Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: jpmesh
  This package provide map data is based on the Digital Map 25000(Map
  Image) published by Geospatial Information Authorityof Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  -- 1. Failure: jpn_pref (@test-spdf_jpn.R#20)  ---------------------------------
  Names of `df_pref2` ('jis_code', 'prefecture', 'geometry') don't match 'jis_code', 'prefecture', '.'
  
  == testthat results  ===========================================================
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: jpn_pref (@test-spdf_jpn.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    geojson  12.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  19: (function (dt, year, month, yday, mday, wday, hour, minute, second, tz = NULL, roll = FALSE, 
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 18, wday = integer(0), 
         hour = 1, minute = 0, second = 0, dt = structure(1487289600, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 62 SKIPPED: 0 FAILED: 1
  1. Error: plot_i_hr_datetime produces a ggplot object (@test_viz_plot.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Running examples in 'lubridate-Ex.R' failed
The error most likely occurred in:

> ### Name: ymd
> ### Title: Parse dates with *y*ear, *m*onth, and *d*ay components
> ### Aliases: ymd ydm mdy myd dmy dym yq
> ### Keywords: chron
> 
> ### ** Examples
> 
> x <- c("09-01-01", "09-01-02", "09-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> x <- c("2009-01-01", "2009-01-02", "2009-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> ymd(090101, 90102)
[1] "2009-01-01" "2009-01-02"
> now() > ymd(20090101)
Warning in with_tz(Sys.time(), tzone) : Unrecognized time zone ''
Error in C_force_tz(time, tz = tzone, roll) : 
  CCTZ: Unrecognized output timezone: ""
Calls: >.POSIXt -> date_to_posix -> force_tz -> C_force_tz -> .Call
Execution halted
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 31, wday = integer(0), 
         hour = 16, minute = 14, second = 5, dt = structure(1522505670.49393, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 31, wday = integer(0), 
         hour = 16, minute = 14, second = 5, dt = structure(1522505691.3244, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2443 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MetaIntegrator.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MRMR.Rcheck/00install.out' for details.
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.
'library' or 'require' calls to packages already attached by Depends:
  'amap' 'clValid' 'cluster' 'fpc' 'xcms'
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'mzR' 'xcms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
    libs   1.5Mb
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 31, wday = integer(0), 
         hour = 16, minute = 34, second = 27.407457113266, dt = structure(1522506865.40746, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 3
  1. Error: character date handling: yyyy-mm-dd hh:mm:ss in past (@test-naptime.R#126) 
  2. Error: character date handling: yyyy-mm-dd hh:mm:ss in future (@test-naptime.R#136) 
  3. Error: Invalid Period throws error (@test-naptime.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.4Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
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-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/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  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.3Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R        2.3Mb
    libs     5.9Mb
    models   4.8Mb
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  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: 18 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 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs   12.1Mb
    share  11.9Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  OK: 33 SKIPPED: 0 FAILED: 28
  1. Error: (unknown) (@test_GTE-summary_by.R#7) 
  2. Error: all queries match expected values (@test_GTE_paper_count.R#132) 
  3. Error: document type = *journal-paper* matches (@test_document_type.R#11) 
  4. Error: document type = *conference-paper* matches (@test_document_type.R#22) 
  5. Error: make_search_url matches number of papers from_year to_year (@test_from_year_to_year.R#12) 
  6. Error: is_dctype_enabled = FALSE (@test_is_dctype_enabled.R#8) 
  7. Error: is_dctype_enabled = TRUE (@test_is_dctype_enabled.R#21) 
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: There were 11 warnings (use warnings() to see them)
  Execution halted
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df -> typeof
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Package required but not available: 'rcqp'

Package suggested but not available for checking: 'polmineR.sampleCorpus'

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

> ### Name: Return24hVolume,PoloniexPublicAPI-method
> ### Title: Returns 24-hour trading volumes for all available markets.
> ###   Additionally, total trading volumes for the 5 primary currencies are
> ###   also retrieved.
> ### Aliases: Return24hVolume,PoloniexPublicAPI-method
> 
> ### ** Examples
> 
> poloniex.public <- PoloniexPublicAPI()
> volume.info <- Return24hVolume(poloniex.public)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10015 milliseconds with 0 out of 0 bytes received
Calls: Return24hVolume ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Rn.eg.db' 'org.Ss.eg.db'
  'org.Bt.eg.db' 'org.Ce.eg.db' 'org.Cf.eg.db' 'org.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'
Running 'run-all.R' [28s]
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  `load.project(override.config = list(data_ignore = ""))` threw an error with unexpected message.
  Expected match: "file is encrypted or is not a database"
  Actual message: "file is not a database"
  
  WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
  WARNING: Perl module Spreadsheet::ParseXLSX cannot be loaded.
  WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
  == testthat results  ===========================================================
  OK: 636 SKIPPED: 4 FAILED: 1
  1. Failure: ignored data files are not loaded (@test-load.R#183) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Error in re-building vignettes:
  ...
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
Running 'tests.R' [7s]
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > op.warn <- getOption("warn")
  > options(warn = 2)
  > quantmod::getSymbols("SPY", src = "google", from = Sys.Date() - 10)
  'getSymbols' currently uses auto.assign=TRUE by default, but will
  use auto.assign=FALSE in 0.5-0. You will still be able to use
  'loadSymbols' to automatically load data. getOption("getSymbols.env")
  and getOption("getSymbols.auto.assign") will still be checked for
  alternate defaults.
  
  This message is shown once per session and may be disabled by setting 
  options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.
  Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  : 
    (converted from warning) cannot open URL 'http://finance.google.com/finance/historical?q=SPY&startdate=Mar+21,+2018&enddate=Mar+31,+2018&output=csv': HTTP status was '403 Forbidden'
  Calls: <Anonymous> -> do.call -> getSymbols.google -> download.file
  Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Package suggested but not available for checking: 'rcom'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/RBPcurve.Rcheck/00install.out' for details.
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
The top-level auxiliary file: RcppGSL-intro.aux
I couldn't open database file Rcpp.bib
---line 151 of file RcppGSL-intro.aux
 : \bibdata{Rcpp
 :              }
I'm skipping whatever remains of this command
The style file: jss.bst
I found no database files---while reading file RcppGSL-intro.aux
Warning--I didn't find a database entry for "GSL"
Warning--I didn't find a database entry for "JSS:Rcpp"
Warning--I didn't find a database entry for "Eddelbuettel:2013:Rcpp"
Warning--I didn't find a database entry for "CRAN:Rcpp"
Warning--I didn't find a database entry for "R:Main"
Warning--I didn't find a database entry for "CRAN:RcppArmadillo"
Warning--I didn't find a database entry for "Eddelbuettel+Sanderson:2013:RcppArmadillo"
Warning--I didn't find a database entry for "Sanderson:2010:Armadillo"
Warning--I didn't find a database entry for "CRAN:RcppEigen"
Warning--I didn't find a database entry for "JSS:RcppEigen"
Warning--I didn't find a database entry for "CRAN:inline"
Warning--I didn't find a database entry for "CRAN:Rcpp:Attributes"
(There were 2 error messages)
Warning: running command '"bibtex" "RcppGSL-intro.aux"' had status 1
Error: processing vignette 'RcppGSL-intro.Rmd' failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.7Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/revdbayes.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
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.
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == testthat results  ===========================================================
  OK: 192 SKIPPED: 0 FAILED: 9
  1. Error: (unknown) (@test-clip_erase.R#41) 
  2. Failure: ms_filter_fields works with polygons (@test-filter_fields.R#32) 
  3. Failure: ms_filter_fields works with lines (@test-filter_fields.R#52) 
  4. Failure: ms_innerlines works with all classes (@test-innerlines.R#45) 
  5. Failure: ms_innerlines works with all classes (@test-innerlines.R#46) 
  6. Failure: ms_lines works with all classes (@test-lines.R#42) 
  7. Failure: ms_lines works with all classes (@test-lines.R#43) 
  8. Failure: ms_lines works with fields specified (@test-lines.R#62) 
  9. Error: (unknown) (@test-simplify.R#208) 
  
