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CHECK report for DeSousa2013 on riesling1

This page was generated on 2021-01-18 15:58:47 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE DeSousa2013 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 92/385HostnameOS / ArchINSTALLBUILDCHECK
DeSousa2013 1.27.0
Xin Wang
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/DeSousa2013
Branch: master
Last Commit: bb7af97
Last Changed Date: 2020-10-27 10:02:18 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: DeSousa2013
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeSousa2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz
StartedAt: 2021-01-18 11:18:59 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:23:00 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 240.6 seconds
RetCode: 0
Status:  OK  
CheckDir: DeSousa2013.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DeSousa2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/DeSousa2013.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeSousa2013/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeSousa2013' version '1.27.0'
* 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 'DeSousa2013' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 44.0Mb
  sub-directories of 1Mb or more:
    data  43.7Mb
* 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
Namespaces in Imports field not imported from:
  'frmaTools' 'hgu133plus2frmavecs' 'rgl'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CRCPipeLine: no visible global function definition for 'data'
CRCPipeLine: no visible global function definition for 'pdf'
CRCPipeLine: no visible global function definition for 'graphics.off'
compGapStats: no visible binding for global variable 'mad'
compGapStats : fun: no visible global function definition for 'hclust'
compGapStats : fun: no visible global function definition for 'as.dist'
compGapStats : fun: no visible global function definition for 'cor'
compGapStats : fun: no visible global function definition for 'cutree'
compGapStats: no visible binding for global variable 'median'
figClassify: no visible global function definition for 'layout'
figClassify: no visible global function definition for 'par'
figClassify: no visible global function definition for 'image'
figClassify: no visible global function definition for 'axis'
figClassify: no visible global function definition for 'box'
figClassify: no visible global function definition for 'gray'
figClassify: no visible global function definition for 'mtext'
figClassify: no visible global function definition for 'barplot'
figClassify: no visible global function definition for 'grid'
figGAP: no visible global function definition for 'par'
figGAP: no visible global function definition for 'lines'
figGAP: no visible global function definition for 'title'
figKM: no visible global function definition for 'axis'
figKM: no visible global function definition for 'box'
figKM: no visible global function definition for 'text'
figKM: no visible global function definition for 'legend'
figPAMCV: no visible global function definition for 'boxplot'
filterSamples: no visible global function definition for 'as.dist'
filterSamples: no visible global function definition for 'cor'
pamClassify: no visible global function definition for 'hclust'
pamClassify: no visible global function definition for 'as.dist'
pamClassify: no visible global function definition for 'cor'
pbs2unigenes: no visible global function definition for 'mappedkeys'
progAMC: no visible global function definition for 'pchisq'
selTopVarGenes: no visible binding for global variable 'mad'
selTopVarGenes: no visible binding for global variable 'median'
Undefined global functions or variables:
  as.dist axis barplot box boxplot cor cutree data graphics.off gray
  grid hclust image layout legend lines mad mappedkeys median mtext par
  pchisq pdf text title
Consider adding
  importFrom("grDevices", "graphics.off", "gray", "pdf")
  importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid",
             "image", "layout", "legend", "lines", "mtext", "par",
             "text", "title")
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "mad",
             "median", "pchisq")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
              user system elapsed
compGapStats 10.04   0.19   10.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
compGapStats 10.18   0.22   10.39
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/DeSousa2013.Rcheck/00check.log'
for details.



Installation output

DeSousa2013.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/DeSousa2013_1.27.0.tar.gz && rm -rf DeSousa2013.buildbin-libdir && mkdir DeSousa2013.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DeSousa2013.buildbin-libdir DeSousa2013_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DeSousa2013_1.27.0.zip && rm DeSousa2013_1.27.0.tar.gz DeSousa2013_1.27.0.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
 39 44.0M   39 17.1M    0     0  45.1M      0 --:--:-- --:--:-- --:--:-- 44.9M
100 44.0M  100 44.0M    0     0  66.6M      0 --:--:-- --:--:-- --:--:-- 66.6M

