted
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QZ-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.72 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘Cairo’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Quitting from lines 21-23 (TextureAnalysis.Rmd) 
Error: processing vignette 'TextureAnalysis.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Packages required but not available: ‘gRbase’ ‘RBGL’ ‘graph’

Package suggested but not available for checking: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘gRbase’ ‘rags2ridges’ ‘graph’ ‘marray’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: pcaPP
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rainbow.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Package suggested but not available for checking: ‘Heatplus’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.23 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'random-essay.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \setpapersize
                 {USletter}                 % use USletter paper^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rngWELL
This is randtoolbox. For overview, type 'help("randtoolbox")'.
Warning in coll.test(runif, 2^7, 2^10, 1, echo = FALSE) :
  p-values will be approximate in the presence of low expected collision number.
Warning in coll.test(congruRand, 2^8, 2^14, 1, echo = FALSE) :
  p-values will be approximate in the presence of low expected collision number.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fullpres.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

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

! Emergency stop.
<read *> 
         
l.80 \usepackage
                {perpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘rgdal’
Errors in running code in vignettes:
when running code in ‘RankAggreg.Rnw’
  ...
The following object is masked from ‘package:kohonen’:

    map

Warning in fanny(DistDel, nc, ...) :
  FANNY algorithm has not converged in 'maxit' = 500 iterations

  When sourcing ‘RankAggreg.R’:
Error: invalid argument type
Execution halted
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: kohonen
Loading required package: mclust
Package 'mclust' version 5.2.3
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘mclust’

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

    map

Warning in fanny(DistDel, nc, ...) :
  FANNY algorithm has not converged in 'maxit' = 500 iterations

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
 chunk 4 
Error in !toroidal : invalid argument type
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rankcluster.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘graph’ ‘RBGL’ ‘NetPreProc’ ‘PerfMeas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
http://code.google.com/p/pbs-software/

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RapidPolygonLookup.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘Biostrings’ ‘Rsamtools’ ‘GenomicRanges’ ‘GenomicAlignments’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RAppArmor.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   8.8Mb
Packages suggested but not available for checking: ‘rgdal’ ‘ncdf4’
Error in re-building vignettes:
  ...
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Raster.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘RGtk2’

Packages suggested but not available for checking:
  ‘cairoDevice’ ‘graph’ ‘gWidgetsRGtk2’ ‘playwith’ ‘RBGL’ ‘rggobi’
  ‘RGtk2Extras’ ‘pkgDepTools’ ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
[getGenePositions.ucscGenome] Adding 'start_codon' and 'stop_codon' positions.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rbamtools.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {hyperref}                       % Index links, should be lo...
!  ==> Fatal error occurred, no output PDF file produced!
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.
Loading required package: sp

Attaching package: 'dplyr'

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

    intersect, select, union

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 16-24 (BGM_Spatial.Rmd) 
Error: processing vignette 'BGM_Spatial.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Packages required but not available: ‘fmcsR’ ‘ChemmineR’ ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘downscale’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcdd.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘git2r’ ‘devtools’
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
Error in re-building vignettes:
  ...
Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rclusterpp.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \lstset
           {language=C++,basicstyle=\footnotesize\ttfamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
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.
Package required but not available: ‘HH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
Running ‘testthat.R’ [56s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  testthat results ================================================================
  OK: 742 SKIPPED: 32 FAILED: 3
  1. Error: loadCMIP5 handles spatial mismatches between ensembles (@test_loadCMIP5.R#104) 
  2. Error: loadCMIP5 handles FUN correctly (@test_loadCMIP5.R#193) 
  3. Error: loadEnsemble handles no files found (@test_loadEnsemble.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   4.8Mb
    libs      1.4Mb
Error in re-building vignettes:
  ...
Loading required package: RcppArmadillo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppArmadillo-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \setmargrb
              {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.6Mb
Error in re-building vignettes:
  ...
Loading required package: RcppClassic
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppClassic-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.382 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppCNPy-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.384 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.6Mb
Running ‘doRUnit.R’ [82s/83s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  Error executing .setUp before test.gsl.vector.view : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.wrappers): ERROR !! 
  Error executing .setUp before test.gsl.vector.wrappers : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  > 
  > ## Return success or failure to R CMD CHECK
  > if (getErrors(tests)$nFail > 0) {
  +    stop("TEST FAILED!")
  + }
  > if (getErrors(tests)$nErr > 0) {
  +    stop("TEST HAD ERRORS!")
  + }
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppGSL-unitTests.Rnw’
  ...

> if (err$nFail > 0) stop(sprintf("unit test problems: %d failures", 
+     err$nFail))

> if (err$nErr > 0) stop(sprintf("unit test problems: %d errors", 
+     err$nErr))

  When sourcing ‘RcppGSL-unitTests.R’:
Error: unit test problems: 14 errors
Execution halted
Error in re-building vignettes:
  ...
Loading required package: inline
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppGSL-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.393 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.7Mb
    libs      7.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppMLPACK-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {epstopdf}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   8.0Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppOctave.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs      2.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    include   6.2Mb
    libs      4.0Mb
Error in re-building vignettes:
  ...
Loading required package: inline

Attaching package: ‘inline’

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

    registerPlugin

Loading required package: highlight
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-FAQ.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.383 \setmargrb
                {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppRedis.Rcheck/00install.out’ for details.
installed size is 76.8Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      48.9Mb
    libs     23.4Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppZiggurat.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

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

! Emergency stop.
<read *> 
         
l.399 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcrypt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rDEA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RDieHarder.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: rDNAse
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Inserting_bibtex_references.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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]="./webshot9ce16a2399ae.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot9ce16a2399ae.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'readJDX.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  10.9Mb
Package required but not available: ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsfonts,hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘interval’ ‘Icens’
Package unavailable to check Rd xrefs: ‘interval’
Packages suggested but not available for checking:
  ‘Rgraphviz’ ‘Rglpk’ ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Running examples in ‘relations-Ex.R’ failed
The error most likely occurred in:

> ### Name: choice
> ### Title: Relation-Based Choices
> ### Aliases: relation_choice
> ### Keywords: math
> 
> ### ** Examples
> 
> data("SVM_Benchmarking_Classification")
> ## Determine the three best classification learners in the above sense.
> relation_choice(SVM_Benchmarking_Classification, k = 3)
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Calls: relation_choice ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘relations.Rnw’
  ...

> data("Felines")

> relations <- as.relation_ensemble(Felines)

> E <- relation_consensus(relations, "SD/E")

  When sourcing ‘relations.R’:
Error: there is no package called ‘Rglpk’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 25 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Error in re-building vignettes:
  ...
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RepeatABEL_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [23s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 25 SKIPPED: 0 FAILED: 27
  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
Package suggested but not available for checking: ‘rsolr’
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Guide_restorepoint.Rmd’, ‘Guide_restorepoint.html’,
    ‘Guide_restorepoint.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RESTguide.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘cairoDevice’
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 (revdbayes-predictive-vignette.Rmd) 
Error: processing vignette 'revdbayes-predictive-vignette.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rexpokit.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Package suggested but not available for checking: ‘BiocParallel’
Package required but not available: ‘PKI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs      77.2Mb
    pictures   1.3Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgeolocate.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rglpk.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    3.5Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rgnuplot.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
(./tufte-handout.cls
Document Class: tufte-handout 2009/12/11 v3.5.0 Tufte-handout class
(./tufte-common.def
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/keyval.tex))))

! LaTeX Error: File `xifthen.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on rgp_introduction.log.
make: *** [pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
Packages suggested but not available for checking:
  ‘graph’ ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’
  ‘rgdal’ ‘rggobi’ ‘Rgraphviz’ ‘SVGAnnotation’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rhosp.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {amsfonts,amsmath,amssymb,amsthm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rhpc.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
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_ReplDLLdo1’, ‘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.
Packages suggested but not available for checking: ‘rggobi’ ‘fftw’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: xlsx
Loading required package: rJava
Loading required package: xlsxjars
Loading required package: ggplot2
Loading required package: stringr
Loading required package: shiny
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RJafroc.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.120 \usepackage
                 {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Note: information on .o files is not available
File ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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 but not available: ‘chopsticks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rkafka.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following apparent object files/libraries:
  src/l64/c.o src/m64/c.o src/w32/c.o src/w64/c.o
Object files/libraries should not be included in a source package.
Found the following executable file:
  src/w32/c.o
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘gmp’

Packages suggested but not available for checking:
  ‘genefilter’ ‘golubEsets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'data.handling.tex' failed.
LaTeX errors:
! LaTeX Error: File `gensymb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rlas.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'Rlda.ltx' failed with diagnostics:
Running 'texi2dvi' on 'Rlda.ltx' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {calrsfs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
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$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Running ‘RMongo-Ex.R’ [3s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$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 ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmosek.Rcheck/00install.out’ for details.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("gmp"): package ‘gmp’ not found

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./mumps_save_restore_C.h:15:9: warning: 'MUMPS_SAVE_RESTORE_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
  Warning: Integer division truncated to constant ‘768614336404’ at (1) [-Winteger-division]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rmumps.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘topGO’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
Package suggested but not available for checking: ‘RnavGraph’
Package required but not available: ‘graph’

Packages suggested but not available for checking:
  ‘PairViz’ ‘RDRToolbox’ ‘Rgraphviz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running examples in ‘RndTexExams-Ex.R’ failed
The error most likely occurred in:

> ### Name: rte.build.rdn.test
> ### Title: Build random tests from LaTeX file
> ### Aliases: rte.build.rdn.test
> 
> ### ** Examples
> 
> # define some options
> latex.dir.out = 'latexOut' # Name of folder where latex files are going (will create if not exists)
> pdf.dir.out = 'PdfOut'     # Name of folder where resulting pdf files are going
> f.out <- 'MyRandomTest_'   # Name of pdfs (MyRandomTest_1.pdf, MyRandomTest_2.pdf, ... )
> n.test <- 1                # Number of tests to build
> n.question <- 2            # Number of questions in each test
> 
> # Get latex example from package
> f.in <- system.file("extdata", "MyRandomTest_examdesign.tex", package = "RndTexExams")
> 
> # Break latex file into a R list
> list.out <- rte.analyze.tex.file(f.in,
+                                  latex.dir.out = latex.dir.out,
+                                  pdf.dir.out = pdf.dir.out)

rte: Changing LaTeX file into dataframe... Done> 
> # Build pdfs
> result.out <- rte.build.rdn.test(list.in = list.out,
+                                  f.out = f.out,
+                                  n.test = n.test,
+                                  n.question = n.question,
+                                  latex.dir.out = latex.dir.out,
+                                  pdf.dir.out = pdf.dir.out)

rte: Checking for error in inputs... Done
rte: pdflatex flavor: texlive
rte: Type of OS: Darwin
rte: Latex compile function: texi2pdf
rte: Type of exam template: examdesign
rte: Number of mchoice questions: 4
rte: Building Test #1...Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
Messages:
/usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
Calls: rte.build.rdn.test -> rte.compile.latex -> <Anonymous> -> texi2dvi
Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  rte: Changing LaTeX file into dataframe... Done
  rte: Checking for error in inputs... Done
  rte: pdflatex flavor: texlive
  rte: Type of OS: Darwin
  rte: Latex compile function: texi2pdf
  rte: Type of exam template: examdesign
  rte: Number of mchoice questions: 4
  rte: Building Test #1...Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
    Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
  Messages:
  /usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
  Calls: test_check ... rte.build.rdn.test -> rte.compile.latex -> <Anonymous> -> texi2dvi
  testthat results ================================================================
  OK: 1 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.
Quitting from lines 121-147 (rte-vignette_creating_exams.Rmd) 
Error: processing vignette 'rte-vignette_creating_exams.Rmd' failed with diagnostics:
Running 'texi2dvi' on 'latexOut/MyRandomTest_1.tex' failed.
Messages:
/usr/local/bin/texi2dvi: pdflatex exited with bad status, quitting.
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rngtools-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 81.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     78.9Mb
Package required but not available: ‘beadarray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rgenoud
##  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. 
##

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘SSOAP’
Error in re-building vignettes:
  ...
Loading required package: robustbase
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fastMcd-kmini.tex' failed.
BibTeX errors:
The top-level auxiliary file: fastMcd-kmini.aux
I couldn't open style file chicago.bst
---line 43 of file fastMcd-kmini.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file fastMcd-kmini.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
cluster_em_outlier: no visible global function definition for ‘qchisq’
jth_dsty: no visible global function definition for ‘mahalanobis’
k_means: no visible global function definition for ‘kmeans’
mix_rcm: no visible global function definition for ‘median’
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
Running examples in ‘robustrank-Ex.R’ failed
The error most likely occurred in:

> ### Name: sim.partially.matched
> ### Title: Simulate Paired, Independent, or Partially Matched Two-Sample
> ###   Data
> ### Aliases: r2sample sim.partially.matched
> 
> ### ** Examples
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="normal",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
> X=dat$X; Y=dat$Y; Yprime=dat$Yprime    
> 
> dat=sim.partially.matched(m=10,n.x=5,n.y=4,distr="logistic",
+     params=c("loc.2"=0,"rho"=0,"scale.2"=1),seed=1)
Error in loadNamespace(name) : there is no package called ‘copula’
Calls: sim.partially.matched ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘gmp’ ‘iterpc’

See section ‘The DESCRIPTION file’ 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 covMcd(.) : could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rchaeology.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test_netlib.R’ [18s/30s]
Running the tests in ‘tests/test_netlib.R’ failed.
Last 13 lines of output:
  wood1p    1.442902e+00
  woodw     1.304476e+00
  > afiro <- netlib("afiro")
  > 
  > if ( length(ROI_applicable_solvers(afiro)) ) {
  + 	## solve a problem
  + 	sol <- ROI_solve(afiro)
  + 	sol
  + 	stopifnot( equal(sol$objval, 
  + 		       as.numeric(netlib("metainfo")["afiro", "optimal_value"])) )
  + }
  Error in SOLVE(x, ROI_translate(control, solver)) : 
    the directions "<", "<=", ">" and ">=" can only be used in combination with the "free" cone! The constraints c(3, 4, 7, 8, 9, 10, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) are inequality constraints but don`t belong to the "free" cone.
  Calls: ROI_solve -> SOLVE
  Execution halted
Package required but not available: ‘clpAPI’

