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CHECK report for cellbaseR on tokay1

This page was generated on 2021-02-22 12:37:17 -0500 (Mon, 22 Feb 2021).

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 250/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.14.0
Mohammed OE Abdallah
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: RELEASE_3_12
Last Commit: 6ecfb00
Last Changed Date: 2020-10-27 11:23:55 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: cellbaseR
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2021-02-22 01:15:03 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 01:20:33 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 329.4 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_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/cellbaseR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.0'
* 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/Rtmpi8xJqp/R.INSTALL273430e37830/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 7.21   0.95    58.9
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 5.64   0.65   59.66
* 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_1.14.0.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_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL cellbaseR_1.14.0.zip && rm cellbaseR_1.14.0.tar.gz cellbaseR_1.14.0.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  14.6M      0 --:--:-- --:--:-- --:--:-- 16.3M

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/Rtmpi8xJqp/R.INSTALL273430e37830/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_1.14.0.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 7.21 0.9558.90
CellBaseParam000
CellBaseR0.120.020.43
createGeneModel0.800.021.58
getCaddScores0.150.000.64
getCellBase-CellBaseR-method0.180.000.67
getCellBaseResourceHelp0.310.000.96
getChromosomeInfo-CellBaseR-method0.140.010.68
getClinical-CellBaseR-method1.480.022.33
getClinicalByRegion2.970.114.39
getConservationByRegion0.240.031.00
getGene-CellBaseR-method0.330.010.96
getGeneInfo0.170.000.68
getMeta-CellBaseR-method0.170.000.66
getProtein-CellBaseR-method0.280.000.87
getProteinInfo0.270.000.88
getRegion-CellBaseR-method0.320.021.03
getRegulatoryByRegion0.380.011.24
getSnp-CellBaseR-method0.110.020.60
getSnpByGene0.220.000.71
getTf-CellBaseR-method0.090.002.98
getTfbsByRegion0.160.000.71
getTranscript-CellBaseR-method0.120.020.64
getTranscriptByGene0.110.000.59
getVariant-CellBaseR-method0.310.000.97
getVariantAnnotation0.360.001.03
getXref-CellBaseR-method0.130.010.62

cellbaseR.Rcheck/examples_x64/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 5.64 0.6559.66
CellBaseParam000
CellBaseR0.210.000.53
createGeneModel0.500.001.24
getCaddScores0.110.000.71
getCellBase-CellBaseR-method0.070.000.61
getCellBaseResourceHelp0.380.010.98
getChromosomeInfo-CellBaseR-method0.120.000.62
getClinical-CellBaseR-method1.360.012.16
getClinicalByRegion2.820.044.36
getConservationByRegion0.180.000.95
getGene-CellBaseR-method0.350.000.98
getGeneInfo0.150.000.68
getMeta-CellBaseR-method0.130.000.62
getProtein-CellBaseR-method0.250.000.86
getProteinInfo0.250.030.84
getRegion-CellBaseR-method0.290.001.00
getRegulatoryByRegion0.320.041.21
getSnp-CellBaseR-method0.170.000.64
getSnpByGene0.170.020.69
getTf-CellBaseR-method0.140.002.96
getTfbsByRegion0.100.000.65
getTranscript-CellBaseR-method0.070.000.57
getTranscriptByGene0.140.000.63
getVariant-CellBaseR-method0.290.001.01
getVariantAnnotation0.370.001.04
getXref-CellBaseR-method0.130.000.60