  Error: testthat unit tests failed
  Execution halted
File 'RMC/libs/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', 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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
Running 'testthat.R' [62s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  cannot open URL 'http://research.jisao.washington.edu/pdo/PDO.latest'
  1: expect_is(download_pdo(), "data.frame") at testthat/test-pdo-download.R:4
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: download_pdo()
  5: pdo_download()
  6: get_pdo()
  7: download.file("http://research.jisao.washington.edu/pdo/PDO.latest", pdo)
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: pdo_download (@test-pdo-download.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
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/3.4/RQuantLib.Rcheck/00install.out' for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
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.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/rsunlight.Rcheck/00install.out' for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Ryacas.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    sample_data   3.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Running examples in 'seoR-Ex.R' failed
The error most likely occurred in:

> ### Name: hrefLang
> ### Title: Function to retrive the hrefLang-Tag for a given URL
> ### Aliases: hrefLang
> 
> ### ** Examples
> 
> hrefLang("https://www.r-project.org/")
Error in open.connection(x, "rb") : 
  Timeout was reached: Operation timed out after 10015 milliseconds with 0 out of 0 bytes received
Error in as.data.frame.default(unlist(lang)) : 
  cannot coerce class ""try-error"" to a data.frame
Calls: hrefLang -> nrow -> as.data.frame -> as.data.frame.default
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   2.9Mb
installed size is 93.2Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    gdal     3.9Mb
    libs    69.9Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   6.3Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Running 'test_scripts.R' [22s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in plot.gam(model1, se = TRUE) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'stability-Ex.R'
Running examples in 'stacomiR-Ex.R' failed
The error most likely occurred in:

> ### Name: split_per_day
> ### Title: Create a dataframe suitable for charts per 24h and day
> ### Aliases: split_per_day
> 
> ### ** Examples
> 
> datatemp<-structure(list(per_dis_identifiant = c(1L, 1L, 1L), 
+ per_date_debut = structure(c(1420056600, 
+ 1420071000, 1420081200), class = c("POSIXct", "POSIXt"), tzone = ""), 
+ per_date_fin = structure(c(1420071000, 1420081200, 1421000000
+ ), class = c("POSIXct", "POSIXt"), tzone = ""), per_commentaires = c("fonct calcul", 
+ "fonct calcul", "fonct calcul"), per_etat_fonctionnement = c(1L, 
+ 0L, 0L), per_tar_code = 1:3, libelle = c("Fonc normal", "Arr ponctuel", 
+ "Arr maint")), .Names = c("per_dis_identifiant", "per_date_debut", 
+ "per_date_fin", "per_commentaires", "per_etat_fonctionnement", 
+ "per_tar_code", "libelle"), row.names = c(NA, 3L), class = "data.frame")
> newdf<-split_per_day(data=datatemp,horodatedebut="per_date_debut",
+ horodatefin="per_date_fin")
Error in (function (dt, year, month, yday, mday, wday, hour, minute, second,  : 
  Invalid timezone of input vector: ""
Calls: split_per_day ... reclass_date.POSIXlt -> as.POSIXlt -> do.call -> <Anonymous> -> .Call
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   8.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
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-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/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
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Package suggested but not available for checking: 'curatedOvarianData'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
File 'svmpath/libs/i386/svmpath.dll':
  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'
File 'svmpath/libs/x64/svmpath.dll':
  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.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs      13.2Mb
    tessdata  20.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running 'testthat.R' [40s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 141 SKIPPED: 2 FAILED: 13
  1. Failure: Test 1 returns tibble with correct rows and columns. (@test_tq_get_compound_getters.R#24) 
  2. Failure: Test 2 returns tibble with correct rows and columns. (@test_tq_get_compound_getters.R#33) 
  3. Failure: Test 3 returns tibble with correct rows and columns. (@test_tq_get_compound_getters.R#42) 
  4. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_financials.R#18) 
  5. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_financials.R#19) 
  6. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_financials.R#23) 
  7. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_financials.R#25) 
  8. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_ratios.R#14) 
  9. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_ratios.R#16) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------- tidyverse_conflicts() --
x lubridate::as.difftime() masks base::as.difftime()
x lubridate::date()        masks base::date()
x dplyr::filter()          masks stats::filter()
x dplyr::first()           masks xts::first()
x lubridate::intersect()   masks base::intersect()
x dplyr::lag()             masks stats::lag()
x dplyr::last()            masks xts::last()
x lubridate::setdiff()     masks base::setdiff()
x lubridate::union()       masks base::union()
Getting data...

Warning in download.file(url, destfile = tmp, quiet = TRUE) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in value[[3L]](cond) :
  Error at nasdaq during call to tq_exchange.
Warning: x = 'AAPL', get = 'stock.prices': Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=", : cannot open URL 'http://finance.google.com/finance/historical?q=AAPL&startdate=Jan+01,+1990&enddate=Mar+31,+2018&output=csv'

Warning: x = 'AAPL', get = 'financials': Error in thead[x]:thead[x + 1]: NA/NaN argument

Quitting from lines 138-142 (TQ01-core-functions-in-tidyquant.Rmd) 
Error: processing vignette 'TQ01-core-functions-in-tidyquant.Rmd' failed with diagnostics:
no applicable method for 'filter_' applied to an object of class "logical"
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', 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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 10 - 9 == 1
  
  -- 2. Failure: random content can be retrieved (@test_udapi.R#10)  -------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10 - 9 == 1
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  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  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.7Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   9.0Mb
    doc      1.0Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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: 'rPython'

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

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/tmp/Rtmp9dg6NZ/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 23058 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmpXDbdPc/x135a0f164dd223/iofile -n -s 2> /dev/null
Warning: running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmpXDbdPc/x135a0f164dd223/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1282e1579
#1  0x1282e0945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Running ‘run-base.R’ [483s/377s]
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  7: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  8: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  9: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3549 SKIPPED: 0 FAILED: 3
  1. Error: measures (@test_base_measures.R#53) 
  2. Error: check measure calculations (@test_base_measures.R#756) 
  3. Error: predict preserves rownames (@test_base_predict.R#92) 
  
  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.

Execution halted
Running ‘testthat.R’ [53s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 230 SKIPPED: 0 FAILED: 1
  1. Error: logistic_floor (@test_prophet.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [43s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    jurkat_06_100731121305
  Starting to work on MS/MS Peak shape ...
  
  Memory [MB] prior|after|max(diff) : 77.8 | 77.5 | 79.4 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 252 SKIPPED: 0 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#39) 
  2. Failure: createReport (@test_computeQC.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘doRUnit.R’ [85s/85s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector): ERROR !! 
  Error executing .setUp before test.gsl.vector : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.input.SEXP): ERROR !! 
  Error executing .setUp before test.gsl.vector.input.SEXP : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.view): ERROR !! 
  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.
  Error: TEST HAD ERRORS!
  Execution halted
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

> ### Name: grmod
> ### Title: Interface for _gretl_ estimation commands
> ### Aliases: grmod
> 
> ### ** Examples
> 
> set.seed(13)
> dfr = data.frame(y = rnorm(20), x = rnorm(20))
> grmod("ols y 0 x --simple-print",dfr)

No valid gretl executable: no output is produced
Error: '/tmp/RtmpCx6dv6/mbundlefea24cb42380.xml' does not exist.
Execution halted
Found the following significant warnings:
  Warning: D:/temp/RtmpGSsD7p/R.INSTALL2bab815e7474d/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
Authors@R field gives persons with no valid roles:
  Anders Hedenström [fnd]
Package suggested but not available for checking: 'gge'
Running examples in 'agridat-Ex.R' failed
The error most likely occurred in:

