James W. MacDonald
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/affycoretools |
| Branch: RELEASE_3_8 |
| Last Commit: 1e1f968 |
| Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:19:47 -0400 (Sat, 13 Apr 2019).
| Package 24/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| affycoretools 1.54.0 James W. MacDonald
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: affycoretools |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycoretools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings affycoretools_1.54.0.tar.gz |
| StartedAt: 2019-04-13 00:23:52 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:31:53 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 480.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affycoretools.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycoretools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings affycoretools_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/affycoretools.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.54.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'affycoretools' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:47: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:50: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:55: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/makeVenn.Rd:72: file link 'glmQLFit' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/writeFit.Rd:35: file link 'write.fit' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/affycoretools.Rcheck/00install.out' for details.
* 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 ... OK
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
plotDeg 4.95 0.08 5.03
* 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 WARNING
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/affycoretools.Rcheck/00check.log'
for details.
affycoretools.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/affycoretools_1.54.0.tar.gz && rm -rf affycoretools.buildbin-libdir && mkdir affycoretools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affycoretools.buildbin-libdir affycoretools_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL affycoretools_1.54.0.zip && rm affycoretools_1.54.0.tar.gz affycoretools_1.54.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 6442k 100 6442k 0 0 62.8M 0 --:--:-- --:--:-- --:--:-- 65.5M
install for i386
* installing *source* package 'affycoretools' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'affycoretools'
finding HTML links ... done
affycoretools-defunct html
affycoretools html
affystart html
annotateEset html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:47: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:50: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/annotateEset.Rd:55: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
dataAndHeatmapPage html
entrezLinks html
fixHeaderAndGo html
geneSetPage html
finding level-2 HTML links ... done
getCols html
getMainProbes html
gsHeatmap html
intNames html
make.cl html
makeGoGeneTable html
makeGoTable html
makeHmap html
makeImages html
makeIndices html
makeVenn html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/makeVenn.Rd:72: file link 'glmQLFit' in package 'edgeR' does not exist and so has been treated as a topic
maplot html
mirna2mrna html
outputRomer html
pca.legend html
plotDeg html
plotPCA html
runRomer html
tableFilt html
venn4Way html
vennCounts2 html
vennInLine html
vennPage html
vennSelect2 html
writeFit html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGOLMQf/R.INSTALL19f41d4e5c45/affycoretools/man/writeFit.Rd:35: file link 'write.fit' in package 'limma' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'affycoretools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affycoretools' as affycoretools_1.54.0.zip
* DONE (affycoretools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'affycoretools' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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affycoretools.Rcheck/examples_i386/affycoretools-Ex.timings
|
affycoretools.Rcheck/examples_x64/affycoretools-Ex.timings
|