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CHECK report for omicRexposome on tokay2

This page was generated on 2018-10-17 08:44:40 -0400 (Wed, 17 Oct 2018).

Package 1020/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omicRexposome 1.2.0
Carles Hernandez-Ferrer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/omicRexposome
Branch: RELEASE_3_7
Last Commit: c1ec477
Last Changed Date: 2018-04-30 10:35:48 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: omicRexposome
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:omicRexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings omicRexposome_1.2.0.tar.gz
StartedAt: 2018-10-17 03:44:01 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:49:03 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 301.7 seconds
RetCode: 0
Status:  OK  
CheckDir: omicRexposome.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:omicRexposome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings omicRexposome_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/omicRexposome.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'omicRexposome/DESCRIPTION' ... OK
* this is package 'omicRexposome' version '1.2.0'
* 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 'omicRexposome' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
association-methods 8.37      0    8.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
association-methods 8.23      0    8.23
* 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

omicRexposome.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/omicRexposome_1.2.0.tar.gz && rm -rf omicRexposome.buildbin-libdir && mkdir omicRexposome.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=omicRexposome.buildbin-libdir omicRexposome_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL omicRexposome_1.2.0.zip && rm omicRexposome_1.2.0.tar.gz omicRexposome_1.2.0.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 1355k  100 1355k    0     0  18.1M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

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

    add_exp-methods                         html  
    asr                                     html  
    association-methods                     html  
    crossomics-methods                      html  
    crs                                     html  
    getIntegration-methods                  html  
    mds                                     html  
    omicRexposome                           html  
    plotAssociation-methods                 html  
    plotHits-methods                        html  
    plotIntegration-methods                 html  
    plotLambda-methods                      html  
    snpToContinuous                         html  
    tableHits-methods                       html  
    tableLambda-methods                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'omicRexposome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'omicRexposome' as omicRexposome_1.2.0.zip
* DONE (omicRexposome)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'omicRexposome' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

omicRexposome.Rcheck/examples_i386/omicRexposome-Ex.timings

nameusersystemelapsed
add_cls-methods0.210.020.43
add_exp-methods0.090.000.44
asr0.050.000.05
association-methods8.370.008.38
crossomics-methods0.730.000.74
crs0.020.000.01
getIntegration-methods000
mds0.000.010.02
plotAssociation-methods0.560.070.62
plotHits-methods0.200.000.21
plotIntegration-methods0.750.000.75
plotLambda-methods0.220.000.22
tableHits-methods0.040.000.05
tableLambda-methods0.050.000.05

omicRexposome.Rcheck/examples_x64/omicRexposome-Ex.timings

nameusersystemelapsed
add_cls-methods0.230.000.23
add_exp-methods0.050.000.05
asr0.030.000.03
association-methods8.230.008.23
crossomics-methods0.410.000.41
crs0.010.000.01
getIntegration-methods000
mds0.020.000.02
plotAssociation-methods0.420.030.45
plotHits-methods0.220.020.24
plotIntegration-methods1.010.001.02
plotLambda-methods0.250.000.25
tableHits-methods0.040.010.07
tableLambda-methods0.070.000.06