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BioC 3.5: CHECK report for cellbaseR on tokay2

This page was generated on 2017-08-14 13:28:07 -0400 (Mon, 14 Aug 2017).

Package 182/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.0.0
Mohammed OE Abdallah
Snapshot Date: 2017-08-13 17:17:53 -0400 (Sun, 13 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cellbaseR
Last Changed Rev: 129126 / Revision: 131908
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: cellbaseR
Version: 1.0.0
Command: rm -rf cellbaseR.buildbin-libdir cellbaseR.Rcheck && mkdir cellbaseR.buildbin-libdir cellbaseR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellbaseR.buildbin-libdir cellbaseR_1.0.0.tar.gz >cellbaseR.Rcheck\00install.out 2>&1 && cp cellbaseR.Rcheck\00install.out cellbaseR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellbaseR.buildbin-libdir --install="check:cellbaseR-install.out" --force-multiarch --no-vignettes --timings cellbaseR_1.0.0.tar.gz
StartedAt: 2017-08-13 21:32:39 -0400 (Sun, 13 Aug 2017)
EndedAt: 2017-08-13 21:38:38 -0400 (Sun, 13 Aug 2017)
EllapsedTime: 359.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellbaseR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf cellbaseR.buildbin-libdir cellbaseR.Rcheck && mkdir cellbaseR.buildbin-libdir cellbaseR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellbaseR.buildbin-libdir cellbaseR_1.0.0.tar.gz >cellbaseR.Rcheck\00install.out 2>&1 && cp cellbaseR.Rcheck\00install.out cellbaseR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cellbaseR.buildbin-libdir --install="check:cellbaseR-install.out" --force-multiarch --no-vignettes --timings cellbaseR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cellbaseR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellbaseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cellbaseR' version '1.0.0'
* 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 'cellbaseR' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                              user system elapsed
getClinical-CellBaseR-method 12.55   0.19   14.18
AnnotateVcf-CellBaseR-method  6.54   1.39   47.16
getClinicalByRegion           5.86   0.08    7.03
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
  Warning: 'rbind.pages' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                              user system elapsed
getClinical-CellBaseR-method 14.07   0.14   15.63
AnnotateVcf-CellBaseR-method  6.55   1.50   51.91
getClinicalByRegion           7.63   0.06    8.89
* 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 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/cellbaseR.Rcheck/00check.log'
for details.

cellbaseR.Rcheck/00install.out:


install for i386

* installing *source* package 'cellbaseR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cellbaseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellbaseR' as cellbaseR_1.0.0.zip
* DONE (cellbaseR)

cellbaseR.Rcheck/examples_i386/cellbaseR-Ex.timings:

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 6.54 1.3947.16
CellBaseParam000
CellBaseR0.190.000.47
createGeneModel0.970.031.53
getCaddScores0.180.000.64
getCellBase-CellBaseR-method0.190.000.61
getCellBaseResourceHelp0.390.000.91
getChromosomeInfo-CellBaseR-method0.170.000.61
getClinical-CellBaseR-method12.55 0.1914.18
getClinicalByGene1.680.012.39
getClinicalByRegion5.860.087.03
getConservationByRegion0.310.000.86
getGene-CellBaseR-method0.440.000.98
getGeneInfo0.160.020.63
getMeta-CellBaseR-method0.200.000.64
getProtein-CellBaseR-method0.280.000.81
getProteinInfo0.300.000.83
getRegion-CellBaseR-method0.360.000.97
getRegulatoryByRegion0.450.001.20
getSnp-CellBaseR-method0.190.000.62
getSnpByGene0.200.000.64
getTf-CellBaseR-method0.140.004.35
getTfbsByRegion0.210.000.68
getTranscript-CellBaseR-method0.170.000.61
getTranscriptByGene0.150.000.63
getVariant-CellBaseR-method0.400.000.95
getVariantAnnotation0.320.000.92
getXref-CellBaseR-method0.190.000.61

cellbaseR.Rcheck/examples_x64/cellbaseR-Ex.timings:

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 6.55 1.5051.91
CellBaseParam000
CellBaseR0.190.000.46
createGeneModel0.890.031.45
getCaddScores0.270.000.72
getCellBase-CellBaseR-method0.200.000.62
getCellBaseResourceHelp0.470.000.97
getChromosomeInfo-CellBaseR-method0.180.000.64
getClinical-CellBaseR-method14.07 0.1415.63
getClinicalByGene1.980.022.67
getClinicalByRegion7.630.068.89
getConservationByRegion0.320.000.89
getGene-CellBaseR-method0.470.001.02
getGeneInfo0.190.000.64
getMeta-CellBaseR-method0.240.000.67
getProtein-CellBaseR-method0.260.000.81
getProteinInfo0.340.000.89
getRegion-CellBaseR-method0.490.001.10
getRegulatoryByRegion0.370.021.17
getSnp-CellBaseR-method0.210.000.64
getSnpByGene0.220.010.70
getTf-CellBaseR-method0.20.02.6
getTfbsByRegion0.230.000.70
getTranscript-CellBaseR-method0.210.000.64
getTranscriptByGene0.170.000.64
getVariant-CellBaseR-method0.370.000.92
getVariantAnnotation0.340.000.90
getXref-CellBaseR-method0.190.000.61