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CHECK report for depmap on riesling1

This page was generated on 2021-01-11 15:59:30 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE depmap PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 90/385HostnameOS / ArchINSTALLBUILDCHECK
depmap 1.5.1
Laurent Gatto
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/depmap
Branch: master
Last Commit: f37525a
Last Changed Date: 2020-11-26 15:36:28 -0500 (Thu, 26 Nov 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: depmap
Version: 1.5.1
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:depmap.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings depmap_1.5.1.tar.gz
StartedAt: 2021-01-11 11:19:56 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:22:59 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 183.2 seconds
RetCode: 0
Status:  OK  
CheckDir: depmap.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:depmap.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings depmap_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/depmap.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'depmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'depmap' version '1.5.1'
* package encoding: UTF-8
* 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 'depmap' 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
** running examples for arch 'x64' ... OK
* 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

depmap.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/depmap_1.5.1.tar.gz && rm -rf depmap.buildbin-libdir && mkdir depmap.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=depmap.buildbin-libdir depmap_1.5.1.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL depmap_1.5.1.zip && rm depmap_1.5.1.tar.gz depmap_1.5.1.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
  2 43468    2  1219    0     0   1320      0  0:00:32 --:--:--  0:00:32  1319
100 43468  100 43468    0     0  47094      0 --:--:-- --:--:-- --:--:-- 47043

install for i386

* installing *source* package 'depmap' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'depmap'
    finding HTML links ... done
    RPPA                                    html  
REDIRECT:topic	 RPPA -> RPPA.html [ SUCCESS ]
REDIRECT:topic	 RPPA_19Q3 -> RPPA.html [ SUCCESS ]
REDIRECT:topic	 RPPA_19Q2 -> RPPA.html [ SUCCESS ]
REDIRECT:topic	 RPPA_19Q1 -> RPPA.html [ SUCCESS ]
REDIRECT:topic	 depmap_RPPA -> RPPA.html [ SUCCESS ]
    TPM                                     html  
REDIRECT:topic	 TPM -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_20Q4 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_20Q3 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_20Q2 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_20Q1 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_19Q4 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_19Q3 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_19Q2 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 TPM_19Q1 -> TPM.html [ SUCCESS ]
REDIRECT:topic	 depmap_TPM -> TPM.html [ SUCCESS ]
    copyNumber                              html  
REDIRECT:topic	 copyNumber -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_20Q4 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_20Q3 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_20Q2 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_20Q1 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_19Q4 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_19Q3 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_19Q2 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 copyNumber_19Q1 -> copyNumber.html [ SUCCESS ]
REDIRECT:topic	 depmap_copyNumber -> copyNumber.html [ SUCCESS ]
    crispr                                  html  
REDIRECT:topic	 crispr -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_20Q4 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_20Q3 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_20Q2 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_20Q1 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_19Q4 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_19Q3 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_19Q2 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 crispr_19Q1 -> crispr.html [ SUCCESS ]
REDIRECT:topic	 depmap_crispr -> crispr.html [ SUCCESS ]
    depmap                                  html  
REDIRECT:topic	 depmap -> depmap.html [ SUCCESS ]
    depmap_release                          html  
REDIRECT:topic	 depmap_release -> depmap_release.html [ SUCCESS ]
    drug_sensitivity                        html  
REDIRECT:topic	 drug_sensitivity -> drug_sensitivity.html [ SUCCESS ]
REDIRECT:topic	 drug_sensitivity_19Q3 -> drug_sensitivity.html [ SUCCESS ]
REDIRECT:topic	 depmap_drug_sensitivity -> drug_sensitivity.html [ SUCCESS ]
    metadata                                html  
REDIRECT:topic	 metadata -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_20Q4 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_20Q3 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_20Q2 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_20Q1 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_19Q4 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_19Q3 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_19Q2 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 metadata_19Q1 -> metadata.html [ SUCCESS ]
REDIRECT:topic	 depmap_metadata -> metadata.html [ SUCCESS ]
    mutationCalls                           html  
REDIRECT:topic	 mutationCalls -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_20Q4 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_20Q3 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_20Q2 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_20Q1 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_19Q4 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_19Q3 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_19Q2 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 mutationCalls_19Q1 -> mutationCalls.html [ SUCCESS ]
REDIRECT:topic	 depmap_mutationCalls -> mutationCalls.html [ SUCCESS ]
    proteomic                               html  
REDIRECT:topic	 proteomic -> proteomic.html [ SUCCESS ]
REDIRECT:topic	 proteomic_20Q2 -> proteomic.html [ SUCCESS ]
REDIRECT:topic	 depmap_proteomic -> proteomic.html [ SUCCESS ]
    rnai                                    html  
REDIRECT:topic	 rnai -> rnai.html [ SUCCESS ]
REDIRECT:topic	 rnai_19Q3 -> rnai.html [ SUCCESS ]
REDIRECT:topic	 rnai_19Q2 -> rnai.html [ SUCCESS ]
REDIRECT:topic	 rnai_19Q1 -> rnai.html [ SUCCESS ]
REDIRECT:topic	 depmap_rnai -> rnai.html [ SUCCESS ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
** testing if installed package can be loaded from final location
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'depmap' ...
** testing if installed package can be loaded
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
snapshotDate(): 2021-01-07
* MD5 sums
packaged installation of 'depmap' as depmap_1.5.1.zip
* DONE (depmap)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'depmap' successfully unpacked and MD5 sums checked

Tests output


Example timings

depmap.Rcheck/examples_i386/depmap-Ex.timings

nameusersystemelapsed
RPPA000
TPM000
copyNumber000
crispr000
metadata000
mutationCalls000
proteomic000
rnai000

depmap.Rcheck/examples_x64/depmap-Ex.timings

nameusersystemelapsed
RPPA000
TPM000
copyNumber000
crispr000
metadata000
mutationCalls000
proteomic000
rnai000