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CHECK report for Pi on tokay2

This page was generated on 2018-10-17 08:42:55 -0400 (Wed, 17 Oct 2018).

Package 1093/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 1.8.0
Hai Fang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Pi
Branch: RELEASE_3_7
Last Commit: 8ec9d0c
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Pi
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pi_1.8.0.tar.gz
StartedAt: 2018-10-17 03:58:25 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:06:53 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 508.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Pi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pi.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Pi_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Pi.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pi' version '1.8.0'
* 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 'Pi' 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
** running examples for arch 'x64' ... OK
* 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

Pi.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Pi_1.8.0.tar.gz && rm -rf Pi.buildbin-libdir && mkdir Pi.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pi.buildbin-libdir Pi_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Pi_1.8.0.zip && rm Pi_1.8.0.tar.gz Pi_1.8.0.zip
###
##############################################################################
##############################################################################


  % 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 3328k  100 3328k    0     0  32.6M      0 --:--:-- --:--:-- --:--:-- 34.9M

install for i386

* installing *source* package 'Pi' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Pi'
    finding HTML links ... done
    cTarget                                 html  
    dTarget                                 html  
    eGSEA                                   html  
    eTarget                                 html  
    pNode                                   html  
    pPerf                                   html  
    sGS                                     html  
    sTarget                                 html  
    xContour                                html  
    xGSEAbarplot                            html  
    xGSEAconciser                           html  
    xGSEAdotplot                            html  
    xGSsimulator                            html  
    finding level-2 HTML links ... done

    xMLcaret                                html  
    xMLcompare                              html  
    xMLdensity                              html  
    xMLdotplot                              html  
    xMLfeatureplot                          html  
    xMLglmnet                               html  
    xMLparameters                           html  
    xMLrandomforest                         html  
    xMLrename                               html  
    xMLzoom                                 html  
    xPCHiCplot                              html  
    xPieplot                                html  
    xPier                                   html  
    xPierAnno                               html  
    xPierCor                                html  
    xPierCross                              html  
    xPierEvidence                           html  
    xPierGRs                                html  
    xPierGSEA                               html  
    xPierGenes                              html  
    xPierKEGG                               html  
    xPierManhattan                          html  
    xPierMatrix                             html  
    xPierPathways                           html  
    xPierROCR                               html  
    xPierSNPs                               html  
    xPierSNPsAdv                            html  
    xPierSNPsConsensus                      html  
    xPierSubnet                             html  
    xPierTrack                              html  
    xPierTrackAdv                           html  
    xPredictCompare                         html  
    xPredictROCR                            html  
    xRWR                                    html  
    xSNP2cGenes                             html  
    xSNP2eGenes                             html  
    xSNPeqtl                                html  
    xSNPhic                                 html  
    xVisEvidence                            html  
    xVisEvidenceAdv                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Pi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pi' as Pi_1.8.0.zip
* DONE (Pi)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Pi' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Pi.Rcheck/examples_i386/Pi-Ex.timings

nameusersystemelapsed
cTarget000
dTarget000
eGSEA000
eTarget000
pNode000
pPerf000
sGS000
sTarget000
xContour0.050.030.08
xGSEAbarplot0.020.000.01
xGSEAconciser000
xGSEAdotplot000
xGSsimulator000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot000
xMLfeatureplot000
xMLglmnet000
xMLparameters0.020.000.02
xMLrandomforest000
xMLrename000
xMLzoom000
xPCHiCplot000
xPieplot000
xPier000
xPierAnno000
xPierCor0.010.000.02
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA0.020.000.01
xPierGenes000
xPierKEGG000
xPierManhattan000
xPierMatrix0.020.000.02
xPierPathways000
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsConsensus000
xPierSubnet000
xPierTrack0.020.000.02
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRWR0.000.010.02
xSNP2cGenes000
xSNP2eGenes000
xSNPeqtl0.010.000.01
xSNPhic000
xVisEvidence000
xVisEvidenceAdv000

Pi.Rcheck/examples_x64/Pi-Ex.timings

nameusersystemelapsed
cTarget0.010.000.02
dTarget000
eGSEA000
eTarget000
pNode000
pPerf000
sGS000
sTarget000
xContour0.030.000.04
xGSEAbarplot000
xGSEAconciser0.010.000.01
xGSEAdotplot000
xGSsimulator000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot000
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename000
xMLzoom000
xPCHiCplot000
xPieplot000
xPier000
xPierAnno000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA000
xPierGenes000
xPierKEGG000
xPierManhattan000
xPierMatrix000
xPierPathways000
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsConsensus000
xPierSubnet000
xPierTrack000
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRWR000
xSNP2cGenes000
xSNP2eGenes000
xSNPeqtl000
xSNPhic000
xVisEvidence000
xVisEvidenceAdv000