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.
Packages suggested but not available for checking:
  ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Packages suggested but not available for checking: ‘proj4’ ‘rgdal’
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 21-27 (rollply.Rmd) 
Error: processing vignette 'rollply.Rmd' failed with diagnostics:
there is no package called 'proj4'
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ROracle.Rcheck/00install.out’ for details.
Packages required but not available: ‘Rglpk’ ‘hitandrun’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rotations-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ?testthat results ================================================================
  OK: 484 SKIPPED: 0 FAILED: 2
  1. Error: can document eager data (@test-rd-data.R#7) 
  2. Error: can document lazy data (@test-rd-data.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rpanel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rpg.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Error in re-building vignettes:
  ...
Loading required package: rphast
Compacting sufficient statistics ...
Fitting tree model to alignment using REV ...
numpar = 13
Done.  log(likelihood) = -5370.320518 numeval=625
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette1.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘TNRSVignette.pdf’, ‘rPlantVignette.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rpms_2017_02_10.tex' failed.
LaTeX errors:
! LaTeX Error: File `tikz-qtree.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rpoppler.Rcheck/00install.out’ for details.
Packages required but not available: ‘RPostgreSQL’ ‘rpostgis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RPostgreSQL.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RPPanalyzer.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RProtoBuf.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RQuantLib.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'RSP_refcard.tex.rsp' failed with diagnostics:
Running 'texi2dvi' on 'RSP_refcard.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.34 \titlespacing
                  {\section}{0pt}{2.0ex}{0.5ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
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 ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSAP.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSclient.Rcheck/00install.out’ for details.
File ‘rscproxy/libs/rscproxy.so’:
  Found non-API calls to R: ‘R_DefParams’, ‘R_ReplDLLinit’,
    ‘R_SetParams’, ‘R_set_command_line_arguments’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘ptr_R_Busy’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘RBGL’ ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSclient’
Note: information on .o files is not available
File ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
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 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.5Mb
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.
sh: squeue: command not found
Quitting from lines 84-86 (rslurm.Rmd) 
Error: processing vignette 'rslurm.Rmd' failed with diagnostics:
slr_job has not been submitted
Execution halted
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  42.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Package required but not available: ‘dbplyr’

Package required and available but unsuitable version: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  59.6Mb
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).

Gradient evaluation took 0.000179 seconds
1000 transitions using 10 leapfrog steps per transition would take 1.79 seconds.
Adjust your expectations accordingly!


Iteration:   1 / 500 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug
Calls: stan_glmer -> stan_glm.fit -> check_stanfit
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  SAMPLING FOR MODEL 'binomial' NOW (CHAIN 1).
  
  Gradient evaluation took 0.000173 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.73 seconds.
  Adjust your expectations accordingly!
  
  
  Iteration:   1 / 500 [  0%]  (Warmup)
  [1] "Error in sampler$call_sampler(args_list[[i]]) : "
  [2] "  c++ exception (unknown reason)"                
  error occurred during calling the sampler; sampling not done
  Error in check_stanfit(stanfit) : 
    Invalid stanfit object produced please report bug
  Calls: example ... eval -> stan_glmer -> stan_glm.fit -> check_stanfit
  Execution halted
Package suggested but not available for checking: ‘shinystan’
installed size is 207.0Mb
  sub-directories of 1Mb or more:
    libs  204.8Mb
Packages unavailable to check Rd xrefs: ‘shinystan’, ‘rstanarm’
Running examples in ‘RStoolbox-Ex.R’ failed
The error most likely occurred in:

> ### Name: getMeta
> ### Title: Extract bandwise information from ImageMetaData
> ### Aliases: getMeta
> 
> ### ** Examples
> 
> ## Import example data
> mtlFile  <- system.file("external/landsat/LT52240631988227CUB02_MTL.txt", package="RStoolbox")
> meta <- readMeta(mtlFile)
> lsat <- stackMeta(mtlFile)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: stackMeta ... lapply -> FUN -> FUN -> .local -> .rasterObjectFromFile
Execution halted
Running ‘testthat.R’ [23s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(RStoolbox) 
  > 
  > 
  > Sys.setenv("R_TESTS" = "") ## needed to pass R CMD check: https://github.com/hadley/testthat/issues/144
  > 
  > test_check("RStoolbox")
  Loading required package: sp
  Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
    Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
  Calls: test_check ... lapply -> FUN -> FUN -> .local -> .rasterObjectFromFile
  testthat results ================================================================
  OK: 62 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: splines

Attaching package: ‘rstpm2’

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

    colon

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rsymphony.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: rtfbs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rtkpp-Arrays.tex' failed.
LaTeX errors:
! LaTeX Error: File `mdframed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.46 \usepackage
                {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Ruchardet.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘devtools’
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RVowpalWabbit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: RWeka
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RWeka.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘rworldmapFAQ.Rnw’
  ...
> mtext("Source: Andy South, The R Journal Vol. 3/1, June 2011", 
+     side = 1, line = -1)

> par(mai = c(0, 0, 0.2, 0), xaxs = "i", yaxs = "i")

> library(rgdal)

  When sourcing ‘rworldmapFAQ.R’:
Error: there is no package called ‘rgdal’
Execution halted
Error in re-building vignettes:
  ...
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
149 codes from your data successfully matched countries in the map
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rworldmap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.37 \usepackage
                [colorlinks=true,urlcolor=blue]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs    4.8Mb
    yacas   1.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ryacas.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sadists.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.91 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: bbmle
Loading required package: stats4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sads_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Warning in sqrt(diag(vc)) : NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'selection.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  Population size       = 10
  Number of Generations = 40
  Elitism               = 2
  Mutation Chance       = 0.05


Warning in sink() : no sink to remove

 *** Sample size :  409.6178
 *** Number of strata :  203
---------------------------
...written output to outstrata.txt
Warning in sink() : no sink to remove
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SamplingStrataVignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: SamplingStrataVignette.aux
I couldn't open style file chicago.bst
---line 23 of file SamplingStrataVignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file SamplingStrataVignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘sampSurf-Ex.R’ failed
The error most likely occurred in:

> ### Name: izGridMirage
> ### Title: Generate Objects of Class "'mirageInclusionZoneGrid'"
> ### Aliases: izGridMirage
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
>  
> tr = Tract(c(x=20,y=20), cellSize=1)
> mtr = mirageTract(tr)
> st = standingTree(centerOffset=c(x=16,y=16))
> ag = angleGauge(4)     #4=baf
> hps.iz = horizontalPointIZ(st, angleGauge=ag)
> hps.izg = izGridMirage(hps.iz, mtr, truncateOverlap=FALSE)
Loading required package: rgeos
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgeos’
Error in gIntersects(North, p.iz) : could not find function "gIntersects"
Calls: izGridMirage -> izGridMirage -> .local
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GettingStarted.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GO.db’ ‘GOstats’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sas7bdat.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20     \usepackage
                    {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘satellite-Ex.R’ failed
The error most likely occurred in:

> ### Name: alignGeometry
> ### Title: Align raster geometry between two data sets
> ### Aliases: alignGeometry alignGeometry,RasterLayer-method
> ###   alignGeometry,RasterStack-method alignGeometry,Satellite-method
> 
> ### ** Examples
> 
> path <- system.file("extdata", package = "satellite")
> files <- list.files(path, pattern = glob2rx("LC8*.tif"), full.names = TRUE)
> sat <- satellite(files)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: satellite ... raster -> raster -> .local -> .rasterObjectFromFile
Execution halted
Running ‘testthat.R’ [18s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 48 SKIPPED: 0 FAILED: 21
  1. Error: calcAtmosCorr for RasterLayers works as expected (@test-calcAtmosCorr.R#8) 
  2. Error: calcAtmosCorr for Satellite works as expected (@test-calcAtmosCorr.R#46) 
  3. Error: Depricated satAtmosCorr for Satellite works as expected (@test-calcAtmosCorr.R#60) 
  4. Error: compDODN works as expected (@test-calcDODN.R#7) 
  5. Error: calcHistMatch for raster works as expected (@test-calcHistMatch.R#10) 
  6. Error: calcPathRadDOS for numeric works as expected (@test-calcPathRadDOS.R#9) 
  7. Error: calcPathRadDOS for Satellite works as expected (@test-calcPathRadDOS.R#93) 
  8. Error: Deprecated satPathRadDOS for Satellite works as expected (@test-calcPathRadDOS.R#108) 
  9. Error: calcTOAIrradModel for satellite works as expected (@test-calcTOAIrrad.R#23) 
  1. ...
  
  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 24-28 (landsat-calibration.Rmd) 
Error: processing vignette 'landsat-calibration.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'saves.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sbrl.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scaRabee.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scglrVignettes.tex' failed.
LaTeX errors:
! LaTeX Error: File `diagbox.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TechnicalDocument.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
SciencesPo 1.4.1
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Quitting from lines 754-756 (Indices.Rmd) 
Error: processing vignette 'Indices.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Error in re-building vignettes:
  ...

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sclero_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.3Mb
Package required but not available: ‘BiocParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘oligoClasses’
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sdcMicro
--------
This is sdcMicro v5.0.2.
For references, please have a look at citation('sdcMicro')
Note: since version 5.0.0, the graphical user-interface is a shiny-app that can be started with sdcApp().
Please submit suggestions and bugs at: https://github.com/sdcTools/sdcMicro/issues
--------
Loading required package: xtable
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sdc_guidelines.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {color,xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Loading required package: sp
sdm 1.0-32 (2016-12-01)
Quitting from lines 45-52 (quick_sdm.Rmd) 
Error: processing vignette 'quick_sdm.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
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.
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [colorlinks = true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Preparing the data.
Fitting model for 04035.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304035.pdf.
Fitting model for 04041.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304041.pdf.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/seewave.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Attaching package: ‘Ecfun’

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

    sign


Attaching package: ‘Ecdat’

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

    Orange

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SeleMix-vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: SeleMix-vignette.aux
I couldn't open style file chicago.bst
---line 30 of file SeleMix-vignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file SeleMix-vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
! LaTeX Error: File `ntheorem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \newtheorem
               {theorem}{Theorem}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
      see ?specifyEquations
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘bugBO.R’ [4s/6s]
  Running ‘bugKEEPdprime.R’ [4s/6s]
  Running ‘testBugResiduals.R’ [79s/123s]
  Running ‘testDprimes.R’ [66s/103s]
  Running ‘testKEEPeffs.R’ [168s/265s]
  Running ‘testMAM.R’ [12m/18m]
Running the tests in ‘tests/testMAM.R’ failed.
Last 13 lines of output:
    |========================================================              |  80%
  
    |                                                                            
    |=============================================================         |  87%
  
    |                                                                            
    |=================================================================     |  93%
  
  Warning messages:
  1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
    unable to evaluate scaled gradient
  2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
    Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
  
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'methodology.tex' failed.
BibTeX errors:
The top-level auxiliary file: methodology.aux
I couldn't open style file chicago.bst
---line 2 of file methodology.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file methodology.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seqDesignInstructions.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [round,authoryear]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘Biostrings’ ‘qvalue’ ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘Biostrings’ ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   5.0Mb
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sequoia.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               [margin=2.7cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.ltx' failed with diagnostics:
Running 'texi2dvi' on 'vignette.ltx' failed.
LaTeX errors:
! LaTeX Error: File `beramono.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is 101.6Mb
  sub-directories of 1Mb or more:
    doc      4.0Mb
    libs    94.1Mb
    sqlite   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘SGP’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sgt.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:quantmod':

    summary

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

    summary

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SharpeRatio.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.72 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   6.2Mb
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinystan)
  Loading required package: shiny
  
  This is shinystan version 2.3.0
  
  > 
  > test_check("shinystan")
  Error in library(rstanarm) : there is no package called 'rstanarm'
  Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'shotGroups.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

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

! Emergency stop.
<read *> 
         
l.80 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘pcalg’ ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [150s/233s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 05:33:43 2017 
  *********************************************** 
  Number of test functions: 28 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  simcausal unit testing - 28 test functions, 1 error, 0 failures
  ERROR in test.MV: Error in loadNamespace(name) : there is no package called 'rCopula'
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

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

    format.pval, round.POSIXt, trunc.POSIXt, units

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simcausal_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `footmisc.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘doMPI’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SimInf.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Packages required but not available:
  ‘Biostrings’ ‘BSgenome’ ‘GenomeInfoDb’ ‘GenomicRanges’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

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

Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Rmpi’ ‘copula’
Running ‘doExtras.R’ [1s/1s]
  Comparing ‘doExtras.Rout’ to ‘doExtras.Rout.save’ ... OK
  Running ‘getArray-swap.R’ [1s/2s]
  Running ‘tst-wrongs.R’ [16s/53s]
  Running ‘tstTGforecasts.R’ [5s/18s]
  Running ‘tstVaRsuperadd.R’ [1s/1s]
Running the tests in ‘tests/tstVaRsuperadd.R’ failed.
Last 13 lines of output:
  > ## manually
  > require(copula) # for the following call of doOne()
  Loading required package: copula
  
  > nonGr <- get.nonGrids(varList)$nonGrids
  
  > dd <- doOne(n= min(nonGr$n, 100), d=4, family="Clayton", tau=0.5,
  +             qmargin=nonGr$qmargin, alpha=nonGr$alpha)
  Error in onacopulaL("Clayton", list(th = iTau(archmCopula("clayton"),  : 
    could not find function "onacopulaL"
  Calls: demo -> source -> withVisible -> eval -> eval -> doOne
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'copula'
  Execution halted
Package unavailable to check Rd xrefs: ‘copula’
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$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.

Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Packages required but not available: ‘polyapost’ ‘rcdd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘dplyr’

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

Package required and available but unsuitable version: ‘dplyr’

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

Packages required and available but unsuitable versions: ‘dplyr’ ‘sjmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

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

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

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

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hitandrun’
Package unavailable to check Rd xrefs: ‘hitandrun’
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/judge-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/shepard-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/perm-plot1-1-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/spp-plot1-1-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! P
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘rhdf5’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.6Mb
Warning: parse error in file '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/snakecase.Rcheck/snakecase/doc/caseconverters.R':
invalid multibyte character in parser at line 28
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pairwiseSNHT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgdal’ ‘RODBC’ ‘rgeos’
Package suggested but not available for checking: ‘meteoForecast’
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) :
  swe:Quantity given without unit of measurement: Salinity

Attaching package: ‘xtable’

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

    label

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sos4R.tex' failed.
LaTeX errors:
! LaTeX Error: File `csquotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.19 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘RPostgreSQL’
Running examples in ‘spacetime-Ex.R’ failed
The error most likely occurred in:

> ### Name: stConstruct
> ### Title: create ST* objects from long or wide tables
> ### Aliases: stConstruct
> ### Keywords: manip
> 
> ### ** Examples
> 
> # example 0: construction of STFDF from long table:
> library(maps)
> states.m = map('state', plot=FALSE, fill=TRUE)
> IDs <- sapply(strsplit(states.m$names, ":"), function(x) x[1])
>  
> library(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()
> states = map2SpatialPolygons(states.m, IDs=IDs)
> 
> library(plm)
Loading required package: Formula
Warning: S3 methods ‘print.sparseSummary’, ‘print.diagSummary’, ‘c.abIndex’, ‘as.array.Matrix’, ‘as.array.sparseVector’, ‘as.matrix.Matrix’, ‘as.matrix.sparseVector’, ‘as.vector.Matrix’, ‘as.vector.sparseVector’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘plm’ in library.dynam(lib, package, package.lib):
 shared object ‘Matrix.so’ not found
Execution halted
Running ‘basic.R’ [3s/5s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ... OK
  Running ‘over.R’ [4s/7s]
  Comparing ‘over.Rout’ to ‘over.Rout.save’ ... OK
  Running ‘raster.R’ [5s/9s]
  Comparing ‘raster.Rout’ to ‘raster.Rout.save’ ... OK
  Running ‘rw.R’ [5s/8s]
  Comparing ‘rw.Rout’ to ‘rw.Rout.save’ ...38,40c38,43
< Warning message:
< In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
<   there is no package called 'rgeos'
---
> rgeos version: 0.3-19, (SVN revision 524)
>  GEOS runtime version: 3.5.0-CAPI-1.9.0 r4084 
>  Linking to sp version: 1.2-3 
>  Polygon checking: TRUE 
> 
> [1] TRUE
  Running ‘stconstruct.R’ [2s/4s]
Running the tests in ‘tests/stconstruct.R’ failed.
Last 13 lines of output:
  >     
  > library(maptools)
  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()
  > states = map2SpatialPolygons(states.m, IDs=IDs)
  > 
  > library(plm)
  Loading required package: Formula
  Error: package or namespace load failed for 'plm' in library.dynam(lib, package, package.lib):
   shared object 'Matrix.so' not found
  In addition: Warning message:
  S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found 
  Execution halted
Errors in running code in vignettes:
when running code in ‘jss816.Rnw’
  ...
+     tz = "GMT")

> library(plm)
Loading required package: Formula
Warning: S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found

  When sourcing 'jss816.R':
Error: package or namespace load failed for 'plm' in library.dynam(lib, package, package.lib):
 shared object 'Matrix.so' not found
Execution halted
Packages suggested but not available for checking: ‘fastshp’ ‘rgdal’
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
Package suggested but not available for checking: ‘rcdd’
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
span: no visible global function definition for ‘complete.cases’
spanr: no visible global function definition for ‘model.frame’
spanr: no visible global function definition for ‘complete.cases’
spanr.hull: no visible global function definition for ‘par’
spanr.hull: no visible global function definition for ‘plot.new’
spanr.hull: no visible global function definition for ‘plot.window’
spanr.hull: no visible global function definition for ‘axis’
spanr.hull: no visible global function definition for ‘title’
spanr.hull: no visible global function definition for ‘points’
spanr.hull: no visible global function definition for ‘lines’
spanr.hull: no visible global function definition for ‘abline’
spanr.hull: no visible global function definition for ‘text’
spanr.hull: no visible global function definition for ‘segments’
spanr.hull: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
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.
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]="./webshotdcab656233c5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdcab656233c5.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 ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sparsebnUtils)
  > 
  > test_check("sparsebnUtils")
  Error in loadNamespace(name) : there is no package called 'graph'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
'library' or 'require' call not declared from: ‘testthat’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sparseHessianFD.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.27 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sparseMVN.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.30 \usepackage
                {array}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in optim(unlist(start), obj.fun, hessian = FALSE, control = control,  :
  unknown names in control: cov11
Warning in Dev * c :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SpatialExtremesGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.2 \usepackage
               {amsmath,amsfonts,amsthm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-SA 3.0 + file LICENSE
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 29-66 (StewartExample.Rmd) 
Error: processing vignette 'StewartExample.Rmd' failed with diagnostics:
there is no package called 'cartography'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Smooth interpolated at 279 time(s).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ST_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [unicode,linktocpage=true,bookmarksnumbered=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      4.8Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  11.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spBayesSurv.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.109 \usepackage
                 {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘MassSpecWavelet’

Package suggested but not available for checking: ‘speaq’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘MAIT’ ‘genefilter’ ‘impute’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
lambda.global: no visible global function definition for ‘mad’
lambda.global: no visible global function definition for ‘quantile’
lambda.global: no visible global function definition for ‘qnorm’
lambda.global: no visible global function definition for ‘pnorm’
ls.comp: no visible global function definition for ‘lsfit’
modterritory: no visible global function definition for ‘median’
newgotterritory: no visible global function definition for ‘median’
newterritory: no visible global function definition for ‘median’
ridge.comp: no visible global function definition for ‘lsfit’
ridge.diacomp: no visible global function definition for ‘ls.diag’
sw.plot: no visible global function definition for ‘par’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘points’
sw.plot: no visible global function definition for ‘image’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘legend’
sw.plot: no visible global function definition for ‘box’
sw.plot: no visible global function definition for ‘title’
thresh.level: no visible global function definition for ‘na.omit’
thresh.level: no visible global function definition for ‘mad’
thresh.level: no visible global function definition for ‘qnorm’
thresh.level: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis box image legend ls.diag lsfit mad median na.omit par plot pnorm
  points qnorm quantile title
Consider adding
  importFrom("graphics", "axis", "box", "image", "legend", "par", "plot",
             "points", "title")
  importFrom("stats", "ls.diag", "lsfit", "mad", "median", "na.omit",
             "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {algorithm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘kirby21.fmri’
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 35-44 (fmri_processing_spm12r.Rmd) 
Error: processing vignette 'fmri_processing_spm12r.Rmd' failed with diagnostics:
there is no package called 'kirby21.fmri'
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.8Mb
Running examples in ‘sp-Ex.R’ failed
The error most likely occurred in:

> ### Name: gridlines
> ### Title: Create N-S and E-W grid lines over a geographic region
> ### Aliases: gridlines gridat text text.SpatialPointsDataFrame labels
> ###   labels.SpatialLines
> ### Keywords: spatial
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) = ~x+y
> plot(meuse)
> plot(gridlines(meuse), add = TRUE)
> text(labels(gridlines(meuse)))
> title("default gridlines within Meuse bounding box")
> 
> proj4string(meuse) <- CRS("+init=epsg:28992")
> crs.longlat <- CRS("+init=epsg:4326")
> meuse_ll <- spTransform(meuse, crs.longlat)
Error in spTransform(meuse, crs.longlat) : 
  package rgdal is required for spTransform methods
Calls: spTransform -> spTransform
Execution halted
Errors in running code in vignettes:
when running code in ‘csdacm.Rnw’
  ...
     2.5%     97.5% 
0.6383983 0.7388898 

> fn <- system.file("pictures/erdas_spnad83.tif", package = "rgdal")[1]

> library(rgdal)

  When sourcing ‘csdacm.R’:
Error: there is no package called ‘rgdal’
Execution halted
Error in re-building vignettes:
  ...
Found more than one class "SpatialMultiPoints" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’
Found more than one class "SpatialMultiPointsDataFrame" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’
Found more than one class "SpatialMultiPointsDataFrame" in cache; using the first, from namespace 'sp'
Also defined by ‘.GlobalEnv’

Error: processing vignette 'csdacm.Rnw' failed with diagnostics:
 chunk 81 
Error in library(rgdal) : there is no package called ‘rgdal’
Execution halted
Package required but not available: ‘CMA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Biostrings’ ‘ShortRead’ ‘golubEsets’ ‘RankProd’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sprint.Rcheck/00install.out’ for details.
.dpssToEigenvalues: no visible global function definition for ‘mvfft’
smooth.construct.sp.smooth.spec: no visible global function definition
  for ‘str’
Undefined global functions or variables:
  mvfft str
Consider adding
  importFrom("stats", "mvfft")
  importFrom("utils", "str")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.

Warning in grts(design = Paneldsgn, DesignID = "UNEQUAL", type.frame = "area",  :
  
Oversample size is not proportional to category sample sizes for stratum
"None".

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CDF_Analysis.tex' failed.
LaTeX errors:
! LaTeX Error: File `chicago.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \bibliographystyle
                      {chicago}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    backsolve, forwardsolve

Loading required package: maps
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'spTest-vig.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabu.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
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
Error in re-building vignettes:
  ...
URL:                http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html
Repository:         CRAN
NeedsCompilation:   no
Packaged:           2016-08-18 16:13:21 UTC; rvaradh1
Date/Publication:   2016-08-18 23:27:39
Built:              R 3.4.0; ; 2017-04-22 00:14:02 UTC; unix

Index:

fpiter                  Fixed-Point Iteration Scheme
squarem                 Squared Extrapolation Methods for Accelerating
                        Slowly-Convergent Fixed-Point Iterations

Further information is available in the following vignettes in
directory
‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SQUAREM.Rcheck/SQUAREM/doc’:

SQUAREM: SQUAREM Tutorial (source, pdf)

Loading required package: setRNG

Error: processing vignette 'SQUAREM.Rnw' failed with diagnostics:
 chunk 27 (label = libinterval) 
Error in library(interval) : there is no package called ‘interval’
Execution halted
draw.srd: no visible global function definition for ‘complete.cases’
draw.srd: no visible global function definition for ‘runif’
draw.srd: no visible global function definition for ‘arrows’
draw.srd: no visible global function definition for ‘text’
draw.srd: no visible global function definition for ‘segments’
draw.srd.enc: no visible global function definition for ‘par’
draw.srd.enc: no visible global function definition for ‘plot.new’
draw.srd.enc: no visible global function definition for ‘plot.window’
draw.srd.enc: no visible global function definition for ‘rgb’
draw.srd.enc: no visible global function definition for ‘polygon’
draw.srd.enc: no visible global function definition for ‘pchisq’
draw.srd.enc: no visible global function definition for ‘text’
draw.srd.enc: no visible global function definition for ‘title’
draw.srd.enc: no visible global function definition for ‘arrows’
drawcell: no visible global function definition for ‘polygon’
drawcell: no visible global function definition for ‘segments’
rotate.srd: no visible global function definition for ‘devAskNewPage’
srd: no visible global function definition for ‘devAskNewPage’
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
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()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: spdep
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ssfavignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘edgeR’ ‘qvalue’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   8.4Mb
Package required but not available: ‘iterpc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘easyNCDF’ ‘s2dverification’
Unavailable namespace imported from by a ':::' call: ‘s2dverification’
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: ‘s2dverification’
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Successfully loaded stepR package version 2.0-1.
Several new functions are added in version 2.0-0. Some older functions are deprecated (still working) and may be defunct in a later version. Please read the documentation for more details.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StepR.tex' failed.
LaTeX errors:
! LaTeX Error: File `floatrow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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)
bos.cat2: no visible global function definition for ‘resid’
bos.cat2: no visible global function definition for ‘lm’
plot.rt: no visible global function definition for ‘plot’
plot.rt: no visible global function definition for ‘text’
plot.rt: no visible global function definition for ‘rect’
plot.rt: no visible global function definition for ‘title’
plot.rt: no visible global function definition for ‘par’
stdata: no visible binding for global variable ‘var’
stima: no visible global function definition for ‘fitted’
stima: no visible global function definition for ‘lm’
stima: no visible global function definition for ‘anova’
stima: no visible global function definition for ‘predict’
stima: no visible global function definition for ‘cor’
stima: no visible global function definition for ‘as.formula’
stima: no visible global function definition for ‘step’
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
stm v1.2.2 (2017-03-28) successfully loaded. See ?stm for help.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'stmVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `placeins.sty' not found.

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

! Emergency stop.
<read *> 
         
l.59 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/tools/bm.sty)

! LaTeX Error: File `tablefootnote.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.22 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on article.log.
make: *** [article.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/stochvol.Rcheck/vign_test/stochvol") : 
  running 'make' failed
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘tigris’
Error in re-building vignettes:
  ...

    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
Warning: Removed 703 rows containing missing values (geom_point).
Warning: Removed 89 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_path).
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 98-100 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'tigris'
Execution halted
Running ‘testthat.R’ [4s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(storr)
  > 
  > test_check("storr")
  Error in redis_connect_tcp(config$host, config$port) : 
    Failed to create context: Connection refused
  Calls: test_check ... redis_connection -> redis_connect -> redis_connect_tcp -> .Call
  testthat results ================================================================
  OK: 634 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
Running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Packages required but not available: ‘Rglpk’ ‘MultAlloc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘limma’ ‘samr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.9Mb
Running ‘test-all.R’ [167s/242s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 00:44:25 2017 
  *********************************************** 
  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
Packages required but not available:
  ‘AnnotationDbi’ ‘GO.db’ ‘biomaRt’ ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'strucchange-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘KFKSDS’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'VignetteSubrank.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               [pdftex]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘genefilter’ ‘sva’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'copulas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, natbib, hyperref, doi}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.2Mb
Error in re-building vignettes:
  ...
Type gamlssNews() to see new features/changes/bug fixes.

