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CHECK report for epihet on tokay2

This page was generated on 2019-04-09 12:43:21 -0400 (Tue, 09 Apr 2019).

Package 500/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epihet 0.99.8
Xiaowen Chen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/epihet
Branch: master
Last Commit: a48385f
Last Changed Date: 2018-12-04 11:54:22 -0400 (Tue, 04 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: epihet
Version: 0.99.8
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epihet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings epihet_0.99.8.tar.gz
StartedAt: 2019-04-09 02:34:47 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:39:38 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 291.1 seconds
RetCode: 0
Status:  OK  
CheckDir: epihet.Rcheck
Warnings: 0

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:epihet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings epihet_0.99.8.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/epihet.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epihet/DESCRIPTION' ... OK
* this is package 'epihet' version '0.99.8'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicRanges', 'IRanges', 'S4Vectors', 'ggplot2', 'foreach',
  'Rtsne', 'igraph'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'epihet' 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
epiPathway 11.56   0.25   11.81
compMatrix  0.22   0.06    8.44
makeGR      0.05   0.00   10.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
epiPathway 11.61   0.71   12.31
compMatrix  0.15   0.00    7.97
makeGR      0.01   0.03   13.59
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/epihet.Rcheck/00check.log'
for details.



Installation output

epihet.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/epihet_0.99.8.tar.gz && rm -rf epihet.buildbin-libdir && mkdir epihet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epihet.buildbin-libdir epihet_0.99.8.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL epihet_0.99.8.zip && rm epihet_0.99.8.tar.gz epihet_0.99.8.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  453k  100  453k    0     0  7386k      0 --:--:-- --:--:-- --:--:-- 8247k

install for i386

* installing *source* package 'epihet' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epihet'
    finding HTML links ... done
    compMatrix                              html  
    data                                    html  
    diffHet                                 html  
    epiBox                                  html  
    epiMA                                   html  
    epiMap                                  html  
    epiNetwork                              html  
    epiPCA                                  html  
    epiPathway                              html  
    epiTSNE                                 html  
    jaccard                                 html  
    makeGR                                  html  
    moduleAnno                              html  
    moduleSim                               html  
    moduleVisual                            html  
    readGR                                  html  
    shannon                                 html  
    splitn                                  html  
    summarize                               html  
    userobj                                 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 'epihet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epihet' as epihet_0.99.8.zip
* DONE (epihet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'epihet' successfully unpacked and MD5 sums checked

Tests output


Example timings

epihet.Rcheck/examples_i386/epihet-Ex.timings

nameusersystemelapsed
compMatrix0.220.068.44
epiBox0.060.020.08
epiMA0.10.00.1
epiMap0.180.020.20
epiPCA0.460.130.58
epiPathway11.56 0.2511.81
epiTSNE0.200.040.25
jaccard0.000.030.03
makeGR 0.05 0.0010.17
moduleAnno0.330.020.35
moduleSim0.060.000.06
moduleVisual0.140.000.14
readGR0.050.010.17
shannon000
splitn000
summarize0.110.000.11
userobj0.010.000.02

epihet.Rcheck/examples_x64/epihet-Ex.timings

nameusersystemelapsed
compMatrix0.150.007.97
epiBox0.040.010.06
epiMA0.090.000.11
epiMap0.160.000.16
epiPCA0.420.000.42
epiPathway11.61 0.7112.31
epiTSNE0.240.010.25
jaccard0.000.020.02
makeGR 0.01 0.0313.59
moduleAnno0.410.000.45
moduleSim0.030.030.06
moduleVisual0.160.000.16
readGR0.060.000.17
shannon000
splitn000
summarize0.150.000.16
userobj0.040.000.03