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CHECK report for cellbaseR on tokay1

This page was generated on 2020-08-13 11:42:16 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cellbaseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 239/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.13.0
Mohammed OE Abdallah
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: e14a517
Last Changed Date: 2020-04-27 15:07:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.13.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
StartedAt: 2020-08-13 04:11:31 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 04:16:45 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 313.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellbaseR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings cellbaseR_1.13.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.13.0'
* 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-3.12-bioc/tmpdir/Rtmp0013G5/R.INSTALL24881d865781/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-3.12-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 (user + system) or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 6.73   0.89   55.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 4.75   0.76   50.45
* 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-3.12-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/3.12/bioc/src/contrib/cellbaseR_1.13.0.tar.gz && rm -rf cellbaseR.buildbin-libdir && mkdir cellbaseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellbaseR.buildbin-libdir cellbaseR_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL cellbaseR_1.13.0.zip && rm cellbaseR_1.13.0.tar.gz cellbaseR_1.13.0.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
100  738k  100  738k    0     0  3637k      0 --:--:-- --:--:-- --:--:-- 3711k

install for i386

* installing *source* package 'cellbaseR' ...
** using staged installation
** 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-3.12-bioc/tmpdir/Rtmp0013G5/R.INSTALL24881d865781/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 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 'cellbaseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellbaseR' as cellbaseR_1.13.0.zip
* DONE (cellbaseR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'cellbaseR' successfully unpacked and MD5 sums checked

Tests output


Example timings

cellbaseR.Rcheck/examples_i386/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 6.73 0.8955.99
CellBaseParam000
CellBaseR0.140.000.42
createGeneModel0.530.011.11
getCaddScores0.160.000.60
getCellBase-CellBaseR-method0.140.000.58
getCellBaseResourceHelp0.370.030.97
getChromosomeInfo-CellBaseR-method0.080.000.55
getClinical-CellBaseR-method1.270.022.06
getClinicalByRegion2.120.093.49
getConservationByRegion0.280.020.95
getGene-CellBaseR-method0.360.010.94
getGeneInfo0.130.000.61
getMeta-CellBaseR-method0.140.020.60
getProtein-CellBaseR-method0.220.000.79
getProteinInfo0.260.000.81
getRegion-CellBaseR-method0.330.000.98
getRegulatoryByRegion0.410.001.22
getSnp-CellBaseR-method0.150.020.63
getSnpByGene0.130.000.61
getTf-CellBaseR-method0.140.003.53
getTfbsByRegion0.190.000.71
getTranscript-CellBaseR-method0.130.000.57
getTranscriptByGene0.120.000.60
getVariant-CellBaseR-method0.280.010.90
getVariantAnnotation0.330.000.97
getXref-CellBaseR-method0.160.000.61

cellbaseR.Rcheck/examples_x64/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 4.75 0.7650.45
CellBaseParam0.020.000.01
CellBaseR0.140.000.41
createGeneModel0.320.020.92
getCaddScores0.150.000.61
getCellBase-CellBaseR-method0.140.000.61
getCellBaseResourceHelp0.400.000.92
getChromosomeInfo-CellBaseR-method0.160.000.61
getClinical-CellBaseR-method1.340.002.13
getClinicalByRegion2.330.024.03
getConservationByRegion0.250.000.92
getGene-CellBaseR-method0.280.000.88
getGeneInfo0.160.000.62
getMeta-CellBaseR-method0.170.000.61
getProtein-CellBaseR-method0.270.000.83
getProteinInfo0.250.000.81
getRegion-CellBaseR-method0.210.010.87
getRegulatoryByRegion0.220.001.00
getSnp-CellBaseR-method0.170.000.75
getSnpByGene0.090.000.56
getTf-CellBaseR-method0.130.023.02
getTfbsByRegion0.170.000.67
getTranscript-CellBaseR-method0.160.000.61
getTranscriptByGene0.140.000.61
getVariant-CellBaseR-method0.250.000.90
getVariantAnnotation0.190.000.82
getXref-CellBaseR-method0.080.000.51