Doing computations: FALSE
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Doing computations: FALSE
Loading required namespace: spdep
Note: range of maximum neighbour order by region is 3-5
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hhh4_spacetime.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Package unavailable to check Rd xrefs: ‘survJamda’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plots.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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.
Error in re-building vignettes:
  ...
Loading required package: SurvRegCensCov
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'weibull.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svUnit.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Packages suggested but not available for checking:
  ‘glpkAPI’ ‘cplexAPI’ ‘clpAPI’
Package unavailable to check Rd xrefs: ‘glpkAPI’
Running examples in ‘sybil-Ex.R’ failed
The error most likely occurred in:

> ### Name: SYBIL_SETTINGS
> ### Title: Set and Get sybil Parameters
> ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
> ###   OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
> ### Keywords: optimize
> 
> ### ** Examples
> 
>   ## show all current parameters
>   SYBIL_SETTINGS()
$MODELORG_VERSION
[1] "2.0"

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

>   
>   ## show current setting for "SOLVER"
>   SYBIL_SETTINGS("SOLVER")
[1] "glpkAPI"
> 
>   ## change current solver to glpkAPI
>   SYBIL_SETTINGS("SOLVER", "glpkAPI")
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver = value, method = "", probType = "",  : 
  package ‘glpkAPI’ not found
Calls: SYBIL_SETTINGS -> checkDefaultMethod
Execution halted
Errors in running code in vignettes:
when running code in ‘sybil.Rnw’
  ...
number of exchange reactions: 20

> optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

  When sourcing ‘sybil.R’:
Error: package ‘glpkAPI’ not found
Execution halted
Error in re-building vignettes:
  ...
sybil::fluxVar          Flux Variability Analysis


Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.




reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

Error: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Execution halted
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sybilSBML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mpoly’
Running examples in ‘symmoments-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Errors in running code in vignettes:
when running code in ‘symmoments.rnw’
  ...
[4,]    1    1    1    2

> evaluate(m1234, c(4, 2, 1, 1, 3, 1, 1, 2, 1, 2))
[1] 3480

> library(mpoly)

  When sourcing ‘symmoments.R’:
Error: there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

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

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    single


Error: processing vignette 'symmoments.rnw' failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages suggested but not available for checking: ‘tigris’ ‘rgdal’
Packages suggested but not available for checking: ‘GISTools’ ‘rgeos’
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
Package required but not available: ‘CNTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘limma’ ‘edgeR’ ‘DESeq2’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘limma’
Running examples in ‘tcgsaseq-Ex.R’ failed
The error most likely occurred in:

> ### Name: voom_weights
> ### Title: Precision weights accounting for heteroscedasticity in RNA-seq
> ###   count data
> ### Aliases: voom_weights
> 
> ### ** Examples
> 
> #rm(list=ls())
> set.seed(123)
> 
> G <- 10000
> n <- 12
> p <- 2
> y <- t(sapply(1:G, FUN=function(x){rnbinom(n=n, size=0.07, mu=200)}))
> 
> x <- sapply(1:p, FUN=function(x){rnorm(n=n, mean=n, sd=1)})
> 
> my_w <-  voom_weights(y, x, doPlot=TRUE)
> w_voom <- limma::voom(counts=y, design=x, plot=TRUE) #slightly faster than us. Same results
Error in loadNamespace(name) : there is no package called ‘limma’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘tcpl_Overview.Rnw’
  ...
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

  When sourcing ‘tcpl_Overview.R’:
Error: argument to 'which' is not logical
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/TDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tdthap-paper.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs       6.7Mb
    tessdata  31.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   5.5Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: textutils

Attaching package: 'textutils'

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

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'btable.tex' failed.
LaTeX errors:
! LaTeX Error: File `libertine.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Tides
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tides.tex' failed.
BibTeX errors:
The top-level auxiliary file: Tides.aux
I couldn't open style file apalike2.bst
---line 14 of file Tides.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file Tides.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘tidytext-Ex.R’ failed
The error most likely occurred in:

> ### Name: lda_tidiers
> ### Title: Tidiers for LDA objects from the topicmodels package
> ### Aliases: augment.LDA glance.LDA lda_tidiers tidy.LDA
> 
> ### ** Examples
> 
> 
> set.seed(2016)
> library(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

> library(topicmodels)
Error in library(topicmodels) : there is no package called ‘topicmodels’
Execution halted
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  Error in library(topicmodels) : there is no package called 'topicmodels'
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 10 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
The following objects are masked from 'package:stats':

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "book"
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 896 rows containing non-finite values (stat_bin).
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: NLP

Attaching package: 'NLP'

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

    annotate

Quitting from lines 23-26 (tidying_casting.Rmd) 
Error: processing vignette 'tidying_casting.Rmd' failed with diagnostics:
there is no package called 'topicmodels'
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: 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
Running examples in ‘tikzDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: getLatexStrWidth
> ### Title: Obtain Font Metrics from LaTeX
> ### Aliases: getLatexCharMetrics getLatexStrWidth
> ### Keywords: character metrics string
> 
> ### ** Examples
> 
> 
>    getLatexStrWidth('{\\\\tiny Hello \\\\LaTeX!}')
Error in getMetricsFromLatex(TeXMetrics, verbose = verbose) : 
TeX was unable to calculate metrics for the following string
or character:

	{\\tiny Hello \\LaTeX!}

Common reasons for failure include:
  * The string contains a character which is special to LaTeX unless
    escaped properly, such as % or $.
  * The string makes use of LaTeX commands provided by a package and
    the tikzDevice was not told to load the package.

The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Calls: getLatexStrWidth -> getMetricsFromLatex
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 73-92 (tikzDevice.Rnw) 
Error: processing vignette 'tikzDevice.Rnw' failed with diagnostics:

TeX was unable to calculate metrics for the following string
or character:

	m

Common reasons for failure include:
  * The string contains a character which is special to LaTeX unless
    escaped properly, such as % or $.
  * The string makes use of LaTeX commands provided by a package and
    the tikzDevice was not told to load the package.

The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Execution halted
Errors in running code in vignettes:
when running code in ‘tileHMM.Rnw’
  ...

> h3k27.data <- as.matrix(simChIP[, 7:14])

> h3k27.data <- log(h3k27.data, 2)

> h3k27.norm <- preprocessCore::normalize.quantiles(h3k27.data)

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

Error: processing vignette 'tileHMM.Rnw' failed with diagnostics:
 chunk 3 
Error in loadNamespace(name) : 
  there is no package called ‘preprocessCore’
Execution halted
'library' or 'require' call to ‘ggplot2’ 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: ‘microbenchmark’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  ‘microbenchmark’
do_timeit: no visible global function definition for ‘Rprof’
do_timeit: no visible global function definition for ‘summaryRprof’
mean.timeit: no visible global function definition for ‘aggregate’
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’
timeit: no visible binding for global variable ‘median’
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
Running ‘simple.R’ [1s/1s]
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
.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 ‘tmcn-Ex.R’ failed
The error most likely occurred in:

> ### Name: revUTF8
> ### Title: Revert UTF-8 string to Chinese character.
> ### Aliases: revUTF8
> 
> ### ** Examples
> 
> revUTF8("1<U+4E8C>3<U+56DB>5")
Error in as.hexmode(str2) : 'x' cannot be coerced to class "hexmode"
Calls: revUTF8 -> intToUtf8 -> as.hexmode
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tmle-npvi.tex' failed.
LaTeX errors:
! LaTeX Error: File `manfnt.sty' not found.

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

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [textwidth=15cm, textheight=23cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘limma’ ‘org.Hs.eg.db’
Running examples in ‘tmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: tmodLimmaTest
> ### Title: Run tmod enrichment tests directly on a limma object
> ### Aliases: tmodLimmaTest
> 
> ### ** Examples
> 
> library(limma)
Error in library(limma) : there is no package called ‘limma’
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 47-57 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
there is no package called 'limma'
Execution halted
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rgraphviz’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Packages unavailable to check Rd xrefs: ‘graph’, ‘Rpoppler’
Running examples in ‘tm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readPDF
> ### Title: Read In a PDF Document
> ### Aliases: readPDF
> ### Keywords: file
> 
> ### ** Examples
> 
> uri <- sprintf("file://%s", system.file(file.path("doc", "tm.pdf"), package = "tm"))
> if(all(file.exists(Sys.which(c("pdfinfo", "pdftotext"))))) {
+     pdf <- readPDF(control = list(text = "-layout"))(elem = list(uri = uri),
+                                                      language = "en",
+                                                      id = "id1")
+     content(pdf)[1:13]
+ }
> VCorpus(URISource(uri, mode = ""),
+         readerControl = list(reader = readPDF(engine = "ghostscript")))
sh: : command not found
Error in system2(gs_cmd, c("-dNODISPLAY -q", sprintf("-sFile=%s", shQuote(file)),  : 
  error in running command
Calls: VCorpus ... mapply -> <Anonymous> -> <Anonymous> -> pdf_info -> system2
Execution halted
Packages required but not available: ‘DESeq’ ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Packages required but not available: ‘graph’ ‘gRbase’ ‘qpgraph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Expanding_TR8.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'traitr.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {amsmath}            % for amslatex stuff^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘OpenStreetMap’
Package unavailable to check Rd xrefs: ‘rgeos’
Running ‘tracks.R’ [2s/3s]
Running the tests in ‘tests/tracks.R’ failed.
Complete output:
  > Sys.setenv(TZ = "Europe/Berlin")
  > # Load required libraries.
  > 
  > library(sp)
  > library(spacetime)
  > library(trajectories)
  > library(rgdal)
  Error in library(rgdal) : there is no package called 'rgdal'
  Execution halted
Error in re-building vignettes:
  ...
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 4 representative(s) selected, coverage=39% (threshold=35%)
 [>] 148 distinct sequence(s)
 [>] number of objects (sum of weights): 99.22
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 5 representative(s) selected, coverage=38% (threshold=35%)
 [>] 89 distinct sequence(s)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.77 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in add.known.TRAMPknowns(x$knowns, x$samples, sample.fk, ...) :
  Mutiple peaks per enzyme/primer combination for sample 221, taking largest peaks only
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TRAMPRdemo.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'trapezoid.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Running examples in ‘treeHFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawViterbiTree
> ### Title: Arranges a Viterbi tree
> ### Aliases: DrawViterbiTree
> ### Keywords: misc
> 
> ### ** Examples
> 
> ## Fit a continous treeHFM ## 
> nHStates = 2;
> ########create observation sequences########
> obs1 <- rbind(runif(10,0,1),runif(10,0,1))
> obs2 <- rbind(runif(8,0,1),runif(8,0,1))
> data=list()
> data[[1]]=obs1
> data[[2]]=obs2
> ######### create guesses for gaussian covariance matrix and means #########
> mc2 <- Mclust(t(cbind(obs1,obs2)), G=2)
> muInit=mc2$parameters$mean;
> SigmaInit=mc2$parameters$variance$sigma
> #########create tree topology####################################
> nodeIndices1=cbind(c(0,1,2,3,3,4,5,6,7,8),c(1,2,3,4,5,6,7,8,9,10));
> nodeIndices2=cbind(c(0,1,2,3,4,4,5,6),c(1,2,3,4,5,6,7,8));
> dataNodeIndices=list()
> dataNodeIndices[[1]]=nodeIndices1;
> dataNodeIndices[[2]]=nodeIndices2;
> ######### create guesses for prior and transition matrices#########
> prior1=array(1,nHStates);
> priorInit = array(1,nHStates)/nHStates;
> transmatInit = matrix(1,nHStates,nHStates)*(1/nHStates);
> transInitDiv= matrix(1,nHStates,nHStates*nHStates)*(1/(nHStates*nHStates))
> #
> hfm=HFMfit(data,nHStates,dataNodeIndices,priorInit,transmatInit,transInitDiv,'c',
+ SigmaInit=SigmaInit, muInit=muInit);

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: .Call("RWrapperBM", priorInit, transmatInit, transInitDiv, emissionProb,     data, nodeIndices, parents, summationIndices, indicesXD,     type, stateIndicesSingle, nHStates, nDStates, nObs, dimData,     nEStates, SigmaInit, muInit)
 2: HFMfit(data, nHStates, dataNodeIndices, priorInit, transmatInit,     transInitDiv, "c", SigmaInit = SigmaInit, muInit = muInit)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Loading required package: EbayesThresh
Loading required package: wavethresh
Loading required package: MASS
WaveThresh: R wavelet software, release 4.6.8, installed

Copyright Guy Nason and others 1993-2016

Note: nlevels has been renamed to nlevelsWT

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'treethresh.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               [margin=3cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Quitting from lines 62-71 (trip.Rmd) 
Error: processing vignette 'trip.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Packages required but not available: ‘AnnotationDbi’ ‘GO.db’ ‘topGO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qexpfamily.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.35 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Running ‘test_code.r’ [0s/2s]
Running the tests in ‘tests/test_code.r’ failed.
Last 13 lines of output:
  +     scoring(fit)
  +   }
  +   if(interv){
  +     interv_test(fit, tau=floor(n/2), delta=0.8, external=FALSE, est_interv=TRUE, ...)
  +     interv_detect(fit, taus=floor(0.45*n):ceiling(0.55*n), delta=0.8, B=3, ...)
  +     interv_multiple(fit, taus=floor(0.45*n):ceiling(0.55*n), deltas=c(0,1), B=3, final.control_bootstrap=NULL, ...)
  +   }
  +   return(TRUE)
  + }
  > 
  > checkfit(model=list(past_obs=1, past_mean=1), param=list(intercept=2, past_obs=0.4, past_mean=0.3), startestims=TRUE, extended=TRUE)
  Error in tsglm.sim(n = n, param = param, model = model, xreg = xreg, link = link,  : 
    could not find function "tsglm.sim"
  Calls: checkfit
  Execution halted
Error in re-building vignettes:
  ...
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 in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {mathabx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’ ‘RPostgreSQL’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSPostgreSQL’, ‘TSodbc’, ‘RPostgreSQL’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Apr 02, 2017 10:18:16 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]]
Apr 02, 2017 10:18:16 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.exceptions.SdmxXmlContentException: 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’
Error in re-building vignettes:
  ...
Error: processing vignette 'tsdisagg2manual.ltx' failed with diagnostics:
Running 'texi2dvi' on 'tsdisagg2manual.ltx' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: knitr
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TurtleGraphics.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘survey’

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

    dotchart

Loading required package: xtable
Loading required package: latticeExtra
Loading required package: RColorBrewer
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mnps.tex' failed.
LaTeX errors:
! LaTeX Error: File `srcltx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'design.tex' failed.
LaTeX errors:
! LaTeX Error: File `apalike.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: logLik.MxModel
> ### Title: logLik.MxModel
> ### Aliases: logLik.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
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: umxRun -> mxRun -> runHelper
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Attaching package: 'umx'
  
