Multiple platform build/check report for BioC 3.6 - CHECK report for cellbaseR on tokay1

Package: cellbaseR

Version: 1.2.0

Command: rm -rf cellbaseR.buildbin-libdir cellbaseR.Rcheck && mkdir cellbaseR.buildbin-libdir cellbaseR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellbaseR.buildbin-libdir cellbaseR_1.2.0.tar.gz >cellbaseR.Rcheck\00install.out 2>&1 && cp cellbaseR.Rcheck\00install.out cellbaseR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cellbaseR.buildbin-libdir --install="check:cellbaseR-install.out" --force-multiarch --no-vignettes --timings cellbaseR_1.2.0.tar.gz

StartedAt: 2018-04-11 22:45:37 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:50:12 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 275.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: cellbaseR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf cellbaseR.buildbin-libdir cellbaseR.Rcheck && mkdir cellbaseR.buildbin-libdir cellbaseR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellbaseR.buildbin-libdir cellbaseR_1.2.0.tar.gz >cellbaseR.Rcheck\00install.out 2>&1 && cp cellbaseR.Rcheck\00install.out cellbaseR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cellbaseR.buildbin-libdir --install="check:cellbaseR-install.out" --force-multiarch --no-vignettes --timings cellbaseR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cellbaseR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.2.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpmkUZHE/R.INSTALLc681085648c/cellbaseR/man/createGeneModel.Rd:23: missing file link 'GeneRegionTrack'
See 'C:/Users/biocbuild/bbs-3.6-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
** 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' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 4.77   0.87   42.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 5.28   1.03   49.34
* 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-3.6-bioc/meat/cellbaseR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'cellbaseR' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpmkUZHE/R.INSTALLc681085648c/cellbaseR/man/createGeneModel.Rd:23: missing file link 'GeneRegionTrack'
    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_1.2.0.zip
* DONE (cellbaseR)
In R CMD INSTALL
In R CMD INSTALL

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	4.77	0.87	42.19
CellBaseParam	0	0	0
CellBaseR	0.11	0.00	0.38
createGeneModel	0.56	0.03	1.18
getCaddScores	0.11	0.00	0.55
getCellBase-CellBaseR-method	0.10	0.00	0.56
getCellBaseResourceHelp	0.40	0.00	0.94
getChromosomeInfo-CellBaseR-method	0.10	0.00	0.55
getClinical-CellBaseR-method	0.78	0.00	1.56
getClinicalByRegion	1.15	0.04	2.36
getConservationByRegion	0.11	0.03	0.83
getGene-CellBaseR-method	0.20	0.01	0.89
getGeneInfo	0.10	0.00	0.57
getMeta-CellBaseR-method	0.07	0.00	0.54
getProtein-CellBaseR-method	0.13	0.00	0.69
getProteinInfo	0.14	0.00	0.69
getRegion-CellBaseR-method	0.17	0.00	0.84
getRegulatoryByRegion	0.19	0.00	1.08
getSnp-CellBaseR-method	0.08	0.00	0.55
getSnpByGene	0.11	0.00	0.57
getTf-CellBaseR-method	0.07	0.00	2.47
getTfbsByRegion	0.08	0.00	0.58
getTranscript-CellBaseR-method	0.11	0.00	0.56
getTranscriptByGene	0.08	0.00	0.55
getVariant-CellBaseR-method	0.16	0.02	0.78
getVariantAnnotation	0.17	0.01	0.77
getXref-CellBaseR-method	0.11	0.00	0.56

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	5.28	1.03	49.34
CellBaseParam	0	0	0
CellBaseR	0.09	0.00	0.34
createGeneModel	0.91	0.05	1.50
getCaddScores	0.11	0.00	0.55
getCellBase-CellBaseR-method	0.09	0.00	0.53
getCellBaseResourceHelp	0.22	0.02	0.77
getChromosomeInfo-CellBaseR-method	0.08	0.00	0.51
getClinical-CellBaseR-method	0.94	0.00	1.58
getClinicalByRegion	1.42	0.00	2.48
getConservationByRegion	0.20	0.00	0.85
getGene-CellBaseR-method	0.42	0.00	0.97
getGeneInfo	0.19	0.00	0.68
getMeta-CellBaseR-method	0.17	0.00	0.61
getProtein-CellBaseR-method	0.24	0.01	0.75
getProteinInfo	0.15	0.02	0.71
getRegion-CellBaseR-method	0.30	0.01	0.93
getRegulatoryByRegion	0.37	0.00	1.14
getSnp-CellBaseR-method	0.10	0.00	0.55
getSnpByGene	0.20	0.00	0.64
getTf-CellBaseR-method	0.13	0.00	2.41
getTfbsByRegion	0.11	0.00	0.56
getTranscript-CellBaseR-method	0.09	0.00	0.53
getTranscriptByGene	0.09	0.00	0.52
getVariant-CellBaseR-method	0.19	0.00	0.73
getVariantAnnotation	0.17	0.00	0.74
getXref-CellBaseR-method	0.08	0.02	0.53

CHECK report for cellbaseR on tokay1

Summary

Command output

Installation output

Tests output

Example timings