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CHECK report for gcapc on tokay1

This page was generated on 2018-04-12 13:29:07 -0400 (Thu, 12 Apr 2018).

Package 519/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gcapc 1.2.0
Mingxiang Teng
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/gcapc
Branch: RELEASE_3_6
Last Commit: 143c089
Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gcapc
Version: 1.2.0
Command: rm -rf gcapc.buildbin-libdir gcapc.Rcheck && mkdir gcapc.buildbin-libdir gcapc.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gcapc.buildbin-libdir gcapc_1.2.0.tar.gz >gcapc.Rcheck\00install.out 2>&1 && cp gcapc.Rcheck\00install.out gcapc-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gcapc.buildbin-libdir --install="check:gcapc-install.out" --force-multiarch --no-vignettes --timings gcapc_1.2.0.tar.gz
StartedAt: 2018-04-12 00:08:03 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:19:51 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 708.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gcapc.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf gcapc.buildbin-libdir gcapc.Rcheck && mkdir gcapc.buildbin-libdir gcapc.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gcapc.buildbin-libdir gcapc_1.2.0.tar.gz >gcapc.Rcheck\00install.out 2>&1 && cp gcapc.Rcheck\00install.out gcapc-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gcapc.buildbin-libdir --install="check:gcapc-install.out" --force-multiarch --no-vignettes --timings gcapc_1.2.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcapc.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gcapc/DESCRIPTION' ... OK
* this is package 'gcapc' version '1.2.0'
* 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 'gcapc' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:92: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:95: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:97: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:47: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:50: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:52: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:42: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:45: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:47: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:93: missing file link 'BSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:96: missing file link 'getBSgenome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:98: missing file link 'getBSgenome'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcapc.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peaksCAT    84.97   3.53   88.50
refinePeaks 48.92   1.52   50.44
gcapcPeaks  46.04   1.09   47.14
gcEffects   38.97   1.49   40.46
bindWidth   10.28   0.47   10.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peaksCAT    87.42   1.83   89.25
refinePeaks 51.66   0.83   52.49
gcapcPeaks  43.98   1.54   45.53
gcEffects   40.28   1.36   41.67
bindWidth    9.77   0.20    9.97
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/gcapc.Rcheck/00check.log'
for details.

Installation output

gcapc.Rcheck/00install.out


install for i386

* installing *source* package 'gcapc' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gcapc'
    finding HTML links ... done
    bindWidth                               html  
    gcEffects                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:92: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:95: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcEffects.Rd:97: missing file link 'getBSgenome'
    gcapcPeaks                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:47: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:50: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/gcapcPeaks.Rd:52: missing file link 'getBSgenome'
    peaksCAT                                html  
    read5endCoverage                        html  
    refinePeaks                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:42: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:45: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refinePeaks.Rd:47: missing file link 'getBSgenome'
    refineSites                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:93: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:96: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp8o1KiE/R.INSTALL1c9433aa757/gcapc/man/refineSites.Rd:98: missing file link 'getBSgenome'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gcapc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gcapc' as gcapc_1.2.0.zip
* DONE (gcapc)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

gcapc.Rcheck/examples_i386/gcapc-Ex.timings

nameusersystemelapsed
bindWidth10.28 0.4710.75
gcEffects38.97 1.4940.46
gcapcPeaks46.04 1.0947.14
peaksCAT84.97 3.5388.50
read5endCoverage0.350.000.35
refinePeaks48.92 1.5250.44

gcapc.Rcheck/examples_x64/gcapc-Ex.timings

nameusersystemelapsed
bindWidth9.770.209.97
gcEffects40.28 1.3641.67
gcapcPeaks43.98 1.5445.53
peaksCAT87.42 1.8389.25
read5endCoverage0.380.000.37
refinePeaks51.66 0.8352.49