  The following object is masked from 'package:stats':
  
      loadings
  
  > 
  > test_check("umx")
  Running One Factor with 10 parameters
  Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
    c++ exception (unknown reason)
  Calls: test_check ... eval -> eval -> umxRun -> mxRun -> runHelper -> .Call
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: reshape
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cap-recap.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
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.
Quitting from lines 126-127 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                	      <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning: 'data' shows efficiency > 1; this looks almost too good to be true
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usl.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [scaled=0.85]{beramono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
'library' or 'require' call to ‘foreach’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for ‘pexp’
ll.coverage.optim.const.post.9m: no visible global function definition
  for ‘dexp’
make.sample.pop: no visible global function definition for ‘runif’
mcmc.converge: no visible global function definition for ‘par’
mcmc.converge: no visible global function definition for ‘plot’
mcmc.converge: no visible global function definition for ‘points’
mcmc.converge: no visible global function definition for ‘density’
mcmc.converge: no visible global function definition for ‘lines’
mcmc.converge : <anonymous>: no visible global function definition for
  ‘sd’
mcmc.estimate : run.chain: no visible global function definition for
  ‘dexp’
mcmc.estimate : run.chain: no visible global function definition for
  ‘rnorm’
mcmc.estimate : run.chain: no visible global function definition for
  ‘runif’
mcmc.estimate : run.chain: no visible global function definition for
  ‘par’
mcmc.estimate : run.chain: no visible global function definition for
  ‘plot’
mcmc.estimate: no visible global function definition for ‘%dopar%’
mcmc.estimate: no visible global function definition for ‘foreach’
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for ‘runif’
vaccinate.sample.pop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘coverageTest.r’ [0s/1s]
Running the tests in ‘tests/coverageTest.r’ failed.
Last 13 lines of output:
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in getTestPaths("vacem", "tests/testUtils.r") : 
    could not find function "getTestPaths"
  Calls: source
  Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘devtools’
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/VBmix.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vdg.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.75 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘vdmR-Ex.R’ failed
The error most likely occurred in:

> ### Name: vcmap
> ### Title: Generate choropleth map with interactive functions
> ### Aliases: vcmap
> 
> ### ** Examples
> 
> data(vsfuk2012)
> shp.path <- file.path(system.file(package="vdmR"), "etc/shapes/kitakyu2012.shp")
> kk2012 <- dplyr::filter(vsfuk2012, CityCode<40110&CityCode>40100)
> vcmap(shp.path, kk2012, "CityCode", "CityCode", "map1", "kk2012")
Warning: use rgdal::readOGR or sf::st_read
Error: isTRUE(gpclibPermitStatus()) is not TRUE
Execution halted
Running ‘run-all.R’ [18s/29s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  1. Error: check vcmap (@test-vdmR.R#20) ----------------------------------------
  isTRUE(gpclibPermitStatus()) is not TRUE
  1: vcmap(shp.path, vsfuk2012, "CityCode", "CityCode", "map01", "vsfuk2012", fill = FertilityRate, 
         ggscale = frcol) at /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/vdmR.Rcheck/vdmR/tests/test-vdmR.R:20
  2: broom::tidy(spdf, region = mid, avoidGEOS = TRUE)
  3: tidy.SpatialPolygonsDataFrame(spdf, region = mid, avoidGEOS = TRUE)
  4: maptools::unionSpatialPolygons(cp, attr[, region])
  5: stopifnot(isTRUE(gpclibPermitStatus()))
  6: stop(msg, call. = FALSE, domain = NA)
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 189-193 (vdmR-vignette.Rnw) 
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
isTRUE(gpclibPermitStatus()) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'decision-vegan.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MedRegExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
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.
Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

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

    RGB

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

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

    layer

Quitting from lines 204-213 (intro-to-viridis.Rmd) 
Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc           3.6Mb
    htmlwidgets   3.5Mb
Error in re-building vignettes:
  ...

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

    backsolve

Loading required package: grid
Warning in structure(ia, dimnames = NULL) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ConfoundingPotential.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {keyval}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘testthat’
  All declared Imports should be used.
Missing or unexported object: ‘dplyr::pull’
Package required but not available: ‘GenomicRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
installed size is 31.7Mb
  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 63-68 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
Stan model 'rw_model' does not contain samples.
Execution halted
Package required but not available: ‘hitandrun’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/wand.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
There are  2000 missing values for 05054000 or 49.78 percent of the data.
The maximum block of missing 05054000 data is 12 days long.
Filled in 2000 values for 05054000
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Watersheds.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \bibliographystyle
                       {apacite}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 (b < 0 | b > e) { : missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Error in re-building vignettes:
  ...
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org/data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WebGestaltR.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Package suggested but not available for checking: ‘rgeolocate’
Error in re-building vignettes:
  ...
     6  training    training    training
 [>] sum of weights: 712 - min/max: 1/50
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
 [>] 490 sequences with 6 distinct events/states
 [>] 490 distinct sequences
 [>] min/max sequence length: 70/70
 [>] computing distances using HAM metric
 [>] total time: 0.208 secs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.78 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘HotDeckImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘impute’ ‘GO.db’ ‘AnnotationDbi’

Packages suggested but not available for checking:
  ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘minet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'funwithfunload.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘genefilter’
Packages suggested but not available for checking:
  ‘devtools’ ‘AnomalyDetection’ ‘BreakoutDetection’
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

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 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.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.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/soccer2-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/goggles-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/swim-plot1-1-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/swim2-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rattle’
Running examples in ‘wsrf-Ex.R’ failed
The error most likely occurred in:

> ### Name: combine.wsrf
> ### Title: Combine Ensembles of Trees
> ### Aliases: combine combine.wsrf
> 
> ### ** Examples
> 
>   library("wsrf")
> 
>   # Prepare parameters.
>   ds     <- rattle::weather
Error in loadNamespace(name) : there is no package called ‘rattle’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘wsrftest.R’ [0s/0s]
Running the tests in ‘tests/wsrftest.R’ failed.
Complete output:
  > suppressMessages(library(wsrf))
  > suppressMessages(library(rattle))
  Error in library(rattle) : there is no package called 'rattle'
  Calls: suppressMessages -> withCallingHandlers -> library
  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 63-67 (wsrf-guide.Rmd) 
Error: processing vignette 'wsrf-guide.Rmd' failed with diagnostics:
there is no package called 'rattle'
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages required but not available:
  ‘dnet’ ‘GenomicRanges’ ‘supraHex’ ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'XiMpLe_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'XLConnect.tex' failed.
LaTeX errors:
! LaTeX Error: File `couriers.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                [colorlinks]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Xmisc

Attaching package: ‘Xmisc’

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

    dir.exists

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Xmisc-ArgumentParser.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OtherPackagesGallery.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {hyperref} % hyperref last^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘biomaRt’ ‘Rsamtools’

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

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Packages required but not available: ‘graph’ ‘PairViz’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/zstdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/RtmpIXtYHI/R.INSTALL28b8cda141e3/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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/asht.Rcheck/00install.out' for details.
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  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/bayesCL.Rcheck/00install.out' for details.
Running examples in 'bikedata-Ex.R' failed
The error most likely occurred in:

> ### Name: bike_daily_trips
> ### Title: Extract daily trip counts for all stations
> ### Aliases: bike_daily_trips
> 
> ### ** Examples
> 
> bike_write_test_data () # by default in tempdir ()
  adding: temp/RtmpEVbTuc/Divvy_Trips_sample/ (stored 0%)
  adding: temp/RtmpEVbTuc/Divvy_Trips_sample/Divvy_Stations.csv (deflated 69%)
  adding: temp/RtmpEVbTuc/Divvy_Trips_sample/Divvy_Trips_sample.csv (deflated 79%)
  adding: temp/RtmpEVbTuc/201604-hubway-tripdata.csv (deflated 84%)
  adding: temp/RtmpEVbTuc/2017-Q1-Trips-History-Data.csv (deflated 78%)
  adding: temp/RtmpEVbTuc/la_metro_gbfs_trips_Q1_2017.csv (deflated 85%)
  adding: temp/RtmpEVbTuc/01aJourneyDataExtract10Jan16-23Jan16.csv (deflated 74%)
  adding: temp/RtmpEVbTuc/201612-citibike-tripdata.csv (deflated 74%)
> # dl_bikedata (city = 'la', data_dir = '.') # or download some real data!
> bikedb <- file.path (tempdir (), 'testdb')
> store_bikedata (data_dir = tempdir (), bikedb = bikedb)
Creating sqlite3 database
Unzipping raw data files for ny ...
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Running examples in 'bikedata-Ex.R' failed
The error most likely occurred in:

> ### Name: bike_daily_trips
> ### Title: Extract daily trip counts for all stations
> ### Aliases: bike_daily_trips
> 
> ### ** Examples
> 
> bike_write_test_data () # by default in tempdir ()
  adding: temp/Rtmpmuvmng/Divvy_Trips_sample/ (stored 0%)
  adding: temp/Rtmpmuvmng/Divvy_Trips_sample/Divvy_Stations.csv (deflated 69%)
  adding: temp/Rtmpmuvmng/Divvy_Trips_sample/Divvy_Trips_sample.csv (deflated 79%)
  adding: temp/Rtmpmuvmng/201604-hubway-tripdata.csv (deflated 84%)
  adding: temp/Rtmpmuvmng/2017-Q1-Trips-History-Data.csv (deflated 78%)
  adding: temp/Rtmpmuvmng/la_metro_gbfs_trips_Q1_2017.csv (deflated 85%)
  adding: temp/Rtmpmuvmng/01aJourneyDataExtract10Jan16-23Jan16.csv (deflated 74%)
  adding: temp/Rtmpmuvmng/201612-citibike-tripdata.csv (deflated 74%)
> # dl_bikedata (city = 'la', data_dir = '.') # or download some real data!
> bikedb <- file.path (tempdir (), 'testdb')
> store_bikedata (data_dir = tempdir (), bikedb = bikedb)
Creating sqlite3 database
Unzipping raw data files for ny ...
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  5. Failure: tripmat-demography (@test-tripmat.R#139) ---------------------------
  tm <- bike_tripmat(bikedb = bikedb, city = "ny", member = 1) produced warnings.
  
  
  testthat results ================================================================
  OK: 134 SKIPPED: 0 FAILED: 5
  1. Error: dplyr read db (@test-db-stats.R#15) 
  2. Error: bike_stations function (@test-stations.R#9) 
  3. Error: write and store data (@test-store-data.R#39) 
  4. Error: stations from downloaded data (@test-store-data.R#50) 
  5. Failure: tripmat-demography (@test-tripmat.R#139) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  5. Failure: tripmat-demography (@test-tripmat.R#151) ---------------------------
  ... <- NULL produced warnings.
  
  
  testthat results ================================================================
  OK: 134 SKIPPED: 0 FAILED: 5
  1. Error: dplyr read db (@test-db-stats.R#15) 
  2. Error: bike_stations function (@test-stations.R#9) 
  3. Error: write and store data (@test-store-data.R#39) 
  4. Error: stations from downloaded data (@test-store-data.R#50) 
  5. Failure: tripmat-demography (@test-tripmat.R#151) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/biomartr.Rcheck/00install.out' for details.
Running 'testthat.R' [203s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading 'brms' package (version 1.7.0). Useful instructions 
  can be found by typing help('brms'). A more detailed introduction 
  to the package is available through vignette('brms_overview').
  > 
  > test_check("brms")
  1. Failure: all S3 methods have reasonable ouputs (@tests.brmsfit-methods.R#145) 
  p <- plot(hyp, plot = FALSE) produced warnings.
  
  
  testthat results ================================================================
  OK: 1089 SKIPPED: 1 FAILED: 1
  1. Failure: all S3 methods have reasonable ouputs (@tests.brmsfit-methods.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [7s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  Error in tbl(lahman_df(), "Batting") : 
    could not find function "lahman_df"
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> tbl
  testthat results ================================================================
  OK: 621 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BRugs.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
pandoc.exe: Could not fetch http://www.canvasxpress.org/images/brand3.png
HttpExceptionRequest Request {
  host                 = "www.canvasxpress.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/images/brand3.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure connect: failed (Connection timed out (WSAETIMEDOUT)))
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS getting_started.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output getting_started.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 67
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "causaleffect.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
running 'texi2dvi' on 'causaleffect.ltx' failed

LaTeX errors:
tes/causaleffect.ltx:81: LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
You're in trouble here.  Try typing  <return>  to proceed.
Execution halted
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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Scanning for packages used in this project
- Discovered 1 packages
Installing packages used in this project 
 - Installing 'MASS'
MASS
checkpoint process complete
---
Error: processing vignette 'managing-checkpoint-archives.Rmd' failed with diagnostics:
there is no package called 'markdown'
Execution halted
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
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/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  8.5Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    bin   3.1Mb
    doc   1.7Mb
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shinyapps   5.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   3.0Mb
Error in re-building vignettes:
  ...