> ### Name: crossa.wheat
> ### Title: Multi-environment trial of wheat for 18 genotypes at 25
> ###   locations
> ### Aliases: crossa.wheat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(crossa.wheat)
> dat <- crossa.wheat
> 
> # AMMI biplot.  Fig 3 of Crossa et al.
> if(require(agricolae)){
+   m1 <- with(dat, AMMI(E=loc, G=gen, R=1, Y=yield))
+   b1 <- m1$biplot[,1:4]
+   b1$PC1 <- -1 * b1$PC1 # Flip vertical
+   plot(b1$yield, b1$PC1, cex=0.0,
+        text(b1$yield, b1$PC1, cex=.5, labels=row.names(b1),col="brown"),
+        main="crossa.wheat AMMI biplot", xlab="Average yield", ylab="PC1", frame=TRUE)
+   mn <- mean(b1$yield)
+   abline(h=0, v=mn, col='wheat')
+ 
+   g1 <- subset(b1,type=="GEN")
+   text(g1$yield, g1$PC1, rownames(g1), col="darkgreen", cex=.5)
+ 
+   e1 <- subset(b1,type=="ENV")
+   arrows(mn, 0,
+          0.95*(e1$yield - mn) + mn, 0.95*e1$PC1,
+          col= "brown", lwd=1.8,length=0.1)
+ }
Loading required package: agricolae
> 
> # GGB example
> library(agridat)
> data(crossa.wheat)
> dat2 <- crossa.wheat
> 
> # FIXME: The loc grouping is now in the data
> 
> # Define mega-environment groups of locations
> dat2$eg <- ifelse(is.element(dat2$loc,
+                              c("KN","NB","PA","BJ","IL","TC",
+                                "JM","PI","AS","ID","SC","SS",
+                                "SJ","MS","MG","MM")), "Grp1", "Grp2")
> 
> library(gge)
Error in library(gge) : there is no package called 'gge'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 44-53 (agridat_examples.Rmd) 
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'gge'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 1. Failure: Downloaded data is as expected (@test_download.R#29)  -----------
  get_fred_series(...) not equal to data.frame(date = as.Date("2009-03-01"), test = 89.1913).
  Component "test": Mean relative difference: 0.002053736
  
  -- 2. Failure: Downloaded data is as expected (@test_download.R#36)  -----------
  dplyr::filter(get_fred_series("INDPRO", "test"), date == "2009-03-01") not equal to data.frame(date = as.Date("2009-03-01"), test = 89.1913).
  Component "test": Mean relative difference: 0.002053736
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Downloaded data is as expected (@test_download.R#29) 
  2. Failure: Downloaded data is as expected (@test_download.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/apaStyle.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'trtf'
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.
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  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.
Found the following significant warnings:
  Warning: replacing previous import 'spam::det' by 'Matrix::det' when loading 'bamlss'
See 'd:/Rcompile/CRANpkg/local/3.3/bamlss.Rcheck/00install.out' for details.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "cont1.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 in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'knitr::knitr') for vignette with name 'cont1'. The following files exist in directory '.': 'bincat.Rnw', 'bincat.aux', 'bincat.bbl', 'bincat.blg', 'bincat.log', 'bincat.out', 'bincat.pdf', 'bincat.tex', 'computing.Rnw', 'computing.aux', 'computing.bbl', 'computing.blg', 'computing.log', 'computing.out', 'computing.pdf', 'computing.tex', 'cont1.Rnw', 'cont1.tex', 'cont2.Rnw', 'hwbart.R', 'hwbart.Rmd', 'hwbart.pdf', 'references.bib', 'time-to-event.Rnw', 'time-to-event.pdfsync'
Calls: buildVignettes -> find_vignette_product
Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
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.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  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.
Authors@R field gives persons with no valid roles:
  Bea Hernández [rev] (Bea reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
  Elaine McVey [rev] (Elaine reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-04-01 09:15:36] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  == testthat results  ===========================================================
  OK: 59 SKIPPED: 0 FAILED: 5
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: initial (@test_install_uilts.R#39) 
  4. Error: dependence (@test_install_uilts.R#88) 
  5. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'bmrm-Ex.R' failed
The error most likely occurred in:

> ### Name: mmc
> ### Title: Convenient wrapper function to solve max-margin clustering
> ###   problem on a dataset
> ### Aliases: mmc
> 
> ### ** Examples
> 
>    # -- Prepare a 2D dataset to cluster with an intercept
>    x <- cbind(intercept=100,scale(data.matrix(iris[c(1,3)]),center=TRUE,scale=FALSE))
> 
>    # -- Find max-margin clusters
>    y <- mmc(x,k=3,LAMBDA=0.001,minClusterSize=10,seeds=5)
Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column
Calls: mmc ... merge.default -> merge -> merge.data.frame -> fix.by
Execution halted
Package suggested but not available for checking: 'ASGS.foyer'
Authors@R field gives persons with no valid roles:
  Brooke Anderson <brooke.anderson@colostate.edu> [rev] (0000-0002-5012-9035)
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   2.7Mb
    lib      69.0Mb
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: eval_bare(get_expr(quo), get_env(quo))
  4: lapply(boxoffice(dates = christmas, site = "mojo", top_n = 10), class)
  5: boxoffice(dates = christmas, site = "mojo", top_n = 10)
  6: httr::GET(paste0(url_start, url_dates[i]), httr::user_agent(useragent))
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  OK: 83 SKIPPED: 0 FAILED: 1
  1. Error: column types are correct (@test-column-types.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'BrailleR-Ex.R' failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Running examples in 'broom-Ex.R' failed
The error most likely occurred in:

> ### Name: kde_tidiers
> ### Title: Tidy a kernel density estimate object from the ks package
> ### Aliases: kde_tidiers tidy.kde
> 
> ### ** Examples
> 
> 
> if (require("ks", quietly = TRUE)) {
+   dat <- replicate(2, rnorm(100))
+   k <- kde(dat)
+   
+   td <- tidy(k)
+   head(td)
+   
+   library(ggplot2)
+   ggplot(td, aes(x1, x2, fill = estimate)) +
+     geom_tile() +
+     theme_void()
+   
+   # also works with 3 dimensions
+   dat3 <- replicate(3, rnorm(100))
+   k3 <- kde(dat3)
+   
+   td3 <- tidy(k3)
+   head(td3)
+ }
Note: method with signature 'Matrix#diagonalMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#ddiMatrix'.
 "sparseMatrix#ANY" would also be valid
Note: method with signature 'dsparseMatrix#dsparseMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#dtTMatrix'.
 "sparseMatrix#TsparseMatrix" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: kde -> Hpi -> gdscalar -> norm -> norm
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File 'camel/libs/i386/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'
File 'camel/libs/x64/camel.dll':
  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.
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:
  ...
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Chicago,%20IL&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Chicago, IL"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=New%20York&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "New York"
Quitting from lines 16-23 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
regularize.values: possible error in xy.coords(x, y, setLab = FALSE):
  unused argument (setLab = FALSE)
Running 'SP500-ex.R' [34s]
Running the tests in 'tests/SP500-ex.R' failed.
Last 13 lines of output:
  +     dim(spWts.non0 <- spWts[rowSums(spWts) > 0 , ])
  +     round(1000 * spWts.non0)
  +     ##
  +     image(spWts.non0, xlab = "turning point", ylab = "asset number")
  +     wts.non0 <- as(spWts.non0, "matrix")
  + }) else {
  +     warning("'Matrix' package not available -- should not happen!")
  +     wts.non0 <- CLs5c.0.120$weights_set[rowSums(CLs5c.0.120$weights_set) > 0 , ]
  +     if(is.null(colnames(wts.non0))) ## empty column names for nice printing:
  +         colnames(wts.non0) <- rep("", ncol(wts.non0))
  +     print.table(round(1000 * wts.non0), zero.print=".")
  + }
  Loading required package: Matrix
  Error: could not find function "withAutoprint"
  Execution halted
Package suggested but not available for checking: 'SingleCellExperiment'
Unknown package 'SingleCellExperiment' in Rd xrefs
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SingleCellExperiment'
Error in .requirePackage(package) : 
  unable to find required package 'SingleCellExperiment'
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 143-147 (clustree.Rmd) 
Error: processing vignette 'clustree.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
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
Authors@R field gives persons with no valid roles:
  Anna Krystalli [rev] (0000-0002-2378-4915)
  Toph Allen [rev] (0000-0003-4580-091X)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/cometExactTest.Rcheck/00install.out' for details.
Packages required and available but unsuitable versions: 'graphics' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Running 'testthat.R' [104s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Cyclops.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/D3GB.Rcheck/00install.out' for details.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         ...), class = structure("nonstandardGenericFunction", package = "methods")), 
         <environment>)
  27: .findInheritedMethods(classes, fdef, mtable)
  28: (function (x) 
     x$.self$finalize())(<environment>)
  
