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CHECK report for cellbaseR on tokay1

This page was generated on 2019-04-13 11:27:49 -0400 (Sat, 13 Apr 2019).

Package 214/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.6.1
Mohammed OE Abdallah
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_8
Last Commit: f01f468
Last Changed Date: 2019-04-08 16:09:41 -0400 (Mon, 08 Apr 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 [ WARNINGS ] 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: cellbaseR
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellbaseR_1.6.1.tar.gz
StartedAt: 2019-04-13 01:02:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:08:09 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 324.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellbaseR.Rcheck
Warnings: 1

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:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cellbaseR_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellbaseR.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 'cellbaseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cellbaseR' 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 'cellbaseR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp2j0m6i/R.INSTALL1bb47da16307/cellbaseR/man/createGeneModel.Rd:23: file link 'GeneRegionTrack' in package 'Gviz' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellbaseR.Rcheck/00install.out' for details.
* 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
AnnotateVcf-CellBaseR-method 6.58   1.36   45.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method  4.3   0.99   45.34
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/cellbaseR.Rcheck/00check.log'
for details.



Installation output

cellbaseR.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/cellbaseR_1.6.1.tar.gz && rm -rf cellbaseR.buildbin-libdir && mkdir cellbaseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellbaseR.buildbin-libdir cellbaseR_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cellbaseR_1.6.1.zip && rm cellbaseR_1.6.1.tar.gz cellbaseR_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  658k  100  658k    0     0  8226k      0 --:--:-- --:--:-- --:--:-- 8668k

install for i386

* installing *source* package 'cellbaseR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cellbaseR'
    finding HTML links ... done
    AnnotateVcf-CellBaseR-method            html  
    CellBaseParam-class                     html  
    CellBaseParam                           html  
    CellBaseR-class                         html  
    CellBaseR                               html  
    cellbaseR-package                       html  
    createGeneModel                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp2j0m6i/R.INSTALL1bb47da16307/cellbaseR/man/createGeneModel.Rd:23: file link 'GeneRegionTrack' in package 'Gviz' does not exist and so has been treated as a topic
    getCaddScores                           html  
    getCellBase-CellBaseR-method            html  
    getCellBaseResourceHelp                 html  
    getChromosomeInfo-CellBaseR-method      html  
    getClinical-CellBaseR-method            html  
    getClinicalByGene                       html  
    getClinicalByRegion                     html  
    getConservationByRegion                 html  
    getGene-CellBaseR-method                html  
    getGeneInfo                             html  
    getMeta-CellBaseR-method                html  
    getProtein-CellBaseR-method             html  
    getProteinInfo                          html  
    getRegion-CellBaseR-method              html  
    getRegulatoryByRegion                   html  
    getSnp-CellBaseR-method                 html  
    getSnpByGene                            html  
    getTf-CellBaseR-method                  html  
    getTfbsByRegion                         html  
    getTranscript-CellBaseR-method          html  
    getTranscriptByGene                     html  
    getVariant-CellBaseR-method             html  
    getVariantAnnotation                    html  
    getXref-CellBaseR-method                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cellbaseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellbaseR' as cellbaseR_1.6.1.zip
* DONE (cellbaseR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cellbaseR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

cellbaseR.Rcheck/examples_i386/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 6.58 1.3645.44
CellBaseParam000
CellBaseR0.120.000.44
createGeneModel0.360.031.00
getCaddScores0.100.000.56
getCellBase-CellBaseR-method0.150.020.65
getCellBaseResourceHelp0.280.090.94
getChromosomeInfo-CellBaseR-method0.130.000.63
getClinical-CellBaseR-method1.040.031.87
getClinicalByRegion2.650.103.99
getConservationByRegion0.180.010.90
getGene-CellBaseR-method0.380.000.96
getGeneInfo0.150.020.64
getMeta-CellBaseR-method0.180.010.64
getProtein-CellBaseR-method0.260.000.83
getProteinInfo0.250.000.82
getRegion-CellBaseR-method0.330.001.03
getRegulatoryByRegion0.310.021.17
getSnp-CellBaseR-method0.190.000.66
getSnpByGene0.170.000.75
getTf-CellBaseR-method0.140.003.05
getTfbsByRegion0.160.020.66
getTranscript-CellBaseR-method0.110.000.59
getTranscriptByGene0.140.000.63
getVariant-CellBaseR-method0.190.020.80
getVariantAnnotation0.180.000.83
getXref-CellBaseR-method0.080.000.55

cellbaseR.Rcheck/examples_x64/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 4.30 0.9945.34
CellBaseParam000
CellBaseR0.080.000.36
createGeneModel0.310.030.92
getCaddScores0.080.020.55
getCellBase-CellBaseR-method0.060.010.56
getCellBaseResourceHelp0.220.020.80
getChromosomeInfo-CellBaseR-method0.060.000.54
getClinical-CellBaseR-method0.820.001.61
getClinicalByRegion2.080.033.38
getConservationByRegion0.140.000.85
getGene-CellBaseR-method0.170.020.76
getGeneInfo0.060.000.56
getMeta-CellBaseR-method0.110.000.56
getProtein-CellBaseR-method0.200.000.78
getProteinInfo0.140.010.72
getRegion-CellBaseR-method0.230.000.94
getRegulatoryByRegion0.390.001.20
getSnp-CellBaseR-method0.190.000.64
getSnpByGene0.190.020.69
getTf-CellBaseR-method0.120.002.80
getTfbsByRegion0.190.000.67
getTranscript-CellBaseR-method0.160.000.62
getTranscriptByGene0.120.020.63
getVariant-CellBaseR-method0.330.030.95
getVariantAnnotation0.250.000.88
getXref-CellBaseR-method0.130.000.61