Attaching package: 'scales'

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

    discard


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'GGally'

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

    nasa

Quitting from lines 337-354 (exploring-election-data.Rmd) 
Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics:
could not find function "dmap"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/EMCC.Rcheck/00install.out' for details.
Running examples in 'emil-Ex.R' failed
The error most likely occurred in:

> ### Name: learning_curve
> ### Title: Learning curve analysis
> ### Aliases: learning_curve
> 
> ### ** Examples
> 
> options(emil_max_indent=3)
> lc <- learning_curve(c(Linear="lda", Quadratic="qda"),
+                      iris[-5], iris$Species, test_fraction=c(.7, .5, .3))
24 Jun 17:33  Learning curve analysis
24 Jun 17:33    Test set test_fraction 1 of 3 (0.7)
24 Jun 17:33      Evaluating modeling performance...
24 Jun 17:33    Test set test_fraction 2 of 3 (0.5)
24 Jun 17:33      Evaluating modeling performance...
24 Jun 17:33    Test set test_fraction 3 of 3 (0.3)
24 Jun 17:33      Evaluating modeling performance...
> plot(lc)
Error in select.list(., test_fraction = TRUE, fold = TRUE, method = TRUE,  : 
  unused arguments (test_fraction = TRUE, fold = TRUE, method = TRUE, performance = "error")
Calls: plot ... withVisible -> <Anonymous> -> select -> select.list
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
ggtree v1.6.11  For help: https://guangchuangyu.github.io/ggtree

If you use ggtree in published research, please cite:
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 38-44 (bias.Rmd) 
Error: processing vignette 'bias.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: etl
> ### Title: Initialize an 'etl' object
> ### Aliases: etl etl.default is.etl print.etl summary.etl
> 
> ### ** Examples
> 
> 
> # Instantiate the etl object
> cars <- etl("mtcars")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\Rtmp0QqOyh\file131807b2a5255.sqlite3
Warning: call dbDisconnect() when finished working with a connection
Error: The dbplyr package is required to communicate with database backends.
Execution halted
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

trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13546 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at D:\temp\RtmpYD2WiJ/eurostat/ten00081_date_code_TF.rds
trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 4255 bytes
==================================================
downloaded 4255 bytes

Quitting from lines 310-336 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
Evaluation error: only 0's may be mixed with negative subscripts.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gamsel.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Running examples in 'geoSpectral-Ex.R' failed
The error most likely occurred in:

> ### Name: spc.Read_NOMAD_v2
> ### Title: Read the NOMAD v2 bio-optical database
> ### Aliases: spc.Read_NOMAD_v2
> 
> ### ** Examples
> 
> ap = spc.Read_NOMAD_v2()
[1] "Reading the NOMAD file D:/temp/RtmpgpvvLE/RLIBS_1aae48ec55a4/geoSpectral/test_data/nomad_seabass_v2.a_2008200.txt.gz off disk."
Error: Variable context not set
Execution halted
Running 'test-all.R' [86s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  testthat results ================================================================
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Running examples in 'gmapsdistance-Ex.R' failed
The error most likely occurred in:

> ### Name: gmapsdistance
> ### Title: gmapsdistance
> ### Aliases: gmapsdistance
> 
> ### ** Examples
> 
> # Example 1
> results = gmapsdistance(origin = "Washington+DC", 
+                         destination = "New+York+City+NY", 
+                         mode = "driving")
> results
$Time
[1] 13656

$Distance
[1] 361721

$Status
[1] "OK"

> 
> # Example 2
> results = gmapsdistance(origin = "38.1621328+24.0029257",
+                         destination = "37.9908372+23.7383394",
+                         mode = "walking")
> results
$Time
[1] 30487

$Distance
[1] 39509

$Status
[1] "OK"

> 
> # Example 3
> results = gmapsdistance(origin = c("Seattle+WA", "Miami+FL"), 
+                         destination = c("Chicago+IL", "Philadelphia+PA"), 
+                         mode = "bicycling", 
+                         dep_date = "2017-08-16", 
+                         dep_time = "20:40:00")
Error in UseMethod("xmlChildren") : 
  no applicable method for 'xmlChildren' applied to an object of class "NULL"
Calls: gmapsdistance -> as -> .class1 -> xmlChildren
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/goftte.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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Running 'testthat.R' [10s]
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-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/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.
3/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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.1Mb
    libs   1.2Mb
NB: this package is only installed for sub-architecture 'x64'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ICSNP.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  13.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     11.6Mb
Running examples in 'imfr-Ex.R' failed
The error most likely occurred in:

> ### Name: imf_data
> ### Title: Download a data from the IMF
> ### Aliases: imf_data
> 
> ### ** Examples
> 
> # Download Real Effective Exchange Rate (CPI base) for the UK and China
> # at an annual frequency
> real_ex <- imf_data(database_id = 'IFS', indicator = 'EREER_IX',
+                country = c('CN', 'GB'), freq = 'A')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failure when receiving data from the peer
Calls: imf_data ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  No variables decoded!
  persnr used as id!
  1. Failure: filter (@test-dplyr_methods.R#13) ----------------------------------
  dplyr::filter(testdata, persnr == 198505043334) inherits from `tbl_df/tbl/data.frame` not `incadata`.
  
  
  Using tempfile: D:\temp\RtmpAlLlBl\ex_data29e505cb32822.csv2
  [1] "ex_data29e505cb32822.csv2"
  file size: 1103 kb
  testthat results ================================================================
  OK: 38 SKIPPED: 1 FAILED: 1
  1. Failure: filter (@test-dplyr_methods.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
StartKappa: 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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/lavaan.survey.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: ensure_db (@test-db.R#12) ------------------------------------------
  ensure_db(db) produced warnings.
  
  
  2. Failure: ensure_queue (@test-queue.R#21) ------------------------------------
  q <- ensure_queue("foo", db = db) produced warnings.
  
  
  testthat results ================================================================
  OK: 506 SKIPPED: 0 FAILED: 2
  1. Failure: ensure_db (@test-db.R#12) 
  2. Failure: ensure_queue (@test-queue.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: (function (...) 
     .subset2(public_bind_env, "finalize")())(<environment>)
  10: .subset2(public_bind_env, "finalize")()
  11: is_open(self$con)
  12: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: The pipe function (@test_nse.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'macleish-Ex.R' failed
The error most likely occurred in:

> ### Name: etl_extract.etl_macleish
> ### Title: Extract weather data
> ### Aliases: etl_extract.etl_macleish etl_load.etl_macleish
> ###   etl_transform.etl_macleish
> 
> ### ** Examples
> 
> 
> macleish <- etl("macleish")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\RtmpI7ZycU\file229186b7971b3.sqlite3
Error: The dbplyr package is required to communicate with database backends.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/mcPAFit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.6Mb
    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 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(mnis)
  > 
  > test_check("mnis")
  1. Failure: mnis_joined_between returns expected format (@tests_joined_between.R#11) 
  nrow(xmjb) == 9 isn't true.
  
  
  testthat results ================================================================
  OK: 13 SKIPPED: 3 FAILED: 1
  1. Failure: mnis_joined_between returns expected format (@tests_joined_between.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'Test.R' [9s]
Running the tests in 'tests/Test.R' failed.
Last 13 lines of output:
  +   Dates <- GetDates(SubsetExample$lat, SubsetExample$long, Product)[1:2]
  + 
  +   GetSubset(Lat = SubsetExample$lat, Long = SubsetExample$long, Product = Product, Band = Band,
  +             StartDate = Dates[1], EndDate = Dates[1], KmAboveBelow = 0, KmLeftRight = 0)
  + 
  +   MODISSubsets(LoadDat = SubsetExample, Product = "MCD12Q1", Bands = c("Land_Cover_Type_1"),
  +                Size = c(1,1), StartDate = TRUE)
  + 
  +   MODISSummaries(LoadDat = SubsetExample, Product = "MCD12Q1", Band = "Land_Cover_Type_1",
  +                  ValidRange = c(0,254), NoDataFill = 255, ScaleFactor = 1, StartDate = TRUE)
  + }
  Error in Product == GetProducts() : 
    comparison of these types is not implemented
  Calls: GetBands
  Execution halted
Running 'testthat.R' [86s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 172 SKIPPED: 1 FAILED: 11
  1. Error: we can connect (@test_03_dplyr.R#14) 
  2. Error: dplyr copy_to() (@test_03_dplyr.R#24) 
  3. Error: dplyr tbl( sql() ) (@test_03_dplyr.R#35) 
  4. Error: dplyr select() (@test_03_dplyr.R#43) 
  5. Error: dplyr filter() (@test_03_dplyr.R#51) 
  6. Error: dplyr arrange() (@test_03_dplyr.R#59) 
  7. Error: dplyr mutate() (@test_03_dplyr.R#67) 
  8. Error: dplyr summarise() (@test_03_dplyr.R#75) 
  9. Error: dplyr multiple objects (@test_03_dplyr.R#84) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [77s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 156 SKIPPED: 1 FAILED: 11
  1. Error: we can connect (@test_03_dplyr.R#14) 
  2. Error: dplyr copy_to() (@test_03_dplyr.R#24) 
  3. Error: dplyr tbl( sql() ) (@test_03_dplyr.R#35) 
  4. Error: dplyr select() (@test_03_dplyr.R#43) 
  5. Error: dplyr filter() (@test_03_dplyr.R#51) 
  6. Error: dplyr arrange() (@test_03_dplyr.R#59) 
  7. Error: dplyr mutate() (@test_03_dplyr.R#67) 
  8. Error: dplyr summarise() (@test_03_dplyr.R#75) 
  9. Error: dplyr multiple objects (@test_03_dplyr.R#84) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [91s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  testthat results ================================================================
  OK: 178 SKIPPED: 1 FAILED: 2
  1. Failure: PlotContribution() works properly with PhyloExpressionSet input... (@test-PlotContribution.R#11) 
  2. Failure: PlotContribution() works properly with DivergenceExpressionSet input... (@test-PlotContribution.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: Brightness works (@test_brightness.R#7) ----------------------------
  round(mean(brightness, na.rm = TRUE), 4) not equal to 1.0263.
  1/1 mismatches
  [1] 1.03 - 1.03 == 0.0026
  
  
  [1] "Now processing: D:/temp/RtmpiyBpj0/RLIBS_3c9c7ba0400a/nandb/extdata/50.tif."
  [1] "Now processing: 50.tif."
  [1] "Done. Please check folder."
  testthat results ================================================================
  OK: 153 SKIPPED: 0 FAILED: 1
  1. Failure: Brightness works (@test_brightness.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: Brightness works (@test_brightness.R#7) ----------------------------
  round(mean(brightness, na.rm = TRUE), 4) not equal to 1.0263.
  1/1 mismatches
  [1] 1.03 - 1.03 == 0.0026
  
  
  [1] "Now processing: D:/temp/RtmpiyBpj0/RLIBS_3c9c7ba0400a/nandb/extdata/50.tif."
  [1] "Now processing: 50.tif."
  [1] "Done. Please check folder."
  testthat results ================================================================
  OK: 153 SKIPPED: 0 FAILED: 1
  1. Failure: Brightness works (@test_brightness.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'netdiffuseR-Ex.R' failed
The error most likely occurred in:

> ### Name: exposure
> ### Title: Ego exposure
> ### Aliases: exposure
> ### Keywords: univar
> 
> ### ** Examples
> 
> # Calculating the exposure based on Structural Equivalence ------------------
> set.seed(113132)
> graph <- rdiffnet(100, 10)
> 
> SE <- lapply(struct_equiv(graph), "[[", "SE")
> SE <- lapply(SE, function(x) {
+    x <- 1/x
+    x[!is.finite(x)] <- 0
+    x
+ })
> 
> # Recall setting valued equal to TRUE!
> expo_se <- exposure(graph, alt.graph=SE , valued=TRUE)
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.4Mb
    R         2.8Mb
    include   3.8Mb
    libs      1.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
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-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/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  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
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:
> ### Title: Weight polls
> ### Aliases: weight_polls
> 
> ### ** Examples
> 
> polldates <- tail(unique(polls$MidDate), 20)
> weight_polls(polldates, method = "curia")
 [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
[20] NaN
> weight_polls(polldates, method = "pundit")
 [1] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
 [8] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
[15] 0.0000000 0.0000000 0.0000000 0.2620402 0.3376533 0.4003065
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.38 0.22 6.1 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/3.3new/OpenCL.Rcheck/00install.out' for details.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs     5.8Mb
    models   4.7Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  standardize_path(x) not equal to `expected`.
  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  8.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.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 13.1Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [138s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     ... complete. 
  Elapsed time: 0 seconds.
  Creating a dfm from a corpus ...
     ... tokenizing texts
     ... lowercasing
     ... found 14 documents, 5,058 features
     ... created a 14 x 5,058 sparse dfm
     ... complete. 
  Elapsed time: 0 seconds.
  testthat results ================================================================
  OK: 1026 SKIPPED: 17 FAILED: 1
  1. Failure: test corpus constructors works for data.frame (@test-corpus.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
    po    2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.4Mb
    libs      1.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.8Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       8.0Mb
    libs      1.0Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
    libs     25.9Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      21.9Mb
    libs      3.9Mb
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.
Package suggested but not available for checking: 'rsolr'
Running 'getFuns.R' [2s]
  Comparing 'getFuns.Rout' to 'getFuns.Rout.save' ... OK
  Running 'ijroi-format.R' [3s]
  Comparing 'ijroi-format.Rout' to 'ijroi-format.Rout.save' ... OK
  Running 'reconstruct.R' [3s]
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
    Backwards path
      i = 377 ; sf/Sf = 0.5 ; sf = 368.306937214058
        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
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    fonts   1.5Mb
    libs    2.0Mb
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-33~1.3/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
.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').
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
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.
Package suggested but not available for checking: 'rnaturalearthhires'
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: httr::GET(url = "http://nrfaapps.ceh.ac.uk/", path = "nrfa/xml/waterml2", query = list(db = "nrfa_public", 
         stn = idx, dt = type))
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 6 SKIPPED: 0 FAILED: 3
  1. Error: Output of cmr function for single station (@test-cmr.R#5) 
  2. Error: Output of cmr function for multiple stations (@test-cmr.R#22) 
  3. Error: Output of gdf function for id 18019 (@test-gdf.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: src_presto(RPresto::Presto(), schema = "test", catalog = "catalog", host = "http://localhost", 
         port = 8000, user = Sys.getenv("USER"), session.timezone = test.timezone(), parameters = list())
  3: dplyr::src_sql
  4: getExportedValue(pkg, name)
  5: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 218 SKIPPED: 24 FAILED: 3
  1. Error: db_explain works with mock (@test-db_explain.R#25) 
  2. Error: db_query_fields works with mock (@test-db_query_fields.R#42) 
  3. Error: as() works (@test-src_translate_env.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
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.
median:
  function(x, na.rm)
median.sym.data.table:
  function(x, na.rm, method, ...)

median:
  function(x, na.rm)
median.sym.data.table:
  function(x, na.rm, method, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Running examples in 'RSDA-Ex.R' failed
The error most likely occurred in:

> ### Name: median.sym.data.table
> ### Title: Symbolic Median
> ### Aliases: median.sym.data.table
> ### Keywords: Median Symbolic
> 
> ### ** Examples
> 
> data(example3)
> sym.data<-example3
> median(sym.data[,2])
[1] 1.5
> median(sym.data[,6] ,method='interval')
Error in median(sym.data[, 6], method = "interval") : 
  unused argument (method = "interval")
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > 
  > test_check("RSDA")
  1. Error: Mediana simbolica (@test.estadisticos.R#56) --------------------------
  unused argument (method = "interval")
  1: expect_equal(median(example3[, 6], method = "interval"), c(F6 = 5, F6.1 = 89), tolerance = 1e-06) at testthat/test.estadisticos.R:56
  2: compare(object, expected, ...)
  3: median(example3[, 6], method = "interval")
  
  testthat results ================================================================
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Error: Mediana simbolica (@test.estadisticos.R#56) 
  
  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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.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()
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       1.8Mb
    projects   2.2Mb
Running examples in 'secrlinear-Ex.R' failed
The error most likely occurred in:

