Alejandro Reyes
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DEXSeq |
| Branch: RELEASE_3_8 |
| Last Commit: 4f592da |
| Last Changed Date: 2019-03-11 10:35:39 -0400 (Mon, 11 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:40 -0400 (Sat, 13 Apr 2019).
| Package 403/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEXSeq 1.28.3 Alejandro Reyes
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEXSeq |
| Version: 1.28.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEXSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEXSeq_1.28.3.tar.gz |
| StartedAt: 2019-04-13 01:46:45 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:53:03 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 377.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEXSeq.Rcheck |
| Warnings: 0 |
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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:DEXSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEXSeq_1.28.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEXSeq.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 'DEXSeq/DESCRIPTION' ... OK
* this is package 'DEXSeq' version '1.28.3'
* 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'
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 ... 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 ... 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 9.25 0.02 9.26
DEXSeqResults 7.34 0.23 7.59
methods-gr 7.00 0.00 7.00
perGeneQValue 6.92 0.00 6.92
testForDEU 6.39 0.01 6.41
estimateDispersions 5.78 0.00 5.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DEXSeqResults 7.47 0 7.47
estimateExonFoldChanges 7.47 0 7.47
testForDEU 7.20 0 7.21
methods-gr 7.19 0 7.19
perGeneQValue 6.86 0 6.86
estimateDispersions 6.56 0 6.56
* 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-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DEXSeq_1.28.3.tar.gz && rm -rf DEXSeq.buildbin-libdir && mkdir DEXSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEXSeq.buildbin-libdir DEXSeq_1.28.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DEXSeq_1.28.3.zip && rm DEXSeq_1.28.3.tar.gz DEXSeq_1.28.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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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
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_1.28.3.zip
* DONE (DEXSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-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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