  Error in (function (x)  : 
    no function to return from, jumping to top level
  == testthat results  ===========================================================
  OK: 113 SKIPPED: 0 FAILED: 2
  1. Error: map shows (@tests_map_bimap.R#32) 
  2. Error: (unknown) (@tests_map_bimap.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  R Consortium [fnd]
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         "stack"), class = "Rcpp_stack_trace")), .Names = c("message", "call", "cppstack"
     ), class = c("Rcpp::exception", "C++Error", "error", "condition")))
  
  Error in stop(list(message = "Failed to connect: Can't connect to MySQL server on 'localhost' (0)",  : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... <Anonymous> -> .local -> connection_create -> .Call
  == testthat results  ===========================================================
  OK: 536 SKIPPED: 11 FAILED: 4
  1. Error: explicit collection returns all data (@test-collect.R#13) 
  2. Error: (unknown) (@test-collect.R#11) 
  3. Error: explicit collection returns all data (@test-collect.R#13) 
  4. Error: (unknown) (@test-collect.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/depth.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.7Mb
Running 'has-devel.R' [3s]
  Running 'test-that.R' [91s]
Running the tests in 'tests/test-that.R' failed.
Last 13 lines of output:
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 399 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    bin   3.1Mb
    doc   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DGVM3D.Rcheck/00install.out' for details.
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     ))), ndim = 4L, lambda = c(0, 0.001, 0.01, 0.1, 1, 10, 100), kernel = "rbfdot", kernel.pars = structure(list(
         sigma = c(0.001, 0.01, 0.1, 1, 10, 100, 1000, 10000)), .Names = "sigma"), pca = TRUE, 
         pca.center = TRUE, pca.scale = FALSE, fastcv = FALSE, cv.folds = 5, fastcv.test = NULL, 
         fastkrr.nblocks = 4, verbose = TRUE)
  8: krrl$learn(data, res[[1]])
  9: krr(data$x[i_indices, ], kernel, data$y[i_indices], params$lambda)
  10: solve(Matrix(K + diag(lambda, N)))
  11: solve(Matrix(K + diag(lambda, N)))
  
  == testthat results  ===========================================================
  OK: 108 SKIPPED: 0 FAILED: 1
  1. Error: rmse_by_ndim (@test_quality.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
package 'diversitree' exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/diversitree.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: expect_identical(summarise(gdf, out = !(!1:2)), tibble(g = c(1, 2), out = 1:2)) at testthat/test-summarise.r:985
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  == testthat results  ===========================================================
  OK: 2876 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: expect_identical(summarise(gdf, out = !(!1:2)), tibble(g = c(1, 2), out = 1:2)) at testthat/test-summarise.r:985
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  == testthat results  ===========================================================
  OK: 2876 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  Execution halted
File 'DPpackage/libs/i386/DPpackage.dll':
  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'
File 'DPpackage/libs/x64/DPpackage.dll':
  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.
Authors@R field gives persons with no valid roles:
  Ben Marwick <bmarwick@uw.edu> [rev]
  Peter Slaughter <slaughter@nceas.ucsb.edu> [rev]
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
File 'EBS/libs/i386/EBS.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'GeneralFunctions.o'
File 'EBS/libs/x64/EBS.dll':
  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.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 108-113 (parsing.Rmd) 
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
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
File 'elrm/libs/i386/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'
File 'elrm/libs/x64/elrm.dll':
  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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/EMAtools.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/EMMIXcskew.Rcheck/00install.out' for details.
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
Missing or unexported object: 'xcms::profMat'
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  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: 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Universidade Federal de Santa Maria <ppgcs@ufsm.br> [fnd]
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FieldSim.Rcheck/00install.out' for details.
Package required but not available: 'CVXR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Warning: invalid input found on input connection 'fivethirtyeight-Ex.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FRESA.CAD.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.5Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3, 3).
  Lengths differ: 5 is not 6
  
  -- 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 2, 3).
  Lengths differ: 5 is not 6
  
  == testthat results  ===========================================================
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#56) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'GAMens-Ex.R' failed
The error most likely occurred in:

> ### Name: GAMens
> ### Title: Applies the GAMbag, GAMrsm or GAMens ensemble classifier to a
> ###   data set
> ### Aliases: GAMens
> ### Keywords: models classif
> 
> ### ** Examples
> 
> 
> ## Load data (mlbench library should be loaded)
> library(mlbench)
> data(Ionosphere)
> 
> ## Train a GAMens ensemble,
> ## estimated using 4 nonparametric terms and 2 linear terms
> Ionosphere.GAMens <- GAMens(Class~s(V3,4)+s(V4,4)+s(V5,3)+s(V6,5)+V7+V8,
+ Ionosphere ,3 , autoform=FALSE, iter=10 )
Error: could not find function "predict.gam"
Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
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 ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/GGEBiplotGUI.Rcheck/00install.out' for details.
Package required but not available: 'gge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nipals'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required and available but unsuitable version: 'grid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'base2grob'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/googledrive.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Neal Richardson <neal.p.richardson@gmail.com> [rev] (Neal reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
  Julia Gustavsen <j.gustavsen@gmail.com> [rev] (Julia reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
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")
Invalid citation information in 'inst/CITATION':
  Error in .citation(rval): attempt to set an attribute on NULL
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/GPoM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Package required but not available: 'hexSticker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
Package required and available but unsuitable version: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggimage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Error in library.dynam(lib, package, package.lib) : 
  DLL 'diversitree' not found: maybe not installed for this architecture?
Quitting from lines 24-37 (hisse-vignette.Rmd) 
Error: processing vignette 'hisse-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'diversitree'
Execution halted
Package suggested but not available for checking: 'trackr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/HiveR.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  The R Consortium [fnd]
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  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'
File 'hSDM/libs/x64/hSDM.dll':
  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.
Running 'testthat.R' [108s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 83 SKIPPED: 17 FAILED: 11
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9) 
  3. Error: phyloseq sim (@test-HTSSIP_sim.R#59) 
  4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75) 
  5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 
  6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#35) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/HUM.Rcheck/00install.out' for details.
Dscores: no visible global function definition for 'filter'
Dscores: no visible global function definition for 'sd'
Gscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'object.size'
RobustScores: no visible global function definition for 'filter'
SplitHalf: no visible global function definition for 'cor'
TestRetest: no visible global function definition for 'filter'
TestRetest: no visible global function definition for 'cor'
WPRscores: no visible global function definition for 'filter'
WPRscores: no visible global function definition for 'quantile'
WPRscores: no visible global function definition for 'sd'
computeMinid: no visible global function definition for 'sd'
doP1P2: no visible global function definition for 'filter'
doP1P2: no visible global function definition for 'sd'
doP1P2P3P4: no visible global function definition for 'filter'
specialvar: no visible global function definition for 'var'
Undefined global functions or variables:
  cor filter object.size quantile sd var
Consider adding
  importFrom("stats", "cor", "filter", "quantile", "sd", "var")
  importFrom("utils", "object.size")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    3.2Mb
    libs   2.9Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         val
     })(Assessment.StockCode = "cod.27.47d20", Assessment.AssessmentYear = 2015L, Assessment.ContactPerson = "colin.millar@ices.dk", 
         Assessment.NameSystemProducedFile = "icesSAG R package version 1.3.2", Assessment.Fish_Data.Year = 2000L, 
         Assessment.Fish_Data.Year = 2001L, Assessment.Fish_Data.Year = 2002L, Assessment.Fish_Data.Year = 2003L, 
         Assessment.Fish_Data.Year = 2004L, Assessment.Fish_Data.Year = 2005L, Assessment.Fish_Data.Year = 2006L, 
         Assessment.Fish_Data.Year = 2007L, Assessment.Fish_Data.Year = 2008L, Assessment.Fish_Data.Year = 2009L, 
         Assessment.Fish_Data.Year = 2010L, Assessment.Fish_Data.Year = 2011L, Assessment.Fish_Data.Year = 2012L, 
         Assessment.Fish_Data.Year = 2013L, Assessment.Fish_Data.Year = 2014L, Assessment.Fish_Data.Year = 2015L)
  
