| Back to the "Multiple platform build/check report" | A [B] C D E F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2015-08-20 13:21:47 -0700 (Thu, 20 Aug 2015).
| Package 99/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| BiocStyle 1.7.6 Bioconductor Package Maintainer
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ ERROR ] | OK | ||||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| Package: BiocStyle |
| Version: 1.7.6 |
| Command: rm -rf BiocStyle.buildbin-libdir BiocStyle.Rcheck && mkdir BiocStyle.buildbin-libdir BiocStyle.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocStyle.buildbin-libdir BiocStyle_1.7.6.tar.gz >BiocStyle.Rcheck\00install.out 2>&1 && cp BiocStyle.Rcheck\00install.out BiocStyle-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocStyle.buildbin-libdir --install="check:BiocStyle-install.out" --force-multiarch --no-vignettes --timings BiocStyle_1.7.6.tar.gz |
| StartedAt: 2015-08-20 01:51:36 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 01:52:16 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 39.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocStyle.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf BiocStyle.buildbin-libdir BiocStyle.Rcheck && mkdir BiocStyle.buildbin-libdir BiocStyle.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocStyle.buildbin-libdir BiocStyle_1.7.6.tar.gz >BiocStyle.Rcheck\00install.out 2>&1 && cp BiocStyle.Rcheck\00install.out BiocStyle-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=BiocStyle.buildbin-libdir --install="check:BiocStyle-install.out" --force-multiarch --no-vignettes --timings BiocStyle_1.7.6.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/BiocStyle.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocStyle/DESCRIPTION' ... OK
* this is package 'BiocStyle' version '1.7.6'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BiocStyle' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': 'rmarkdown:::metadata'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'rmarkdown:::from_rmarkdown' 'rmarkdown:::normalize_path'
'rmarkdown:::pandoc_html_highlight_args'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [0s] OK
** running examples for arch 'x64' ... [0s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_tests.R' [3s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "run_tests.R" "run_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/run_tests.R' failed.
Last 13 lines of output:
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Test files with failing tests
test_latex.R
test_maketitle
Error in BiocGenerics:::testPackage("BiocStyle") :
unit tests failed for package BiocStyle
Execution halted
** running tests for arch 'x64' ...
Running 'run_tests.R' [2s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "run_tests.R" "run_tests.Rout"' had status 1
ERROR
Running the tests in 'tests/run_tests.R' failed.
Last 13 lines of output:
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Test files with failing tests
test_latex.R
test_maketitle
Error in BiocGenerics:::testPackage("BiocStyle") :
unit tests failed for package BiocStyle
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/BiocStyle.Rcheck/00check.log'
for details.
BiocStyle.Rcheck/tests_i386/run_tests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("BiocStyle")
Writing to file maketitle_test_1.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_1.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_1.tex'
Timing stopped at: 0.05 0.03 0.78
Error : running 'texi2dvi' on 'maketitle_test_1.tex' failed
LaTeX errors:
D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpUZjbgV/maketitle_test_1.tex:9: LaTeX Error:
Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help
! LaTeX Error: File `D:/biocbld/BBS-3\unhbox\voidb@x \penalty \@M \ {}1.2-B/R/s
hare/texmf/tex/latex/Sweave.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
In addition: Warning message:
running command '"C:\PROGRA˜2\MIKTEX˜1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "maketitle_test_1.tex" --max-iterations=20 -I "D:/biocbld/BBS-3˜1.2-B/R/share/texmf/tex/latex" -I "D:/biocbld/BBS-3˜1.2-B/R/share/texmf/bibtex/bst"' had status 1
RUNIT TEST PROTOCOL -- Thu Aug 20 01:52:07 2015
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
BiocStyle RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_maketitle: Error : running 'texi2dvi' on 'maketitle_test_1.tex' failed
LaTeX errors:
D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpUZjbgV/maketitle_test_1.tex:9: LaTeX Error:
Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help
! LaTeX Error: File `D:/biocbld/BBS-3\unhbox\voidb@x \penalty \@M \ {}1.2-B/R/s
hare/texmf/tex/latex/Sweave.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Test files with failing tests
test_latex.R
test_maketitle
Error in BiocGenerics:::testPackage("BiocStyle") :
unit tests failed for package BiocStyle
Execution halted
BiocStyle.Rcheck/tests_x64/run_tests.Rout.fail:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("BiocStyle")
Writing to file maketitle_test_1.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_1.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_1.tex'
Timing stopped at: 0.06 0.02 0.67
Error : running 'texi2dvi' on 'maketitle_test_1.tex' failed
LaTeX errors:
D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpQ3aPYk/maketitle_test_1.tex:9: LaTeX Error:
Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help
! LaTeX Error: File `D:/biocbld/BBS-3\unhbox\voidb@x \penalty \@M \ {}1.2-B/R/s
hare/texmf/tex/latex/Sweave.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
In addition: Warning message:
running command '"C:\PROGRA˜2\MIKTEX˜1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "maketitle_test_1.tex" --max-iterations=20 -I "D:/biocbld/BBS-3˜1.2-B/R/share/texmf/tex/latex" -I "D:/biocbld/BBS-3˜1.2-B/R/share/texmf/bibtex/bst"' had status 1
RUNIT TEST PROTOCOL -- Thu Aug 20 01:52:10 2015
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
BiocStyle RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test_maketitle: Error : running 'texi2dvi' on 'maketitle_test_1.tex' failed
LaTeX errors:
D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpQ3aPYk/maketitle_test_1.tex:9: LaTeX Error:
Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help
! LaTeX Error: File `D:/biocbld/BBS-3\unhbox\voidb@x \penalty \@M \ {}1.2-B/R/s
hare/texmf/tex/latex/Sweave.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Test files with failing tests
test_latex.R
test_maketitle
Error in BiocGenerics:::testPackage("BiocStyle") :
unit tests failed for package BiocStyle
Execution halted
BiocStyle.Rcheck/00install.out:
install for i386 * installing *source* package 'BiocStyle' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'BiocStyle' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'BiocStyle' as BiocStyle_1.7.6.zip * DONE (BiocStyle)
BiocStyle.Rcheck/examples_i386/BiocStyle-Ex.timings:
| name | user | system | elapsed | |
| html_document | 0 | 0 | 0 | |
| latex | 0 | 0 | 0 | |
| markdown | 0 | 0 | 0 | |
| pdf_document | 0 | 0 | 0 | |
BiocStyle.Rcheck/examples_x64/BiocStyle-Ex.timings:
| name | user | system | elapsed | |
| html_document | 0 | 0 | 0 | |
| latex | 0 | 0 | 0 | |
| markdown | 0 | 0 | 0 | |
| pdf_document | 0 | 0 | 0 | |