Alejandro Reyes
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DEXSeq |
| Branch: RELEASE_3_7 |
| Last Commit: 1b16e47 |
| Last Changed Date: 2018-04-30 10:35:19 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:27 -0400 (Wed, 17 Oct 2018).
| Package 379/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEXSeq 1.26.0 Alejandro Reyes
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEXSeq |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEXSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DEXSeq_1.26.0.tar.gz |
| StartedAt: 2018-10-17 01:34:17 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:40:32 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 374.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DEXSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEXSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DEXSeq_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DEXSeq.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocParallel' 'Biobase' 'SummarizedExperiment' 'IRanges'
'GenomicRanges' 'DESeq2' 'AnnotationDbi' 'RColorBrewer' 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'DEXSeq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGU6axZ/R.INSTALL17bc78491b/DEXSeq/man/methods-gr.Rd:32: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGU6axZ/R.INSTALL17bc78491b/DEXSeq/man/methods-gr.Rd:36: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DEXSeq.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
Examples with CPU or elapsed time > 5s
user system elapsed
estimateExonFoldChanges 11.89 0.00 11.91
methods-gr 11.48 0.01 11.50
DEXSeqResults 10.72 0.50 11.24
perGeneQValue 11.19 0.00 11.19
testForDEU 10.42 0.00 10.42
estimateDispersions 7.77 0.00 7.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
estimateExonFoldChanges 12.03 0.03 12.67
DEXSeqResults 10.50 0.05 10.55
testForDEU 9.33 0.00 9.33
methods-gr 8.25 0.00 8.25
estimateDispersions 7.09 0.00 7.10
perGeneQValue 6.88 0.00 6.87
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/DEXSeq.Rcheck/00check.log'
for details.
DEXSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DEXSeq_1.26.0.tar.gz && rm -rf DEXSeq.buildbin-libdir && mkdir DEXSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEXSeq.buildbin-libdir DEXSeq_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DEXSeq_1.26.0.zip && rm DEXSeq_1.26.0.tar.gz DEXSeq_1.26.0.zip
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install for i386
* installing *source* package 'DEXSeq' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEXSeq'
finding HTML links ... done
DEXSeq-defunct html
DEXSeq html
DEXSeqDataSet html
DEXSeqHTML html
DEXSeqResults html
accessors html
counts html
estimateDispersions html
estimateExonFoldChanges html
estimateSizeFactors html
methods-gr html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGU6axZ/R.INSTALL17bc78491b/DEXSeq/man/methods-gr.Rd:32: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGU6axZ/R.INSTALL17bc78491b/DEXSeq/man/methods-gr.Rd:36: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
otherMethods html
perGeneQValue html
plotDEXSeq html
plotDispEsts html
plotMA html
testForDEU html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DEXSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEXSeq' as DEXSeq_1.26.0.zip
* DONE (DEXSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DEXSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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DEXSeq.Rcheck/examples_i386/DEXSeq-Ex.timings
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DEXSeq.Rcheck/examples_x64/DEXSeq-Ex.timings
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