install for i386

* installing *source* package 'DeSousa2013' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DeSousa2013'
    finding HTML links ... done
    CRCPipeLine                             html  
REDIRECT:topic	 CRCPipeLine -> CRCPipeLine.html [ SUCCESS ]
REDIRECT:topic	 DeSousa2013 -> CRCPipeLine.html [ SUCCESS ]
    buildClassifier                         html  
REDIRECT:topic	 buildClassifier -> buildClassifier.html [ SUCCESS ]
REDIRECT:topic	 figPAMCV -> buildClassifier.html [ SUCCESS ]
    compGapStats                            html  
REDIRECT:topic	 compGapStats -> compGapStats.html [ SUCCESS ]
REDIRECT:topic	 figGAP -> compGapStats.html [ SUCCESS ]
    conClust                                html  
REDIRECT:topic	 conClust -> conClust.html [ SUCCESS ]
    data-AMC                                html  
REDIRECT:topic	 AMC_CRC_clinical -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 AMC_sample_head -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 ge.all -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 selPbs -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 gapsmat -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 gapsSE -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 sdat -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 uniGenes -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 clus -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 clus.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 sdat.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 silh -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 diffGenes -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 diffGenes.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 pam.rslt -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 signature -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 thresh -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 err -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 cents -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 clu.pred -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 sdat.sig -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 pred -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 gclu.f -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 nam.ord -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 surv -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 survstats -> data-AMC.html [ SUCCESS ]
REDIRECT:topic	 data4surv -> data-AMC.html [ SUCCESS ]
REDIRECT:file	 data-AMC.html -> data-AMC.html [ SUCCESS ]
    filterDiffGenes                         html  
REDIRECT:topic	 filterDiffGenes -> filterDiffGenes.html [ SUCCESS ]
    filterSamples                           html  
REDIRECT:topic	 filterSamples -> filterSamples.html [ SUCCESS ]
REDIRECT:topic	 figSilh -> filterSamples.html [ SUCCESS ]
    findDiffGenes                           html  
REDIRECT:topic	 findDiffGenes -> findDiffGenes.html [ SUCCESS ]
    geneExpPre                              html  
REDIRECT:topic	 geneExpPre -> geneExpPre.html [ SUCCESS ]
    getCentroids                            html  
REDIRECT:topic	 getCentroids -> getCentroids.html [ SUCCESS ]
    pamClassify                             html  
REDIRECT:topic	 pamClassify -> pamClassify.html [ SUCCESS ]
REDIRECT:topic	 figClassify -> pamClassify.html [ SUCCESS ]
    pbs2unigenes                            html  
REDIRECT:topic	 pbs2unigenes -> pbs2unigenes.html [ SUCCESS ]
    progAMC                                 html  
REDIRECT:topic	 progAMC -> progAMC.html [ SUCCESS ]
REDIRECT:topic	 figKM -> progAMC.html [ SUCCESS ]
    selTopVarGenes                          html  
REDIRECT:topic	 selTopVarGenes -> selTopVarGenes.html [ SUCCESS ]
** 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 'DeSousa2013' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DeSousa2013' as DeSousa2013_1.27.0.zip
* DONE (DeSousa2013)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'DeSousa2013' successfully unpacked and MD5 sums checked

Tests output


Example timings

DeSousa2013.Rcheck/examples_i386/DeSousa2013-Ex.timings

nameusersystemelapsed
CRCPipeLine000
buildClassifier1.950.062.02
compGapStats10.04 0.1910.24
conClust0.570.000.62
data-AMC000
filterDiffGenes0.70.00.7
filterSamples0.090.000.09
findDiffGenes0.500.010.51
geneExpPre000
pamClassify0.100.000.11
pbs2unigenes2.940.213.23
progAMC0.030.010.04
selTopVarGenes3.040.003.05

DeSousa2013.Rcheck/examples_x64/DeSousa2013-Ex.timings

nameusersystemelapsed
CRCPipeLine000
buildClassifier2.090.052.14
compGapStats10.18 0.2210.39
conClust0.500.020.58
data-AMC000
filterDiffGenes0.700.030.73
filterSamples0.070.010.09
findDiffGenes0.550.070.61
geneExpPre000
pamClassify0.110.010.12
pbs2unigenes3.460.423.89
progAMC0.050.000.04
selTopVarGenes3.150.033.19