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CHECK report for GeneExpressionSignature on tokay2

This page was generated on 2019-10-16 12:25:36 -0400 (Wed, 16 Oct 2019).

Package 626/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneExpressionSignature 1.30.0
Yang Cao , Fei Li
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GeneExpressionSignature
Branch: RELEASE_3_9
Last Commit: e6b4266
Last Changed Date: 2019-05-02 11:53:29 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneExpressionSignature
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneExpressionSignature.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneExpressionSignature_1.30.0.tar.gz
StartedAt: 2019-10-16 03:53:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:55:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 133.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneExpressionSignature.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneExpressionSignature.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneExpressionSignature_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.30.0'
* 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 'GeneExpressionSignature' 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'PGSEA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RankMerging: no visible global function definition for 'exprs'
RankMerging: no visible global function definition for 'as'
RankMerging: no visible global function definition for 'phenoData'
RankMerging: no visible global function definition for 'new'
ScoreGSEA : PRL.Distance: no visible global function definition for
  'exprs'
ScoreGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'new'
ScorePGSEA: no visible global function definition for 'PGSEA'
ScorePGSEA: no visible global function definition for 'pnorm'
getRLs : Check.Log: no visible global function definition for 'median'
integratePRL: no visible global function definition for 'phenoData'
integratePRL: no visible global function definition for 'exprs'
integratePRL: no visible global function definition for 'new'
integratePRL: no visible global function definition for 'as'
Undefined global functions or variables:
  PGSEA as exprs median new phenoData pnorm
Consider adding
  importFrom("methods", "as", "new")
  importFrom("stats", "median", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ScoreGSEA         5.68   0.18    5.84
SignatureDistance 5.54   0.06    5.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
ScoreGSEA 5.49   0.07    5.56
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.



Installation output

GeneExpressionSignature.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneExpressionSignature_1.30.0.tar.gz && rm -rf GeneExpressionSignature.buildbin-libdir && mkdir GeneExpressionSignature.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneExpressionSignature_1.30.0.zip && rm GeneExpressionSignature_1.30.0.tar.gz GeneExpressionSignature_1.30.0.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 2323k  100 2323k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 14.2M

install for i386

* installing *source* package 'GeneExpressionSignature' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneExpressionSignature'
    finding HTML links ... done
    GeneExpressionSignature                 html  
    RankMerging                             html  
    ScoreGSEA                               html  
    ScorePGSEA                              html  
    SignatureDistance                       html  
    exampleSet                              html  
    getRLs                                  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 'GeneExpressionSignature' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneExpressionSignature' as GeneExpressionSignature_1.30.0.zip
* DONE (GeneExpressionSignature)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneExpressionSignature' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneExpressionSignature.Rcheck/examples_i386/GeneExpressionSignature-Ex.timings

nameusersystemelapsed
RankMerging2.040.032.08
ScoreGSEA5.680.185.84
ScorePGSEA3.700.033.73
SignatureDistance5.540.065.59
exampleSet0.450.010.47
getRLs0.910.131.24

GeneExpressionSignature.Rcheck/examples_x64/GeneExpressionSignature-Ex.timings

nameusersystemelapsed
RankMerging1.680.101.78
ScoreGSEA5.490.075.56
ScorePGSEA3.380.103.47
SignatureDistance4.940.034.97
exampleSet0.420.020.43
getRLs0.670.140.82