> ### Name: Arvicola
> ### Title: Water Vole Capture Dataset
> ### Aliases: arvicola
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> head(traps(arvicola))
          x      y
0.A  164.86 609.69
0.B  164.86 609.69
20.A 163.85 629.66
20.B 163.85 629.66
40.A 164.88 649.19
40.B 164.88 649.19
> 
> ## for speed, pre-compute distance matrix
> userd <- networkdistance (traps(arvicola), glymemask, glymemask)
> ## fit model
> glymefit <- secr.fit(arvicola, mask = glymemask, trace = FALSE,
+                      details = list(userdist = userd))
Warning in check3D(object) :
  secr 3.0 requires 3-D capthist; using updateCH() to convert
Warning in autoini(ch, msk, binomN = details$binomN, ignoreusage = details$ignoreusage) :
  'autoini' failed to find g0; setting initial g0 = 0.1
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/selectr.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
Package required and available but unsuitable version: 'parallel'

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

> ### Name: calcBaseline
> ### Title: Calculate the BASELINe PDFs
> ### Aliases: calcBaseline
> 
> ### ** Examples
> 
> # Subset example data
> data(ExampleDb, package="alakazam")
> db <- subset(ExampleDb, ISOTYPE %in% c("IgA", "IgG") & SAMPLE == "+7d")
>  
> # Calculate BASELINe
> baseline <- calcBaseline(db, 
+                          sequenceColumn="SEQUENCE_IMGT",
+                          germlineColumn="GERMLINE_IMGT_D_MASK", 
+                          testStatistic="focused",
+                          regionDefinition=IMGT_V,
+                          targetingModel=HH_S5F,
+                          nproc=1)
Collapsing clonal sequences...
Error in `colnames<-`(`*tmp*`, value = "OBSERVED") : 
  length of 'dimnames' [2] not equal to array extent
Calls: calcBaseline -> observedMutations -> colnames<-
Execution halted
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/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 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.2Mb
Missing or unexported objects:
  'dplyr::build_sql' 'dplyr::translate_sql'
Running examples in 'sqlscore-Ex.R' failed
The error most likely occurred in:

> ### Name: create_statement
> ### Title: Generate a CREATE TABLE statement from a model
> ### Aliases: create_statement
> 
> ### ** Examples
> 
> # Basic create statements
> mod <- glm(Sepal.Length ~ Sepal.Width + Petal.Length + Petal.Width + Species,
+            data=datasets::iris)
> create_statement(mod, src_table="tbl_name", dest_table="target_tbl")
Error: The dbplyr package is required to communicate with database backends.
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sqlscore)
  > 
  > test_check("sqlscore")
  Error: The dbplyr package is required to communicate with database backends.
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/StatMatch.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  	siaf parameter 3: TRUE 
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  argument "new" is missing, with no default
  1: update(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1)) at testthat/test-tiafs.R:45
  2: update.list(imdfit_steptiafInf, tiaf = tiaf.step(c(7, 20), maxRange = maxepst + 0.1))
  
  Error in update.list(model, siaf = NULL, tiaf = NULL, epidemic = ~1, epilink = "log") : 
    argument "new" is missing, with no default
  Calls: test_check ... source_file -> eval -> eval -> update -> update.list
  testthat results ================================================================
  OK: 233 SKIPPED: 1 FAILED: 1
  1. Error: Step kernel with maxRange>max(eps.t) is equivalent to maxRange=Inf (@test-tiafs.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
Running examples in 'tidyjson-Ex.R' failed
The error most likely occurred in:

> ### Name: companies
> ### Title: Startup company information for 1,000 companies
> ### Aliases: companies
> 
> ### ** Examples
> 
> library(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

> library(jsonlite)

Attaching package: 'jsonlite'

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

    read_json

> 
> # Print the first record (do not run automatically)
> # companies[[1]] %>% prettify
> 
> # Get the key employees data
> key_employees <- companies %>%
+   spread_values(
+     name = jstring("name")
+   ) %>%
+   mutate(
+     company.sort_order = rank(name)
+   ) %>%
+   enter_object("relationships") %>%
+   gather_array("relationship.index") %>%
+   spread_values(
+     is.past = jlogical("is_past"),
+     name = jstring("person", "permalink"),
+     title = jstring("title")
+   )
Error in eval(expr, envir, enclos) : 
  argument "json.column" is missing, with no default
Calls: %>% ... tryCatchList -> tryCatchOne -> doTryCatch -> eval -> eval
Execution halted
Running 'testthat.R' [58s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  nrow(test2) not equal to 208.
  1/1 mismatches
  [1] 206 - 208 == -2
  
  
  testthat results ================================================================
  OK: 185 SKIPPED: 2 FAILED: 5
  1. Error: Test prints warning message on invalid x input. (@test_tq_get_dividends.R#23) 
  2. Error: Test returns NA on invalid x input. (@test_tq_get_dividends.R#27) 
  3. Failure: Test prints warning message on invalid x input. (@test_tq_get_splits.R#23) 
  4. Failure: Test 1 returns tibble with correct rows and columns. (@test_tq_get_stock_prices.R#19) 
  5. Failure: Test 2 returns tibble with correct rows and columns. (@test_tq_get_stock_prices.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  testthat results ================================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: 'cross' works (@test-anchor.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc           3.6Mb
    htmlwidgets   3.5Mb
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
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.
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.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  13: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
  14: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  15: open(x, "rb")
  16: open.connection(x, "rb")
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: Test that current version is still latest version (@tests.R#9) 
  
  Error: testthat unit tests failed
  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 '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/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.
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.
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ARTP2.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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.6Mb
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/baseballDBR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 8-9 (./child/ex5-2.Rnw) 
Quitting from lines 44-44 (./child/ex5-2.Rnw) 
Error: processing vignette 'article2-vignette.Rnw' failed with diagnostics:
cannot open connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bayesCL.Rcheck/00install.out’ for details.
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 23.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  18.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BayesTwin.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
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.
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 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/biclique.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.1Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.2Mb
Running examples in ‘Biocomb-Ex.R’ failed
The error most likely occurred in:

> ### Name: Biocomb-package
> ### Title: Tools for Data Mining
> ### Aliases: Biocomb-package Biocomb
> ### Keywords: package feature selection classification information gain
> ###   Relative cost curves HUM roc auc
> 
> ### ** Examples
> 
> data(data_test)
> # class label must be factor
> data_test[,ncol(data_test)]<-as.factor(data_test[,ncol(data_test)])
> 
> # Perform the feature selection using the fast correlation-based filter algorithm
> disc="MDL"
> threshold=0.2
> attrs.nominal=numeric()
> out=select.fast.filter(data_test,disc.method=disc,threshold=threshold,
+ attrs.nominal=attrs.nominal)
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: select.fast.filter ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Package required and available but unsuitable version: ‘configr’

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/bios2mds.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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/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
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 29.8Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
installed size is 243.0Mb
  sub-directories of 1Mb or more:
    include    2.7Mb
    lib      240.0Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breakfast.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breathtestcore.Rcheck/00install.out’ for details.
Package required but not available: ‘breathtestcore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  to the package is available through vignette('brms_overview').
  > 
  > test_check("brms")
  1. Failure: all S3 methods have reasonable ouputs (@tests.brmsfit-methods.R#145) 
  p <- plot(hyp, plot = FALSE) produced warnings.
  
  
  testthat results ================================================================
  OK: 1089 SKIPPED: 1 FAILED: 1
  1. Failure: all S3 methods have reasonable ouputs (@tests.brmsfit-methods.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in ‘tests/test_all.R’ failed.
Last 13 lines of output:
  1. Failure: Test that bsm give identical results with gssm (@test_bootstrap_filter.R#10) 
  2. Failure: Test that bsm give identical results with gssm (@test_bootstrap_filter.R#13) 
  3. Failure: Test that poisson ng_bsm give identical results with ngssm (@test_bootstrap_filter.R#27) 
  4. Failure: Test that binomial ng_bsm give identical results with ngssm (@test_bootstrap_filter.R#36) 
  5. Failure: Test that negative binomial ng_bsm give identical results with ngssm (@test_bootstrap_filter.R#45) 
  6. Failure: Test that still svm works (@test_bootstrap_filter.R#55) 
  7. Failure: Test that poisson ng_bsm give identical results with ngssm (@test_is.R#18) 
  8. Failure: Test that svm still works (@test_is.R#29) 
  9. Failure: MCMC results for Gaussian model are correct (@test_mcmc.R#16) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    libs  54.6Mb
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
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-5, (SVN revision 648)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-4 
Warning in engine$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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/capm.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
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/catSurv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
Running 'texi2dvi' on 'causaleffect.ltx' failed.
LaTeX errors:
! Undefined control sequence.
l.81 \DOI
         {10.18637/jss.v076.i12}
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.
 ...                                              
Execution halted
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.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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/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.
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
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/childsds.Rcheck/00install.out’ for details.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clusterSEs.Rcheck/00install.out’ for details.
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corehunter.Rcheck/00install.out’ for details.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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
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.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
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:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 510 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 511 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 519 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ctsem.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[OO^^S<dd>^^W>^^L"^^V<a1><ed><8d><c4>4<98>ڦ<89>yCBZ<92><ae>\<98>
                                           <ba><e8><ce>ĸ1n\<f3>^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80><99>8L^^...
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 ...O^^S<dd>^^W>^^L"^^V<a1><ed><8d><c4>4<98>ڦ<89>yCBZ<92><ae>\<98><ba><e8><ce>ĸ1n\<f3>
                                                  ^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80><99>8L^^H<da>...
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 ...<c4>4<98>ڦ<89>yCBZ<92><ae>\<98><ba><e8><ce>ĸ1n\<f3>^^UtIܹa/_<a1><bb>&<ee><ba><e8>H\<80>
                                                  <99>8L^^H<da>(<93>N^^GR <81>ˌP'<f8><a3><fd>-<9e><f4>...
The control sequence at the end of the top lin
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cudaBayesreg.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:
  9: http_error(HEAD(x, ...))
  10: HEAD(x, ...)
  11: request_perform(req, hu$handle$handle)
  12: request_fetch(req$output, req$url, handle)
  13: request_fetch.write_memory(req$output, req$url, handle)
  14: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 8 SKIPPED: 4 FAILED: 1
  1. Error: d3_dep-* src href is a valid url (@test_deps.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘d3r’
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot16c4d558b2e19.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c4d558b2e19.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/datasus.Rcheck/datasus/doc/Introduction_to_datasus.R':
invalid multibyte character in parser at line 50
Error in re-building vignettes:
  ...
Warning in engine$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  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dc3net.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
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
Package required and available but unsuitable version: ‘ftsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   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.

Attaching package: 'desctable'

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

    datatable

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

    IQR, chisq.test, fisher.test

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]="./webshot5fb33084ba6f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5fb33084ba6f.png': No such file or directory
Quitting from lines 66-73 (desctable.Rmd) 
Error: processing vignette 'desctable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfcomb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfmta.Rcheck/00install.out’ for details.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.6Mb
Package required but not available: ‘ALL’

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/dggridR.Rcheck/00install.out’ for details.
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/didrooRFM.Rcheck/00install.out’ for details.
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  10.3Mb
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/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.
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
.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
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
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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/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 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   9.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs     2.4Mb
    models   4.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/easyDes.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/edrGraphicalTools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eechidna.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
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’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EMCC.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.8Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  testthat results ================================================================
  OK: 62 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: Person Carl Boettiger <cboettig@gmail.com> was not given any role. 
  2: Person Matthew B. Jones was not given any role. 
  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.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:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot26a02d32b059.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot26a02d32b059.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...<e5><81>h	ԂXqI<a9><c9><c0>H^^H<b5>N<93>K<c6>C<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7>9<dc><e7>/}
                                                  <c4>v,Gg!<c6>wν<ba><e7><9e><df>=<f7>|\ydkk<8b>N.<8d>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.15 ...<99><e0>^^D_i<aa>:<d3>&<96><df><
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: Argument mod1 is deprecated; please use mods and which instead. 
2: Argument mod2 is deprecated; please use mods and which instead. 
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 390 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 391 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 405 is invalid in this locale
6: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 406 is invalid in this locale
7: 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
Packages required and available but unsuitable versions:
  ‘SNPRelate’ ‘gdsfmt’

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

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/EventStudy.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/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
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         magic_character = magic_character, output_path = output_path, allow_pep8 = allow_pep8, 
         prefix = prefix, postfix = postfix, run_pandoc = run_pandoc, compile_latex = compile_latex, 
         pandoc_formats = as.list(pandoc_formats))
  3: python.exec(python.command)
  4: stop(ret$error.desc)
  
  testthat results ================================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Error: pandoc_formats (@test_basic.R#48) 
  2. Error: pandoc_formats_list (@test_basic.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘expands-Ex.R’ failed
The error most likely occurred in:

> ### Name: cellfrequency_pdf
> ### Title: Computes the probability distribution of cellular frequencies
> ###   for a single mutation.
> ### Aliases: cellfrequency_pdf
> 
> ### ** Examples
> 
> freq=seq(0.1,1.0,by=0.01);
> cfd=cellfrequency_pdf(af=0.26,cnv=1.95,pnb=0,freq=freq, max_PM=6)
Error in .jcall("core.utils.Common", "V", "setALLOWED_FREQUENCIES", .jarray(as.double(freq))) : 
  RcallMethod: cannot determine object class
Calls: cellfrequency_pdf -> .jcall -> .External
Execution halted
Errors in running code in vignettes:
when running code in ‘expands.Rnw’
  ...
+     all))

> SPs = clusterCellFrequencies(cfd$densities[toUseIdx, 
+     ], precision)
[1] "Clustering  0 probability distributions..."
[1] "Clustering agglomeration method: average"

  When sourcing ‘expands.R’:
Error: object must be a numeric matrix
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'expands.Rnw' failed with diagnostics:
 chunk 5 
Error in .local(object, ...) : object must be a numeric matrix

Execution halted
Package suggested but not available for checking: ‘golubEsets’
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
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  12.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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.
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  7.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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  8.8Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    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.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fitur.Rcheck/00install.out’ for details.
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 did 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
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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frequencies.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
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/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
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: read_model_frame_into_Weka(mf)
  11: read_data_into_Weka(mf, 1L)
  12: .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List"))
  
  testthat results ================================================================
  OK: 70 SKIPPED: 0 FAILED: 4
  1. Error: Discretization - basic (@test-discretize.R#27) 
  2. Error: Discretization - single NA (independent variable) (@test-discretize.R#42) 
  3. Error: Comparsion with FSelector (@test-information_gain.R#9) 
  4. Error: Test character table (@test-information_gain.R#38) 
  
  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/fso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ftsa.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fullfact.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
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
Packages required and available but unsuitable versions:
  ‘grDevices’ ‘graphics’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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 11.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gastempt.Rcheck/00install.out’ for details.
installed size is 59.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.5Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    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/gdimap.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ggdmc.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/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 ‘ggformula-Ex.R’ failed
The error most likely occurred in:

> ### Name: gf_spline
> ### Title: Formula interface to geom_spline()
> ### Aliases: gf_spline
> 
> ### ** Examples
> 
> if (require(mosaic)) {
+   gf_spline(births ~ date, color = ~wday, data = Births78)
+   gf_spline(births ~ date, color = ~wday, data = Births78, df = 20)
+   gf_spline(births ~ date, color = ~wday, data = Births78, df = 4)
+ }
Loading required package: mosaic
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: lattice
Loading required package: mosaicData
Loading required package: Matrix

The 'mosaic' package masks several functions from core packages in order to add additional features.  
The original behavior of these functions should not be affected by this.