  == testthat results  ===========================================================
  OK: 1334 SKIPPED: 0 FAILED: 1
  1. Error: SAG upload (@test-test.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Andee Kaplan [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
  Carl Ganz [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     11.6Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\Rtmp2vPLhm\ex_data9af86bd45a14.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\Rtmp2vPLhm\ex_data9af86bd45a14.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
Package required and available but unsuitable version: 'libcoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace with empty importFrom: 'miscTools'
Found the following significant warnings:
  Warning: S3 methods '.DollarNames.Message', '.DollarNames.Descriptor', '.DollarNames.EnumDescriptor', '.DollarNames.EnumValueDescriptor', '.DollarNames.FileDescriptor', '.DollarNames.FieldDescriptor', '.DollarNames.ServiceDescriptor', '.DollarNames.MethodDescriptor', '.DollarNames.ZeroCopyInputStream', '.DollarNames.ZeroCopyOutputStream', 'with.Message', 'within.Message', 'as.list.Message', 'as.list.Descriptor', 'as.list.EnumDescriptor', 'as.list.FileDescriptor', 'as.list.ServiceDescriptor' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.3/jmvcore.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant number: MR/M013227/1)
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant numbers: G0400615 and MR/M013227/1)
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: jpmesh
  This package provide map data is based on the Digital Map 25000(Map
  Image) published by Geospatial Information Authorityof Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  -- 1. Failure: jpn_pref (@test-spdf_jpn.R#20)  ---------------------------------
  Names of `df_pref2` ('jis_code', 'prefecture', 'geometry') don't match 'jis_code', 'prefecture', '.'
  
  == testthat results  ===========================================================
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: jpn_pref (@test-spdf_jpn.R#20) 
  
  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.
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:
> # Basic usage with default arguments
> result = knockoff.filter(X, y, knockoffs=knockoffs,
+                            statistic=stat.stability_selection)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 89 99
> 
> # Advanced usage with custom arguments
> foo = stat.stability_selection
> k_stat = function(X, X_k, y) foo(X, X_k, y, fitfun=stabs::lars.lasso)
> result = knockoff.filter(X, y, knockoffs=knockoffs, statistic=k_stat)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 65 89 99
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  53.51 1.31 54.6 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 ?) ========
Running examples in 'ks-Ex.R' failed
The error most likely occurred in:

> ### Name: Hpi
> ### Title: Plug-in bandwidth selector
> ### Aliases: Hpi Hpi.diag hpi
> ### Keywords: smooth
> 
> ### ** Examples
> 
> data(unicef)
> Hpi(unicef, pilot="dscalar")
Note: method with signature 'ANY#sparseMatrix' chosen for function 'kronecker',
 target signature 'dgeMatrix#dtTMatrix'.
 "Matrix#ANY" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: Hpi -> gdscalar -> norm -> norm
Execution halted
Error in re-building vignettes:
  ...
Loading required package: boot
Loading required package: MASS
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "laeken-intro.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 in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'laeken-intro'. The following files exist in directory '.': 'laeken-intro-018.pdf', 'laeken-intro-023.pdf', 'laeken-intro.Rnw', 'laeken-intro.tex', 'laeken-pareto.Rnw', 'laeken-standard.Rnw', 'laeken-variance.Rnw', 'laeken.bib'
Calls: buildVignettes -> find_vignette_product
Execution halted
Authors@R field gives persons with no valid roles:
  Laura Graham [rev] (Laura reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
  Jeffrey Hollister [rev] (Jeffrey reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/languageserver.Rcheck/00install.out' for details.
File 'leaps/libs/i386/leaps.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'leaps.o'
File 'leaps/libs/x64/leaps.dll':
  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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in 'lmem.gwaser-Ex.R' failed
The error most likely occurred in:

> ### Name: mq.g.diagnostics
> ### Title: Performs molecular markers quality diagnostics.
> ### Aliases: mq.g.diagnostics
> 
> ### ** Examples
> 
> data (QA_geno)
> data (QA_map)
> data (QA_pheno)
> 
> P.data <- QA_pheno
> G.data <- QA_geno
> map.data <- QA_map
> 
> cross.data  <- gwas.cross (P.data, G.data, map.data,
+ cross='gwas', heterozygotes=FALSE)
 --Read the following data:
	 179  individuals
	 811  markers
	 3  phenotypes
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
 --Cross type: bc 
> summary (cross.data)
Warning in summary.cross(cross.data) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
    Doubled haploids

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    7 
        Autosomes:      1 2 3 4 5 6 7 

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in mq_missinggenotype_plot(crossobj) : 
  could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Running examples in 'LOGIT-Ex.R' failed
The error most likely occurred in:

> ### Name: confusion_stat
> ### Title: Display confusion or classification matrix following logistic
> ###   regression using glm with binomial family.
> ### Aliases: confusion_stat
> ### Keywords: models
> 
> ### ** Examples
> 
> library(MASS)
> library(LOGIT)
> data(R84)
> R84$cage <- R84$age - mean(R84$age)
> R84$cdoc <- R84$docvis - mean(R84$docvis)
> mylogit <- glm(outwork ~ cdoc + female + kids + cage + factor(edlevel),
+ family=binomial, data=R84)
> mu <- predict(mylogit, type="response")
> cutpoint<-ROCtest(mylogit, fold=10, type="Sensitivity")$cut
> mu[mu>=cutpoint]<-1
> mu[mu<cutpoint]<-0
> confusion_stat(mu, R84$outwork)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
Package required and available but unsuitable version: 'partykit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 30, wday = integer(0), 
         hour = 11, minute = 30, second = 5, dt = structure(1522402204.92533, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2429 SKIPPED: 4 FAILED: 6
  1. Error: Comparison operators work with POSIX and Date objects (@test-ops-compare.R#4) 
  2. Error: difftime comparison with periods works (@test-ops-compare.R#63) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  4. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  5. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  6. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 30, wday = integer(0), 
         hour = 11, minute = 30, second = 5, dt = structure(1522402231.56438, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  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 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: row_ievora(x = x, g = grp)
  7: row_t_welch(x[, g == 1, drop = FALSE], x[, g == 0, drop = FALSE])
  8: rowSums((x - mxs)^2, na.rm = TRUE)
  9: stop("'x' must be an array of at least two dimensions")
  
