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CHECK report for dcGSA on tokay2

This page was generated on 2019-10-16 12:34:34 -0400 (Wed, 16 Oct 2019).

Package 392/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dcGSA 1.12.0
Jiehuan sun
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/dcGSA
Branch: RELEASE_3_9
Last Commit: 01ad4ca
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: dcGSA
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dcGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dcGSA_1.12.0.tar.gz
StartedAt: 2019-10-16 03:04:28 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:05:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 64.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: dcGSA.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dcGSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dcGSA_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dcGSA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dcGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dcGSA' version '1.12.0'
* 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 'dcGSA' can be installed ... OK
* checking installed package size ... OK
* checking package 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'dcGSA.Rmd', 'dcGSA.bib'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/dcGSA.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/dcGSA.Rcheck/00check.log'
for details.



Installation output

dcGSA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/dcGSA_1.12.0.tar.gz && rm -rf dcGSA.buildbin-libdir && mkdir dcGSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dcGSA.buildbin-libdir dcGSA_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL dcGSA_1.12.0.zip && rm dcGSA_1.12.0.tar.gz dcGSA_1.12.0.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 35526  100 35526    0     0   259k      0 --:--:-- --:--:-- --:--:--  273k

install for i386

* installing *source* package 'dcGSA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dcGSA'
    finding HTML links ... done
    LDcov                                   html  
    dcGSA                                   html  
    finding level-2 HTML links ... done

    dcGSAtest                               html  
    readGMT                                 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 'dcGSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dcGSA' as dcGSA_1.12.0.zip
* DONE (dcGSA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'dcGSA' successfully unpacked and MD5 sums checked

Tests output


Example timings

dcGSA.Rcheck/examples_i386/dcGSA-Ex.timings

nameusersystemelapsed
LDcov0.040.000.03
dcGSA0.580.030.62
dcGSAtest000
readGMT0.020.000.02

dcGSA.Rcheck/examples_x64/dcGSA-Ex.timings

nameusersystemelapsed
LDcov0.030.000.03
dcGSA0.690.000.68
dcGSAtest0.000.020.02
readGMT000