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CHECK report for cnvGSAdata on riesling1

This page was generated on 2021-01-14 15:59:07 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE cnvGSAdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 69/385HostnameOS / ArchINSTALLBUILDCHECK
cnvGSAdata 1.27.0
Joseph Lugo
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/cnvGSAdata
Branch: master
Last Commit: d259bce
Last Changed Date: 2020-10-27 09:55:27 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: cnvGSAdata
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cnvGSAdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cnvGSAdata_1.27.0.tar.gz
StartedAt: 2021-01-14 11:11:21 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:12:20 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 59.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cnvGSAdata.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cnvGSAdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings cnvGSAdata_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/cnvGSAdata.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 'cnvGSAdata/DESCRIPTION' ... OK
* this is package 'cnvGSAdata' version '1.27.0'
* 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 'cnvGSAdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      5.2Mb
    extdata   3.8Mb
* 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
* 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 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  cnvGSA_input_example.RData     2.4Mb    1.2Mb       xz
  cnvGSA_output_example.RData    2.5Mb    768Kb       xz
  gs_data_example.RData          310Kb    207Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/cnvGSAdata.Rcheck/00check.log'
for details.



Installation output

cnvGSAdata.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/cnvGSAdata_1.27.0.tar.gz && rm -rf cnvGSAdata.buildbin-libdir && mkdir cnvGSAdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cnvGSAdata.buildbin-libdir cnvGSAdata_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL cnvGSAdata_1.27.0.zip && rm cnvGSAdata_1.27.0.tar.gz cnvGSAdata_1.27.0.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 6391k  100 6391k    0     0  54.2M      0 --:--:-- --:--:-- --:--:-- 54.7M

install for i386

* installing *source* package 'cnvGSAdata' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'cnvGSAdata'
    finding HTML links ... done
    cnvGSA_input_example                    html  
REDIRECT:topic	 cnvGSA_input_example.RData -> cnvGSA_input_example.html [ SUCCESS ]
REDIRECT:topic	 cnvGSA.in -> cnvGSA_input_example.html [ SUCCESS ]
REDIRECT:file	 cnvGSA_input_example.html -> cnvGSA_input_example.html [ SUCCESS ]
    cnvGSA_output_example                   html  
REDIRECT:topic	 cnvGSA_output_example.RData -> cnvGSA_output_example.html [ SUCCESS ]
REDIRECT:topic	 cnvGSA.out -> cnvGSA_output_example.html [ SUCCESS ]
REDIRECT:file	 cnvGSA_output_example.html -> cnvGSA_output_example.html [ SUCCESS ]
    cnvGSAdata-package                      html  
REDIRECT:topic	 cnvGSAdata-package -> cnvGSAdata-package.html [ SUCCESS ]
REDIRECT:topic	 cnvGSAdata -> cnvGSAdata-package.html [ SUCCESS ]
    cnv_AGP_demo.txt                        html  
REDIRECT:topic	 cnv_AGP_demo.txt -> cnv_AGP_demo.txt.html [ SUCCESS ]
    enrGMT_AGP_demo.gmt                     html  
REDIRECT:topic	 enrGMT_AGP_demo.gmt -> enrGMT_AGP_demo.gmt.html [ SUCCESS ]
    enrGeneric_AGP_demo.txt                 html  
REDIRECT:topic	 enrGeneric_AGP_demo.txt -> enrGeneric_AGP_demo.txt.html [ SUCCESS ]
    gene_ID_demo.txt                        html  
REDIRECT:topic	 gene_ID_demo.txt -> gene_ID_demo.txt.html [ SUCCESS ]
    gs_data_example                         html  
REDIRECT:topic	 gs_data_example.RData -> gs_data_example.html [ SUCCESS ]
REDIRECT:topic	 gsData -> gs_data_example.html [ SUCCESS ]
REDIRECT:file	 gs_data_example.html -> gs_data_example.html [ SUCCESS ]
    kl_gene_AGP_demo.txt                    html  
REDIRECT:topic	 kl_gene_AGP_demo.txt -> kl_gene_AGP_demo.txt.html [ SUCCESS ]
    kl_loci_AGP_demo.txt                    html  
REDIRECT:topic	 kl_loci_AGP_demo.txt -> kl_loci_AGP_demo.txt.html [ SUCCESS ]
    ph_AGP_demo.txt                         html  
REDIRECT:topic	 ph_AGP_demo.txt -> ph_AGP_demo.txt.html [ SUCCESS ]
** building package indices
** 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 'cnvGSAdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cnvGSAdata' as cnvGSAdata_1.27.0.zip
* DONE (cnvGSAdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'cnvGSAdata' successfully unpacked and MD5 sums checked

Tests output


Example timings

cnvGSAdata.Rcheck/examples_i386/cnvGSAdata-Ex.timings

nameusersystemelapsed
cnv_AGP_demo.txt0.020.000.02
enrGMT_AGP_demo.gmt3.230.033.27
enrGeneric_AGP_demo.txt000
gene_ID_demo.txt0.080.010.09
kl_gene_AGP_demo.txt000
kl_loci_AGP_demo.txt000
ph_AGP_demo.txt000

cnvGSAdata.Rcheck/examples_x64/cnvGSAdata-Ex.timings

nameusersystemelapsed
cnv_AGP_demo.txt0.010.000.01
enrGMT_AGP_demo.gmt2.310.052.36
enrGeneric_AGP_demo.txt000
gene_ID_demo.txt0.090.000.10
kl_gene_AGP_demo.txt000
kl_loci_AGP_demo.txt000
ph_AGP_demo.txt0.020.000.02