  == testthat results  ===========================================================
  OK: 820 SKIPPED: 0 FAILED: 4
  1. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cases.R#48) 
  2. Error: groups can all be NA (@test-parameters-special-cases.R#103) 
  3. Error: groups can all be NaN (@test-parameters-special-cases.R#113) 
  4. Error: all observations can be in the same group (@test-parameters-special-cases.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
File 'maxent/libs/i386/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'
File 'maxent/libs/x64/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.2     v dplyr   0.7.4
v tidyr   0.8.0     v stringr 1.3.0
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Loading required package: lattice
Error in unloadNamespace(package) : 
  namespace 'lattice' is imported by 'nlme', 'Matrix', 'psych', 'mosaic' so cannot be unloaded
Error : .onAttach failed in attachNamespace() for 'mdsr', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package 'lattice' version 0.20.35 cannot be unloaded
Error: package or namespace load failed for 'mdsr'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
File 'MigClim/libs/i386/MigClim.dll':
  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'
File 'MigClim/libs/x64/MigClim.dll':
  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.
Missing or unexported object: 'tools::CRAN_package_db'
Package required and available but unsuitable version: 'S4Vectors'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run-base.R' [567s]
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  7: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  8: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  9: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  == testthat results  ===========================================================
  OK: 3549 SKIPPED: 0 FAILED: 3
  1. Error: measures (@test_base_measures.R#53) 
  2. Error: check measure calculations (@test_base_measures.R#756) 
  3. Error: predict preserves rownames (@test_base_predict.R#92) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'run-base.R' [589s]
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  7: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  8: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  9: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  == testthat results  ===========================================================
  OK: 3549 SKIPPED: 0 FAILED: 3
  1. Error: measures (@test_base_measures.R#53) 
  2. Error: check measure calculations (@test_base_measures.R#756) 
  3. Error: predict preserves rownames (@test_base_predict.R#92) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [230s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  DONE
  Predicting locations (and uncertainty) for 1 track(s) using crawl::crwPredict...DONE
  Fitting 1 track(s) using crawl::crwMLE... 
  DONE
  Predicting locations (and uncertainty) for 1 track(s) using crawl::crwPredict...DONE
  Fitting 2 track(s) using crawl::crwMLE... 
  DONE
  Predicting locations (and uncertainty) for 2 track(s) using crawl::crwPredict...DONE
  Decoding state sequence... DONE
  == testthat results  ===========================================================
  OK: 205 SKIPPED: 0 FAILED: 1
  1. Failure: Exceptions are thrown (@test_MIfitHMM.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/monoreg.Rcheck/00install.out' for details.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [2s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
     38, 38, 38), second = c(17.5454881191254, 17.5454881191254, 17.5454881191254, 17.5454881191254, 
     17.5454881191254, 17.5454881191254), dt = structure(c(1017466697.54549, 1017466697.54549, 
     1017466697.54549, 1048999097.54549, 1048999097.54549, 1080621497.54549), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 3
  1. Error: Cumulative measures (@test-TriangleConstruction.R#5) 
  2. Error: Incremental measures (@test-TriangleConstruction.R#23) 
  3. Error: Multiple stochastic measures (@test-TriangleConstruction.R#41) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  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.
Authors@R field gives persons with no valid roles:
  YouGov [fnd]
Running examples in 'NAM-Ex.R' failed
The error most likely occurred in:

> ### Name: GWP
> ### Title: Genome-wide prediction
> ### Aliases: wgr ben
> 
> ### ** Examples
> 
> # Load data
> data(tpod)
> 
> # BLUP
> BRR = wgr(y,gen,iv=FALSE,pi=0,it=200,bi=50)
> cor(y,BRR$hat)
          [,1]
[1,] 0.6981897
> 
> # BayesA
> BayesA = wgr(y,gen,iv=TRUE,pi=0,it=200,bi=50)
> cor(y,BayesA$hat)
          [,1]
[1,] 0.6919416
> 
> # BayesB
> BayesB = wgr(y,gen,iv=TRUE,pi=.95,it=200,bi=50)
> cor(y,BayesB$hat)
          [,1]
[1,] 0.5943869
> 
> # BayesC
> BayesC = wgr(y,gen,iv=FALSE,pi=.95,it=200,bi=50)
> cor(y,BayesC$hat)
          [,1]
[1,] 0.4894693
> 
> # BayesL
> BayesL = wgr(y,gen,de=TRUE,it=200,bi=50)
> cor(y,BayesL$hat)
          [,1]
[1,] 0.6558428
> 
> # Bagging  BLUP
> Bag = wgr(y,gen,bag=0.999,it=200,bi=50)
> cor(y,Bag$hat)
          [,1]
[1,] 0.5964858
> 
> # Subsampling  BLUP
> Sub = wgr(y,gen,bag=0.5,it=200,bi=50)
Error in crossprod(x, y) : 
  requires numeric/complex matrix/vector arguments
Calls: wgr -> crossprod
Execution halted
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 30, wday = integer(0), 
         hour = 12, minute = 6, second = 16.5243508815765, dt = structure(1522404374.52435, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 3
  1. Error: character date handling: yyyy-mm-dd hh:mm:ss in past (@test-naptime.R#126) 
  2. Error: character date handling: yyyy-mm-dd hh:mm:ss in future (@test-naptime.R#136) 
  3. Error: Invalid Period throws error (@test-naptime.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  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.
File 'NetSim/libs/i386/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'
File 'NetSim/libs/x64/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             cat(msg)
         if (length(msg) == 0) {
             e = simpleError(paste(1:length(messages), messages, sep = ": ", collapse = ""))
             class(e) = c(class, class(e))
             stop(e)
         }
         messages <<- c(messages, msg)
     })(character(0))
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-NFP.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.3Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
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
Authors@R field gives persons with no valid roles:
  Julia Silge [rev] (Julia Silge reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/36.)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMPController.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMx.Rcheck/00install.out' for details.
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  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: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'CVXR'

Package suggested but not available for checking: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 556 SKIPPED: 0 FAILED: 2
  1. Error: interval: year (@test_thicken_integration.R#7) 
  2. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 572 SKIPPED: 0 FAILED: 1
  1. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required and available but unsuitable versions: 'libcoin' 'inum'

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:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  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: 18 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  8.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Error: (unknown) (@test_GTE-summary_by.R#7) 
  2. Error: all queries match expected values (@test_GTE_paper_count.R#132) 
  3. Error: document type = *journal-paper* matches (@test_document_type.R#11) 
  4. Error: document type = *conference-paper* matches (@test_document_type.R#22) 
  5. Error: make_search_url matches number of papers from_year to_year (@test_from_year_to_year.R#12) 
  6. Error: is_dctype_enabled = FALSE (@test_is_dctype_enabled.R#8) 
  7. Error: is_dctype_enabled = TRUE (@test_is_dctype_enabled.R#21) 
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 5 (https://www.onepetro.org/search?q=smartwell&peer_reviewed=&published_between=&from_year=&to_year=) 
  Execution halted
Package required and available but unsuitable version: 'qusage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  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.
pointdensity: no visible global function definition for
  'txtProgressBar'
pointdensity: no visible global function definition for
  'setTxtProgressBar'
pointdensity: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "flush.console", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
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'
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ..
  ..
  == testthat results  ===========================================================
  OK: 8417 SKIPPED: 53 FAILED: 8
  1. Error: compile (@test_add_connected_constraints.R#12) 
  2. Error: (unknown) (@test_add_connected_constraints.R#3) 
  3. Error: compile (@test_add_connected_constraints.R#12) 
  4. Error: (unknown) (@test_add_connected_constraints.R#3) 
  5. Error: compile (@test_add_connected_constraints.R#12) 
  6. Error: (unknown) (@test_add_connected_constraints.R#3) 
  7. Error: compile (@test_add_connected_constraints.R#12) 
  8. Error: (unknown) (@test_add_connected_constraints.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
Running examples in 'psychmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: correct_d
> ### Title: Correct _d_ values for range restriction and/or measurement
> ###   error
> ### Aliases: correct_d
> 
> ### ** Examples
> 
> ## Correction for measurement error only
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
    dgy   dgp   dGy   dGp
1 0.458 0.516 0.512 0.578
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = NULL, pa = .5, n1 = 100, n2 = 200)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
  value CI_LL_95 CI_UL_95   n n_effective
1 0.595      0.3    0.912 300         183
> 
> ## Correction for direct range restriction in the continuous variable
> correct_d(correction = "uvdrr_y", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)
Error in indirect_rr | rxxa_consistency : 
  operations are possible only for numeric, logical or complex types
Calls: correct_d -> correct_r -> correct_r_uvdrr
Execution halted
Authors@R field gives persons with no valid roles:
  Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see https://github.com/openjournals/joss-reviews/issues/470)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   2.4Mb
Error in re-building vignettes:
  ...
downloaded 0 bytes

Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot download all files
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    contrib   3.6Mb
    doc       2.9Mb
Running examples in 'quantable-Ex.R' failed
The error most likely occurred in:

