David S Fischer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ImpulseDE2 |
| Branch: RELEASE_3_10 |
| Last Commit: 1cc86d1 |
| Last Changed Date: 2019-10-29 13:10:23 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:28:20 -0400 (Wed, 15 Apr 2020).
| Package 842/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ImpulseDE2 1.10.0 David S Fischer
| malbec1 | Linux (Ubuntu 18.04.4 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: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ImpulseDE2_1.10.0.tar.gz |
| StartedAt: 2020-04-15 04:02:25 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:11:47 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 562.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ImpulseDE2.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ImpulseDE2_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ImpulseDE2.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.10.0'
* 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 '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
updateDEAnalysis 28.57 0.01 28.59
plotGenes 26.53 0.01 26.55
plotHeatmap 26.51 0.02 26.53
get_accessors 22.07 0.00 22.10
list_accession 20.21 0.04 21.95
fitSigmoidModels 19.52 0.71 20.25
writeReportToFile 14.74 0.00 14.74
runImpulseDE2 14.41 0.00 14.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotHeatmap 30.34 0.00 30.35
updateDEAnalysis 27.87 0.00 27.88
plotGenes 24.69 0.00 24.68
fitSigmoidModels 17.06 0.04 17.11
list_accession 16.36 0.00 16.36
writeReportToFile 15.78 0.01 15.81
get_accessors 15.09 0.00 15.10
runImpulseDE2 15.02 0.02 15.03
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.10-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/3.10/bioc/src/contrib/ImpulseDE2_1.10.0.tar.gz && rm -rf ImpulseDE2.buildbin-libdir && mkdir ImpulseDE2.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ImpulseDE2_1.10.0.zip && rm ImpulseDE2_1.10.0.tar.gz ImpulseDE2_1.10.0.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 59364 100 59364 0 0 912k 0 --:--:-- --:--:-- --:--:-- 982k
install for i386
* installing *source* package 'ImpulseDE2' ...
** using staged installation
** 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 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 'ImpulseDE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImpulseDE2' as ImpulseDE2_1.10.0.zip
* DONE (ImpulseDE2)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ImpulseDE2' successfully unpacked and MD5 sums checked
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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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