David S Fischer
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ImpulseDE2 |
| Branch: RELEASE_3_8 |
| Last Commit: 06b8982 |
| Last Changed Date: 2019-01-04 13:15:12 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:47 -0400 (Sat, 13 Apr 2019).
| Package 773/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ImpulseDE2 1.6.1 David S Fischer
| 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: ImpulseDE2 |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ImpulseDE2_1.6.1.tar.gz |
| StartedAt: 2019-04-13 03:10:44 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:20:19 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 574.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ImpulseDE2.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:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ImpulseDE2_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ImpulseDE2.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 'ImpulseDE2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ImpulseDE2' version '1.6.1'
* package encoding: UTF-8
* 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 'ImpulseDE2' 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 ... NOTE
plotGenes: no visible global function definition for 'error'
plotGenes: no visible binding for global variable 'normCounts'
plotGenes: no visible binding for global variable 'Condition'
plotGenes: no visible binding for global variable 'Batch'
plotGenes: no visible binding for global variable 'value'
plotGenes: no visible binding for global variable 'BatchFit'
Undefined global functions or variables:
Batch BatchFit Condition error normCounts value
* 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
plotHeatmap 29.75 0.02 29.76
updateDEAnalysis 24.58 0.03 24.61
plotGenes 21.47 0.01 21.49
get_accessors 18.72 0.02 18.73
fitSigmoidModels 17.74 0.36 18.10
list_accession 13.45 0.00 13.45
writeReportToFile 13.42 0.00 13.42
runImpulseDE2 13.24 0.00 13.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
updateDEAnalysis 29.53 0.00 29.53
plotHeatmap 28.68 0.02 28.70
plotGenes 23.49 0.00 23.48
get_accessors 17.89 0.00 17.89
runImpulseDE2 16.38 0.00 16.38
list_accession 15.97 0.00 15.97
writeReportToFile 15.20 0.00 15.21
fitSigmoidModels 14.86 0.08 14.93
* 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/ImpulseDE2.Rcheck/00check.log'
for details.
ImpulseDE2.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/ImpulseDE2_1.6.1.tar.gz && rm -rf ImpulseDE2.buildbin-libdir && mkdir ImpulseDE2.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ImpulseDE2_1.6.1.zip && rm ImpulseDE2_1.6.1.tar.gz ImpulseDE2_1.6.1.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 59373 100 59373 0 0 747k 0 --:--:-- --:--:-- --:--:-- 783k
install for i386
* installing *source* package 'ImpulseDE2' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ImpulseDE2'
finding HTML links ... done
ImpulseDE2Object-class html
append_strReport html
computeNormConst html
computeSizeFactors html
estimateImpulseParam html
estimateSigmoidParam html
evalImpulse html
evalImpulse_comp html
evalLogLikImpulse html
evalLogLikImpulse_comp html
evalLogLikMu html
evalLogLikMu_comp html
evalLogLikSigmoid html
evalLogLikSigmoid_comp html
evalSigmoid html
evalSigmoid_comp html
fitConstImpulse html
fitConstImpulseGene html
fitConstModel html
fitImpulseModel html
fitModels html
fitSigmoidGene html
fitSigmoidModel html
fitSigmoidModels html
get_accessors html
list_accession html
plotGenes html
plotHeatmap html
processData html
runDEAnalysis html
runDESeq2 html
runImpulseDE2 html
set_accessors html
simulateDataSetImpulseDE2 html
updateDEAnalysis html
writeReportToFile html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ImpulseDE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImpulseDE2' as ImpulseDE2_1.6.1.zip
* DONE (ImpulseDE2)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ImpulseDE2' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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ImpulseDE2.Rcheck/examples_i386/ImpulseDE2-Ex.timings
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ImpulseDE2.Rcheck/examples_x64/ImpulseDE2-Ex.timings
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