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This page was generated on 2022-01-24 13:06:00 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for cellbaseR on tokay2


To the developers/maintainers of the cellbaseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellbaseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 264/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.18.0  (landing page)
Mohammed OE Abdallah
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/cellbaseR
git_branch: RELEASE_3_14
git_last_commit: 5598bf6
git_last_commit_date: 2021-10-26 12:35:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellbaseR
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cellbaseR_1.18.0.tar.gz
StartedAt: 2022-01-23 16:37:25 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:42:41 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 316.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cellbaseR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellbaseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cellbaseR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cellbaseR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.18.0'
* 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
* 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 5.93   0.97   50.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
AnnotateVcf-CellBaseR-method 5.52   0.99   50.24
* 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: OK


Installation output

cellbaseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cellbaseR_1.18.0.tar.gz && rm -rf cellbaseR.buildbin-libdir && mkdir cellbaseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellbaseR.buildbin-libdir cellbaseR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cellbaseR_1.18.0.zip && rm cellbaseR_1.18.0.tar.gz cellbaseR_1.18.0.zip
###
##############################################################################
##############################################################################


  % 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  734k  100  734k    0     0  1975k      0 --:--:-- --:--:-- --:--:-- 1980k

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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/cellbaseR.buildbin-libdir/00LOCK-cellbaseR/00new/cellbaseR/help/cellbaseR.html
    createGeneModel                         html  
    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_1.18.0.zip
* DONE (cellbaseR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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 5.93 0.9750.86
CellBaseParam000
CellBaseR0.140.000.50
createGeneModel0.390.021.10
getCaddScores0.160.000.72
getCellBase-CellBaseR-method0.170.010.75
getCellBaseResourceHelp0.330.031.03
getChromosomeInfo-CellBaseR-method0.140.020.71
getClinical-CellBaseR-method1.020.142.12
getClinicalByRegion2.500.054.25
getConservationByRegion0.310.001.17
getGene-CellBaseR-method0.390.001.10
getGeneInfo0.170.010.78
getMeta-CellBaseR-method0.170.020.73
getProtein-CellBaseR-method0.240.030.99
getProteinInfo0.290.030.98
getRegion-CellBaseR-method0.350.001.17
getRegulatoryByRegion0.450.001.46
getSnp-CellBaseR-method0.200.000.78
getSnpByGene0.210.020.78
getTf-CellBaseR-method0.150.003.09
getTfbsByRegion0.210.000.82
getTranscript-CellBaseR-method0.180.000.75
getTranscriptByGene0.180.000.75
getVariant-CellBaseR-method0.390.001.17
getVariantAnnotation0.390.011.12
getXref-CellBaseR-method0.150.000.74

cellbaseR.Rcheck/examples_x64/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method 5.52 0.9950.24
CellBaseParam000
CellBaseR0.130.000.49
createGeneModel0.360.001.08
getCaddScores0.150.010.73
getCellBase-CellBaseR-method0.180.030.77
getCellBaseResourceHelp0.400.001.06
getChromosomeInfo-CellBaseR-method0.140.000.70
getClinical-CellBaseR-method1.100.052.08
getClinicalByRegion2.370.063.91
getConservationByRegion0.240.021.07
getGene-CellBaseR-method0.290.001.03
getGeneInfo0.160.010.72
getMeta-CellBaseR-method0.140.000.71
getProtein-CellBaseR-method0.250.000.92
getProteinInfo0.250.020.94
getRegion-CellBaseR-method0.340.001.17
getRegulatoryByRegion0.410.001.38
getSnp-CellBaseR-method0.150.000.73
getSnpByGene0.190.000.77
getTf-CellBaseR-method0.120.013.06
getTfbsByRegion0.210.000.81
getTranscript-CellBaseR-method0.150.000.72
getTranscriptByGene0.180.000.72
getVariant-CellBaseR-method0.340.001.24
getVariantAnnotation0.410.001.17
getXref-CellBaseR-method0.140.000.70