Attaching package: ‘mosaic’

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

    mean

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

    count, do, tally

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

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test, quantile,
    sd, t.test, var

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

    max, mean, min, prod, range, sample, sum

Error: StatSpline 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 engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc05e7bb77beb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc05e7bb77beb.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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]="./webshote9984fee492e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshote9984fee492e.png': No such file or directory
Quitting from lines 16-30 (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  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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
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 'glmertree.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Oh
           ^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
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>\Oh^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>
                                I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
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 ...<95>R<9a><a6>y<f7><ee>]<ce><f9><f5><eb><d7>oܸa^^X^^F<be>^^B<df>^^E^^@x<81><d7>8!<e7>\<d3>
                                                  <b4>T^^]<8d><96><be><b6>3LOO^^?<fd><fa>u'O<bd>y<f3>f<87>...
The control sequence at the end of the top line
of your error message was never 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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
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.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/II_PreProcessing.R':
invalid multibyte character in parser at line 59
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/IV_VisualizeOutputs.R':
invalid multibyte character in parser at line 30
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:
  base log float matrix elements not equivalent
  
  testthat results ================================================================
  OK: 891 SKIPPED: 717 FAILED: 6
  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. Failure: gpuVector Single Precision Element-Wise Logs (@test_gpuVector_math.R#133) 
  4. Error: vclMatrix Integer Matrix multiplication (@test_vclMatrix_algebra.R#307) 
  5. Error: vclMatrix Single Precision Matrix Cholesky Decomposition (@test_vclMatrix_chol.R#25) 
  6. Failure: vclVector Single Precision Matrix Element-Wise Logs (@test_vclVector_math.R#134) 
  
  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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GrammR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
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/groupsubsetselection.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/grt.Rcheck/00install.out’ for details.
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.
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 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
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.
Running examples in ‘helixvis-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw_wenxiang
> ### Title: Create wenxiang diagrams to visualize alpha helical sequences.
> ### Aliases: draw_wenxiang
> 
> ### ** Examples
> 
> draw_wenxiang("TestWenxiang", "AREKHLVLLKREGDIWKL")
Error in rJava::.jnew("Sequence") : 
  java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
Calls: draw_wenxiang -> <Anonymous> -> .External
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 146-147 (Visualization.Rmd) 
Error: processing vignette 'Visualization.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
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/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.
Running examples in ‘HIBPwned-Ex.R’ failed
The error most likely occurred in:

> ### Name: account_breaches
> ### Title: Search for data breaches associated with one or more accounts.
> ### Aliases: account_breaches
> 
> ### ** Examples
> 
> account_breaches(c("steff.sullivan@gmail.com","stephanie.g.locke@gmail.com"))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: account_breaches ... 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: 31 SKIPPED: 0 FAILED: 7
  1. Error: account_breaches works for a single account (@test-account_breaches.R#8) 
  2. Error: account_breaches works for multiple accounts (@test-account_breaches.R#54) 
  3. Error: breached_site works (@test-breached_site.R#6) 
  4. Error: breached_sites works (@test-breached_sites.R#6) 
  5. Error: data_classes works (@test-data_classes.R#4) 
  6. Error: pastes works for a single account (@test-pastes.R#8) 
  7. Error: pastes works for multiple accounts (@test-pastes.R#26) 
  
  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 23-24 (HIBP.Rmd) 
Error: processing vignette 'HIBP.Rmd' failed with diagnostics:
Peer certificate cannot be authenticated with given CA certificates
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiCblock.Rcheck/00install.out’ for details.
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
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  6.8Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   4.3Mb
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: pdftools
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 163-166 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HURDAT.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/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  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.1Mb
    libs   8.3Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
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/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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.5Mb
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
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
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 29.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     18.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/interactionTest.Rcheck/00install.out’ for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred-class QSPRpred
> 
> ### ** 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
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
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  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:
  ...
 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  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/JumpTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KappaGUI.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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmcudaR.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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/laGP.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs          11.1Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ldhmm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lfl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/libstableR.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [using universal kriging]
  2284747 bytes written
  1. Failure: Test if I/O are equal (@test-writeLAS.R#15) ------------------------
  i@data not equal to o@data.
  Column 'Z': Mean relative difference: 0.001260578
  
  
  testthat results ================================================================
  OK: 148 SKIPPED: 0 FAILED: 1
  1. Failure: Test if I/O are equal (@test-writeLAS.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
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
Package which this enhances but not available for checking: ‘reactR’
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      18.7Mb
    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 $.
l.17 Ԓ<da>[}
          <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
I've deleted a group-closing 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'localsolver.Rmd'
Warning in (if (grepl("\\.[Rr]md$", 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.
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.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  9: .subset2(public_bind_env, "finalize")()
  10: is_open(self$con)
  11: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: symbol replacement works (@test_nse.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
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 20.8Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  13.7Mb
objc[19155]: 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 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
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]="./webshot11424aa2620f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot11424aa2620f.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
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  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   5.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mdpeer.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
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
Package required but not available: ‘RODBC’

Package required and available but unsuitable version: ‘mem’

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/mem.Rcheck/00install.out’ for details.
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 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.2Mb
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 15.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    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.
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
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.
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlrMBO’
Package unavailable to check Rd xrefs: ‘mlrMBO’
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  18: .jnew("weka/core/Attribute", attname[i])
  
  testthat results ================================================================
  OK: 2473 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:
  ...
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 'mlt.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ok
           ^^[<d7>^^V?^^]?c^^\<8d>.<86><e2><a4>O<91>zy<c1><81>^^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.17 <82> <9b><cd><c2>/<e9>^^R<9d>^^PB^^HQ.<97><e7><e6><e6><98>^^?)e<b9>\N
                                      &<93>D<84><d1>\<d7>%<a2><a5><a5>%L<81><be>Q<e1><f3>\<fd><88><8e>^^F<b2>{W<af>^%"<cf><f3><b0> &<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.17 <82> <9b><cd><c2>/<e9>^^R<9d>^^PB^^HQ.<97><e7><e6><e6><98>^^?)e<b9>\N&<93>D<84><d1>\<d7>
                                             %<a2><a5><a5>%L<81><be>Q<e1><f3>\<fd><88><8e>^^F<b2>{W<af>^%"<cf><f3><b0> &<d7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control s
Calls: buildVignettes -> texi2pdf -> texi2dvi
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  6.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.0Mb
    libs   2.5Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Failure: Exceptions are thrown (@test_plotSat.R#5) --------------------------
  plotSat(...) threw an error.
  GeomRasterAnn was built with an incompatible version of ggproto.
  Please reinstall the package that provides this extension.
  
  
  Decoding states sequence... DONE
  testthat results ================================================================
  OK: 178 SKIPPED: 0 FAILED: 1
  1. Failure: Exceptions are thrown (@test_plotSat.R#5) 
  
  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/monogeneaGM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mopa.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
Packages suggested but not available for checking: ‘asreml’ ‘happy.hbrem’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Package suggested but not available for checking: ‘org.Mm.eg.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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mudfold.Rcheck/00install.out’ for details.
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 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
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
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  [1] "Now processing: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nandb.Rcheck/nandb/extdata/50.tif."
  [1] "Now processing: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nandb.Rcheck/nandb/extdata/50.tif."
  [2] "Now processing: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nandb.Rcheck/nandb/extdata/50.tif."
  [1] "Now processing: 50.tif."
  [1] "Done. Please check folder."
  testthat results ================================================================
  OK: 174 SKIPPED: 0 FAILED: 2
  1. Failure: Brightness works (@test_brightness.R#7) 
  2. Failure: CorrectForBleachingFolder works (@test_detrend.R#28) 
  
  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/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
Package required but not available: ‘standardize’

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/NB.MClust.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/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.
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
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.0Mb
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 29.7Mb
  sub-directories of 1Mb or more:
    CppCode       12.0Mb
    R              2.8Mb
    classic-bugs   1.5Mb
    include        3.8Mb
    libs           8.5Mb
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
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  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
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/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 74.9Mb
  sub-directories of 1Mb or more:
    libs  74.5Mb
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 148.3Mb
  sub-directories of 1Mb or more:
    libs    140.1Mb
    models    4.6Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.8Mb
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 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
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pafdR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PanJen.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Linking to GEOS 3.4.2, GDAL 2.1.2, proj.4 4.9.1

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

Downloading MP data
Downloading constituency data
Warning in left_join_impl(x, y, by$x, by$y, suffix$x, suffix$y) :
  joining factor and character vector, coercing into character vector
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]="./webshot10ab84ba1d96c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10ab84ba1d96c.png': No such file or directory
Quitting from lines 19-64 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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
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.
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.
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 ‘PeakSegOptimal/libs/PeakSegOptimal.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘PeakSegFPOPLog.o’, ‘PeakSegPDPALog.o’,
      ‘funPieceListLog.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘PeakSegFPOPLog.o’, ‘PeakSegPDPALog.o’,
      ‘funPieceListLog.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 ‘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$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permPATH.Rcheck/00install.out’ for details.
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pi0.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pifpaf.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshotb385608472c8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb385608472c8.png': No such file or directory
Quitting from lines 61-64 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required and available but unsuitable versions: ‘tools’ ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plink.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.
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:
  5: value[[3L]](cond)
  6: errorHandler(req, res, e)
  7: .makeMessage(..., domain = domain)
  8: lapply(list(...), as.character)
  9: FUN(X[[i]], ...)
  10: as.character.default(X[[i]], ...)
  
  testthat results ================================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: htmlwidgets serialize properly (@test-serializer-htmlwidgets.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
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$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$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

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/polypoly.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/portes.Rcheck/00install.out’ for details.
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.5Mb
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.
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
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 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
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.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Attaching package: 'Biobase'
  
  The following object is masked from 'package:propr':
  
      abstract
  
  [1] "operating in serial mode"
  Error in aldex.clr(as.data.frame(t(mail)), conds = rep("A", 5), denom = 2) : 
    unused arguments (conds = rep("A", 5), denom = 2)
  Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> aldex.clr
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.4Mb
  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
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.
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 11.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   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/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
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
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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/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
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
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.5Mb
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.
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 26.6Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.1Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.0Mb
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 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.15 ....<ba><e9>&<8b><aa><9b><92>m+<a1>zg<a9>ـ*<bb><95><fa>^^DbT۲^^H~<84><89><87>)^^Y<e2>6\<8f>
                                                  q<cc>$Ğ<b7><f8><89>+<8b>$<d8>^^F<93>Ɣ<b3><b0>f<ae><ef><9c>{<cf>...
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 ...^^B^^[^^_<e1>h_<9e><83><f1>W.ʯ_~<ea><95><f0>N<d3>^^Y<9a><a6>1<c6>dY<c6>vEQ\XX
                                                  <f8>ꫯ<88>HQ^^T<fc>~<fa>駁@<e0><b3><cf>>[YY<d1>4...
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.15 ...˲<aa><aa><df>~<fb><ed><ca>ʊ<a2>(+++8Ʒn<dd><da><dc><dc><ec><eb><eb><fb><e2><8b>/:<b6><a1><8b>xg'`}}}
                                                  }}^^]<d7><cb><cb>˧<cc>츄w<98>{o^^[<fc><ed><ed>^W
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 13.6Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs      4.7Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    include   6.2Mb
    libs      3.3Mb
Missing or unexported object: ‘tools::package_native_routine_registration_skeleton’
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
Package suggested but not available for checking: ‘RcppMsgPack’
installed size is 88.1Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      52.2Mb
    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/Rcriticor.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/rcv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rdoxygen.Rcheck/00install.out’ for details.
Running examples in ‘Rdrools-Ex.R’ failed
The error most likely occurred in:

> ### Name: Rdrools-package
> ### Title: A Rules Engine for R based on the popular Java based Drools
> ### Aliases: Rdrools-package Rdrools
> ### Keywords: rulesSession runRules Rdrools
> 
> ### ** Examples
> 
> library(Rdrools)
> data(class)
> data(rules)
> input.columns<-c("name", "class", "grade", "email")
> output.columns<-c("address", "subject", "body")
> rules.session<-rulesSession(rules, input.columns, output.columns)
Error in .jnew("org/math/r/drools/DroolsService", rules, input.columns,  : 
  java.lang.UnsupportedClassVersionError: org/math/r/drools/DroolsService : Unsupported major.minor version 51.0
Calls: rulesSession -> .jnew -> .External
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]="./webshot540327f7e726.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot540327f7e726.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/redR.Rcheck/00install.out’ for details.
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reportROC.Rcheck/00install.out’ for details.
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.
Package required and available but unsuitable version: ‘S4Vectors’

Package suggested but not available for checking: ‘rsolr’

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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/revdbayes.Rcheck/00install.out’ for details.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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 12.0Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    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 ...
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RGtk2.Rcheck/00install.out’ for details.
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.
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.
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
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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rlas.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/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RLT.Rcheck/00install.out’ for details.
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.
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 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/rMouse.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.
Found the following significant warnings:
  Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
  ./mumps_save_restore_C.h:15:9: warning: 'MUMPS_SAVE_RESTORE_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmumps.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/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
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
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