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CHECK report for sampleClassifier on tokay1

This page was generated on 2019-04-13 11:27:30 -0400 (Sat, 13 Apr 2019).

Package 1381/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sampleClassifier 1.6.1
Khadija El Amrani
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/sampleClassifier
Branch: RELEASE_3_8
Last Commit: 282b044
Last Changed Date: 2019-01-04 13:48:01 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sampleClassifier
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sampleClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sampleClassifier_1.6.1.tar.gz
StartedAt: 2019-04-13 05:17:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:26:21 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 518.7 seconds
RetCode: 0
Status:  OK  
CheckDir: sampleClassifier.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sampleClassifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sampleClassifier_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sampleClassifier.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 'sampleClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sampleClassifier' version '1.6.1'
* 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 'sampleClassifier' 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
classifyProfile.rnaseq     74.99   0.57   75.61
classifyProfile            25.84   1.07   26.90
classifyProfile.svm        24.47   0.51   24.98
get.heatmap                22.46   0.33   22.80
classifyProfile.rnaseq.svm 12.35   0.10   12.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
classifyProfile.rnaseq     82.00   0.53   82.54
get.heatmap                34.21   0.47   34.69
classifyProfile            32.17   0.66   32.86
classifyProfile.svm        24.34   0.41   24.75
classifyProfile.rnaseq.svm 13.96   0.34   14.30
* 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: OK


Installation output

sampleClassifier.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/sampleClassifier_1.6.1.tar.gz && rm -rf sampleClassifier.buildbin-libdir && mkdir sampleClassifier.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sampleClassifier.buildbin-libdir sampleClassifier_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sampleClassifier_1.6.1.zip && rm sampleClassifier_1.6.1.tar.gz sampleClassifier_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  219k  100  219k    0     0  1693k      0 --:--:-- --:--:-- --:--:-- 1745k

install for i386

* installing *source* package 'sampleClassifier' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sampleClassifier'
    finding HTML links ... done
    classifyProfile                         html  
    classifyProfile.rnaseq                  html  
    classifyProfile.rnaseq.svm              html  
    classifyProfile.svm                     html  
    get.heatmap                             html  
    sampleClassifier-internal               html  
    sampleClassifier-package                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sampleClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sampleClassifier' as sampleClassifier_1.6.1.zip
* DONE (sampleClassifier)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sampleClassifier' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

sampleClassifier.Rcheck/examples_i386/sampleClassifier-Ex.timings

nameusersystemelapsed
classifyProfile25.84 1.0726.90
classifyProfile.rnaseq74.99 0.5775.61
classifyProfile.rnaseq.svm12.35 0.1012.43
classifyProfile.svm24.47 0.5124.98
get.heatmap22.46 0.3322.80
sampleClassifier-package000

sampleClassifier.Rcheck/examples_x64/sampleClassifier-Ex.timings

nameusersystemelapsed
classifyProfile32.17 0.6632.86
classifyProfile.rnaseq82.00 0.5382.54
classifyProfile.rnaseq.svm13.96 0.3414.30
classifyProfile.svm24.34 0.4124.75
get.heatmap34.21 0.4734.69
sampleClassifier-package000