> ### Name: determineCut
> ### Title: determine best Accuracy cuttoff
> ### Aliases: determineCut
> 
> ### ** Examples
> 
> library(pROC)
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, smooth, var

> cases <- rnorm(100,-1,1.1)
> controls <- rnorm(500,1,1.1)
> cut <- determineCut(cases,controls)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
Running 'testthat.R' [129s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: new("dfm", x, docvars = data.frame(row.names = rownames(x)))
  13: initialize(value, ...)
  14: initialize(value, ...)
  15: callNextMethod()
  16: .nextMethod(.Object = .Object, ... = ...)
  17: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  18: asMethod(object, Class, value)
  19: slot(value, what)
  
  == testthat results  ===========================================================
  OK: 1938 SKIPPED: 27 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: new("dfm", x, docvars = data.frame(row.names = rownames(x)))
  13: initialize(value, ...)
  14: initialize(value, ...)
  15: callNextMethod()
  16: .nextMethod(.Object = .Object, ... = ...)
  17: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  18: asMethod(object, Class, value)
  19: slot(value, what)
  
  == testthat results  ===========================================================
  OK: 1938 SKIPPED: 27 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'tests.R' [7s]
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > op.warn <- getOption("warn")
  > options(warn = 2)
  > quantmod::getSymbols("SPY", src = "google", from = Sys.Date() - 10)
  'getSymbols' currently uses auto.assign=TRUE by default, but will
  use auto.assign=FALSE in 0.5-0. You will still be able to use
  'loadSymbols' to automatically load data. getOption("getSymbols.env")
  and getOption("getSymbols.auto.assign") will still be checked for
  alternate defaults.
  
  This message is shown once per session and may be disabled by setting 
  options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.
  Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  : 
    (converted from warning) cannot open URL 'http://finance.google.com/finance/historical?q=SPY&startdate=Mar+20,+2018&enddate=Mar+30,+2018&output=csv': HTTP status was '403 Forbidden'
  Calls: <Anonymous> -> do.call -> getSymbols.google -> download.file
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
    po    2.1Mb
Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
Running examples in 'RCzechia-Ex.R' failed
The error most likely occurred in:

> ### Name: okresy
> ### Title: Districts (okresy)
> ### Aliases: okresy
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3
> 
> hranice <- okresy()
Error: unknown input format
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: expect_that(is.data.frame(casti()), is_true()) at testthat/test-jla.R:5
  2: condition(object)
  3: expect_true(x)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: is.data.frame(casti())
  7: casti()
  8: readRDS(url(remote_df))
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-jla.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
-- Attaching packages ---------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.2     v dplyr   0.7.4
v tidyr   0.8.0     v stringr 1.3.0
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3
Quitting from lines 27-52 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unknown input format
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'rsolr'
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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 required and available but unsuitable versions: 'grid' 'utils'

See section 'The DESCRIPTION file' 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/3.3/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
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/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.
Running 'testthat.R' [67s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  4: ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv = use_iconv, swapAxisOrder = swapAxisOrder, 
         require_geomType = require_geomType)
  
  == testthat results  ===========================================================
  OK: 290 SKIPPED: 0 FAILED: 6
  1. Error: (unknown) (@test-clip_erase.R#41) 
  2. Error: ms_filter_fields works with polygons (@test-filter_fields.R#30) 
  3. Error: ms_filter_fields works with points (@test-filter_fields.R#40) 
  4. Error: ms_filter_fields works with lines (@test-filter_fields.R#50) 
  5. Failure: ms_filter_fields fails correctly (@test-filter_fields.R#58) 
  6. Error: (unknown) (@test-simplify.R#208) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rmetasim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Rmpfr.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error : Oops, API did not return json after calling '§dldl  ':
        check your query - or api.oadoi.org may experience problems
Quitting from lines 177-178 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Oops, API did not return json after calling '10.1016/j.trc.2013.12.009':
        check your query - or api.oadoi.org may experience problems
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RockFab.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Andrew MacDonald [rev] (Andrew MacDonald reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
  Andy  Teucher [rev] (Andy Teucher reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Warning in self$configPolyhedraSource(source.config = sources.config[[source]],  :
  bytecode version mismatch; using eval

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.
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.
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.
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.
Running examples in 'RSMET-Ex.R' failed
The error most likely occurred in:

> ### Name: meteofranceSynop
> ### Title: SYNOP Weather Data in France
> ### Aliases: meteofranceSynop
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofranceSynop)
> 
> 
> 
> 
> data=meteofranceSynop[meteofranceSynop$timestamp==meteofranceSynop$timestamp[250],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.Rcheck/00install.out' for details.
Running 'testthat.R' [328s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [399s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsunlight.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()
Authors@R field gives persons with no valid roles:
  ERC Grant Agreement number 336167 - the CHAI Project [fnd]
  Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
  Kara  Woo [rev] (Kara Woo reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
Package required and available but unsuitable version: 'RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/s2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/selectiveInference.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Entries with different classification: 1 (0.1%)
  Correlation between scores of matching entries: 0.5
  Average sentiment: 0.25 vs -0.4
  -- 1. Failure: dictionary generations works correctly (@test.generateDictionary.
  dictionary$scores not equal to c(-0.4190744, 0.3955698).
  2/2 mismatches (average diff: 0.0711)
  [1] -0.344 - -0.419 == 0.0746
  [2]  0.463 -  0.396 == 0.0675
  
  == testthat results  ===========================================================
  OK: 386 SKIPPED: 0 FAILED: 1
  1. Failure: dictionary generations works correctly (@test.generateDictionary.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
File 'sequoia/libs/i386/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.o'
File 'sequoia/libs/x64/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.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.
Authors@R field gives persons with no valid roles:
  Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1)
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Running CCA
  Computing nearest neighbor graph
  Computing SNN
  == testthat results  ===========================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_preprocessing.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Running CCA
  Computing nearest neighbor graph
  Computing SNN
  == testthat results  ===========================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_preprocessing.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/shapes.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: D:/temp/RtmpCowpeK/R.INSTALL1b7207d1d3c8f/sharpr2/man/sharpr2-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/sharpr2.Rcheck/00install.out' for details.
prepare_Rd: sharpr2-package.Rd:1: All text must be in a section
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
Running 'testthat.R' [21s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    |============================                                          |  40%
    |                                                                            
    |==========================================                            |  60%[1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  257087"
  [1] "Estimated replications per hour:  2117147"
  [1] "Estimated replications per hour:  246866"
  [1] "Estimated replications per hour:  2307274"
  [1] "Estimated replications per hour:  230730"
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 0 FAILED: 1
  1. Failure: summary.fun can handel logical data and returning vector 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test_scripts.R' [26s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in eval(expr, envir, enclos) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
Running 'test_scripts.R' [27s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in eval(expr, envir, enclos) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
contact_matrix: possible error in xtabs(data = contacts.sample, formula
  = weight ~ agegroup + cnt.agegroup, addNA = TRUE): unused argument
  (addNA = TRUE)
contact_matrix: possible error in xtabs(data = part.sample, formula =
  weight ~ agegroup, addNA = TRUE): unused argument (addNA = TRUE)
Running examples in 'socialmixr-Ex.R' failed
The error most likely occurred in:

> ### Name: contact_matrix
> ### Title: Generate a contact matrix from diary survey data
> ### Aliases: contact_matrix
> 
> ### ** Examples
> 
> data(polymod)
> contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 1, 5, 15))
Using Polymod Social Contact Data. To cite this in a publication, use the 'cite' function
Sampling the age of contacts with missing age from other participants of the same age group.
  To change this behaviour, set the 'missing.contact.age' option
Error in xtabs(data = contacts.sample, formula = weight ~ agegroup + cnt.agegroup,  : 
  unused argument (addNA = TRUE)
Calls: contact_matrix -> xtabs
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    @Misc{,
      title = {Polymod Social Contact Data},
      author = {Joël Mossong and Niel Hens and Mark Jit and Philippe Beutels and Kari Auranen and Rafael Mikolajczyk and Marco Massari and Stefania Salmaso and Gianpaolo Scalia Tomba and Jacco Wallinga and Janneke Heijne and Malgorzata Sadkowska-Todys and Magdalena Rosinska and W. John Edmunds},
      doi = {10.5281/zenodo.1059920},
      publisher = {Zenodo},
      note = {Version 1.1},
      year = {2017},
    }
  
