| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:09 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BiocStyle PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 167/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BiocStyle 2.16.1 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: BiocStyle |
| Version: 2.16.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocStyle.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BiocStyle_2.16.1.tar.gz |
| StartedAt: 2020-10-17 01:58:20 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:00:23 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 123.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocStyle.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocStyle.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BiocStyle_2.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BiocStyle.Rcheck' * using R version 4.0.3 (2020-10-10) * 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 '2.16.1' * package encoding: UTF-8 * 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 Unexported object imported by a ':::' call: 'rmarkdown:::partition_yaml_front_matter' 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'run_tests.R' OK ** running tests for arch 'x64' ... Running 'run_tests.R' OK * 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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BiocStyle.Rcheck/00check.log' for details.
BiocStyle.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BiocStyle_2.16.1.tar.gz && rm -rf BiocStyle.buildbin-libdir && mkdir BiocStyle.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocStyle.buildbin-libdir BiocStyle_2.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BiocStyle_2.16.1.zip && rm BiocStyle_2.16.1.tar.gz BiocStyle_2.16.1.zip
###
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install for i386
* installing *source* package 'BiocStyle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocStyle'
finding HTML links ... done
BiocStyle-defunct html
helpers html
html_document html
latex html
macros html
markdown html
md_document html
output html
pdf_document html
finding level-2 HTML links ... done
use_vignette html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BiocStyle' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocStyle' as BiocStyle_2.16.1.zip
* DONE (BiocStyle)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BiocStyle' successfully unpacked and MD5 sums checked
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BiocStyle.Rcheck/tests_i386/run_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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'
Writing to file maketitle_test_2.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_2.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_2.tex'
Writing to file maketitle_test_3.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_3.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_3.tex'
Writing to file maketitle_test_4.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_4.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_4.tex'
Writing to file maketitle_test_5.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_5.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_5.tex'
processing file: file2a447cbc61ea.Rmd
inline R code fragments
label: plot (with options)
List of 2
$ fig.cap: chr "Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title."
$ echo : logi FALSE
ordinary text without R code
label: small (with options)
List of 3
$ fig.cap : chr "Small figure. A plot produced by a code chunk with option `fig.small = TRUE`."
$ fig.small: logi TRUE
$ echo : logi FALSE
ordinary text without R code
label: wide (with options)
List of 3
$ fig.cap : chr "Wide figure. A plot produced by a code chunk with option `fig.wide = TRUE`."
$ fig.wide: logi TRUE
$ echo : logi FALSE
ordinary text without R code
label: sessionInfo (with options)
List of 1
$ echo: logi FALSE
output file: file2a447cbc61ea.knit.md
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS file2a447cbc61ea.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file2a447cbc61ea.tex --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpwrmumU\2a4414ce3b55.tex" --variable graphics --wrap preserve --variable subparagraph --template "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpwrmumU/BiocStyle/template.tex" --variable tables=yes --standalone --variable "compact-title:yes"
Output created: file2a447cbc61ea.pdf
RUNIT TEST PROTOCOL -- Sat Oct 17 01:59:33 2020
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocStyle RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
Warning message:
LaTeX Warning: You have requested package `C:/Users/biocbuild/bbs-3.11-bioc/R/l
ibrary/BiocStyle/resources/tex/Bioconductor',
but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
`width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 162.
>
> proc.time()
user system elapsed
1.48 0.17 37.31
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BiocStyle.Rcheck/tests_x64/run_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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'
Writing to file maketitle_test_2.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_2.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_2.tex'
Writing to file maketitle_test_3.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_3.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_3.tex'
Writing to file maketitle_test_4.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_4.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_4.tex'
Writing to file maketitle_test_5.tex
Processing code chunks with options ...
1 : keep.source term tex (label = style, maketitle_test_5.Rnw:5)
You can now run (pdf)latex on 'maketitle_test_5.tex'
processing file: file100438541a8.Rmd
inline R code fragments
label: plot (with options)
List of 2
$ fig.cap: chr "Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title."
$ echo : logi FALSE
ordinary text without R code
label: small (with options)
List of 3
$ fig.cap : chr "Small figure. A plot produced by a code chunk with option `fig.small = TRUE`."
$ fig.small: logi TRUE
$ echo : logi FALSE
ordinary text without R code
label: wide (with options)
List of 3
$ fig.cap : chr "Wide figure. A plot produced by a code chunk with option `fig.wide = TRUE`."
$ fig.wide: logi TRUE
$ echo : logi FALSE
ordinary text without R code
label: sessionInfo (with options)
List of 1
$ echo: logi FALSE
output file: file100438541a8.knit.md
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS file100438541a8.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output file100438541a8.tex --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --table-of-contents --toc-depth 2 --number-sections --highlight-style tango --pdf-engine pdflatex --include-in-header "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpWKBIUL\100461ee2efc.tex" --variable graphics --wrap preserve --variable subparagraph --template "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpWKBIUL/BiocStyle/template.tex" --variable tables=yes --standalone --variable "compact-title:yes"
Output created: file100438541a8.pdf
RUNIT TEST PROTOCOL -- Sat Oct 17 02:00:09 2020
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocStyle RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
Warning message:
LaTeX Warning: You have requested package `C:/Users/biocbuild/bbs-3.11-bioc/R/l
ibrary/BiocStyle/resources/tex/Bioconductor',
but the package provides `Bioconductor'.
Package geometry Warning: Over-specification in `h'-direction.
`width' (384.1122pt) is ignored.
Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use
less on input line 162.
>
> proc.time()
user system elapsed
1.39 0.21 35.20
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BiocStyle.Rcheck/examples_i386/BiocStyle-Ex.timings
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BiocStyle.Rcheck/examples_x64/BiocStyle-Ex.timings
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