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-matrix.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 57-58 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unused argument (addNA = TRUE)
Execution halted
Running 'run-all.R' [198s]
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
  To use backup site...
  Downloading spark-2.3.0 for Hadoop 2.7 from:
  - http://www-us.apache.org/dist/spark/spark-2.3.0/spark-2.3.0-bin-hadoop2.7.tgz
  trying URL 'http://www-us.apache.org/dist/spark/spark-2.3.0/spark-2.3.0-bin-hadoop2.7.tgz'
  Content type 'application/x-gzip' length 226128401 bytes (215.7 MB)
  ==================================
  downloaded 147.6 MB
  
  downloaded length 154776315 != reported length 226128401
  Unable to download from default mirror site: http://www-us.apache.org/dist/spark
  Error in robustDownloadTar(mirrorUrl, version, hadoopVersion, packageName,  : 
    Unable to download Spark spark-2.3.0 for Hadoop 2.7. Please check network connection, Hadoop version, or provide other mirror sites.
  Calls: install.spark -> robustDownloadTar
  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').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sparsesvd.Rcheck/00install.out' for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sphereplot.Rcheck/00install.out' for details.
Warning: invalid input found on input connection 'stability-Ex.R'
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
Authors@R field gives persons with no valid roles:
  Scott  Chamberlin [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Running examples in 'survtmle-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in `colnames<-`(`*tmp*`, value = c("t", "group", "value")) : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
Package suggested but not available for checking: 'tidyquant'
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 11
  1. Error: (unknown) (@test_sw_sweep.R#3) 
  2. Error: (unknown) (@test_tidiers_StructTS.R#3) 
  3. Error: (unknown) (@test_tidiers_arima.R#3) 
  4. Error: (unknown) (@test_tidiers_bats_tbats.R#3) 
  5. Error: (unknown) (@test_tidiers_decomposed_ts.R#3) 
  6. Error: (unknown) (@test_tidiers_ets.R#3) 
  7. Error: (unknown) (@test_tidiers_hw.R#3) 
  8. Error: (unknown) (@test_tidiers_lm.R#3) 
  9. Error: (unknown) (@test_tidiers_nnetar.R#3) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-30 (SW00_Introduction_to_sweep.Rmd) 
Error: processing vignette 'SW00_Introduction_to_sweep.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
Packages required and available but unsuitable versions:
  'parallel' 'phyloseq' 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  Luke Winslow [rev] (Reviewed for rOpenSci)
  Laura DeCicco [rev] (Reviewed for rOpenSci)
Package required but not available: 'alphavantager'

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

> ### Name: tk_augment_timeseries
> ### Title: Augment the time series signature to the data
> ### Aliases: tk_augment_timeseries tk_augment_timeseries_signature
> 
> ### ** Examples
> 
> library(tidyquant)
Error in library(tidyquant) : there is no package called 'tidyquant'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 9
  1. Error: (unknown) (@test_tk_augment_timeseries.R#2) 
  2. Error: (unknown) (@test_tk_get_timeseries.R#2) 
  3. Error: (unknown) (@test_tk_index.R#3) 
  4. Error: (unknown) (@test_tk_make_future_timeseries.R#2) 
  5. Error: (unknown) (@test_tk_tbl.R#6) 
  6. Error: (unknown) (@test_tk_ts.R#4) 
  7. Error: (unknown) (@test_tk_xts.R#4) 
  8. Error: (unknown) (@test_tk_zoo.R#4) 
  9. Error: (unknown) (@test_tk_zooreg.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-29 (TK00_Time_Series_Coercion.Rmd) 
Error: processing vignette 'TK00_Time_Series_Coercion.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Package required but not available: 'rsolr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'Coxph-Ex.R' [3s]
Running the tests in 'tests/Coxph-Ex.R' failed.
Complete output:
  > 
  > library("tram")
  Loading required package: mlt
  Loading required package: basefun
  Loading required package: variables
  > library("survival")
  > library("trtf")
  Error in library("trtf") : there is no package called 'trtf'
  Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'TH.data'

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

    geyser

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'quantreg'

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

    untangle.specials

Quitting from lines 22-51 (tram.Rnw) 
Error: processing vignette 'tram.Rnw' failed with diagnostics:
there is no package called 'trtf'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/treethresh.Rcheck/00install.out' for details.
Running examples in 'TukeyRegion-Ex.R' failed
The error most likely occurred in:

> ### Name: TukeyRegion-package
> ### Title: Computation of the Tukey Region and the Tukey Median
> ### Aliases: TukeyRegion-package TukeyRegion-package
> ### Keywords: Tukey region Tukey depth Halfspace depth Location depth
> ###   Halfspace contour Tukey median Barycenter Depth-weighted trimmed mean
> 
> ### ** Examples
> 
> # Load required packages
> require(TukeyRegion)
> require(MASS)
> # Generate data
> set.seed(1)
> X <- mvrnorm(100, rep(0, 3), diag(3))
> # Compute and visualize two Tukey regions
> Tr1 <- TukeyRegion(X, 5, "bfs", 
+   retFacets = TRUE, retVolume = TRUE, retBarycenter = TRUE)
Status:0
> Tr2 <- TukeyRegion(X, 25, "bfs", 
+   retFacets = TRUE, retVolume = TRUE, retBarycenter = TRUE)
Status:0
> plot(Tr1, colorFacets = "red", colorRidges = "red", 
+   colorPoints = "blue", alpha = 0.35)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 10 - 9 == 1
  
  -- 2. Failure: random content can be retrieved (@test_udapi.R#10)  -------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10 - 9 == 1
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  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  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  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  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
Running examples in 'wbstats-Ex.R' failed
The error most likely occurred in:

> ### Name: wbdatacatalog
> ### Title: Download an updated list of the World Bank data catalog
> ### Aliases: wbdatacatalog
> 
> ### ** Examples
> 
> wbdatacatalog()
Error in sprintf("World Bank API request failed for indicator %s\nmessage: %s\ncategory: %s\nreason: %s \nurl: %s",  : 
  argument "indicator" is missing, with no default
Calls: wbdatacatalog -> wbget_dc -> lapply -> FUN -> call_api
Execution halted
Running examples in 'WufooR-Ex.R' failed
The error most likely occurred in:

> ### Name: fields_info
> ### Title: Return details about form's fields
> ### Aliases: fields_info
> 
> ### ** Examples
> 
> fields_info(formIdentifier = "z5kqx7h1gtvg4g", showRequestURL = TRUE)
Error in http_statuses[[as.character(status)]] : subscript out of bounds
Calls: fields_info -> doRequest -> stop_for_status
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: stop_for_status(getResponse)
  4: stop(http_condition(x, "error", task = task, call = call))
  5: http_condition(x, "error", task = task, call = call)
  6: http_status(status)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 5
  1. Error: Fields request returns 17 rows, always (@test-fieldsAndreports.R#9) 
  2. Error: Reports have 11 fields (@test-fieldsAndreports.R#16) 
  3. Error: Form request returns 17 rows, always (@test-forms.R#9) 
  4. Error: Form returns entries, with the requested URL (@test-forms.R#14) 
  5. Error: User request returns 17 rows, always (@test-users.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-47 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Package suggested but not available for checking: 'GenomicScores'
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'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/xptr.Rcheck/00install.out' for details.
Running examples in 'yCrypticRNAs-Ex.R' failed
The error most likely occurred in:

> ### Name: annotationsSet
> ### Title: Create a geneAnnotation object.
> ### Aliases: annotationsSet
> 
> ### ** Examples
> 
> annotationsSet()
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  scerevisiae_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: annotationsSet -> <Anonymous> -> useDataset
Execution halted