Back to Multiple platform build/check report for BioC 3.12
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for gcapc on tokay1

This page was generated on 2021-01-19 11:55:19 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE gcapc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 667/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gcapc 1.14.0
Mingxiang Teng
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/gcapc
Branch: RELEASE_3_12
Last Commit: 6c7d83d
Last Changed Date: 2020-10-27 11:20:02 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gcapc
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gcapc.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gcapc_1.14.0.tar.gz
StartedAt: 2021-01-19 03:09:10 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 03:21:55 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 765.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gcapc.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gcapc.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gcapc_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gcapc.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.14.0'
* 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-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:92: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:95: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:97: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:47: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:50: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:52: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:42: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:45: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:47: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:93: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:96: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:98: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-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
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
peaksCAT    87.06   3.35   90.55
refinePeaks 48.93   1.16   50.13
gcapcPeaks  47.14   1.37   48.87
gcEffects   35.77   2.08   37.88
bindWidth    7.59   0.50    8.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
peaksCAT    85.84   2.50   88.36
refinePeaks 64.73   1.36   66.43
gcapcPeaks  43.69   1.56   45.87
gcEffects   35.33   2.38   37.70
bindWidth    9.20   0.17    9.38
* 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-3.12-bioc/meat/gcapc.Rcheck/00check.log'
for details.



Installation output

gcapc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/gcapc_1.14.0.tar.gz && rm -rf gcapc.buildbin-libdir && mkdir gcapc.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gcapc.buildbin-libdir gcapc_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL gcapc_1.14.0.zip && rm gcapc_1.14.0.tar.gz gcapc_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3418k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3418k  100 3418k    0     0  6229k      0 --:--:-- --:--:-- --:--:-- 6260k

install for i386

* installing *source* package 'gcapc' ...
** using staged installation
** R
** inst
** byte-compile and prepare 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-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:92: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:95: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcEffects.Rd:97: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    gcapcPeaks                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:47: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:50: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/gcapcPeaks.Rd:52: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    peaksCAT                                html  
    read5endCoverage                        html  
    refinePeaks                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:42: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:45: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refinePeaks.Rd:47: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    refineSites                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:93: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:96: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpgbq5UY/R.INSTALL185c125010cb/gcapc/man/refineSites.Rd:98: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
** 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 'gcapc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gcapc' as gcapc_1.14.0.zip
* DONE (gcapc)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'gcapc' successfully unpacked and MD5 sums checked

Tests output


Example timings

gcapc.Rcheck/examples_i386/gcapc-Ex.timings

nameusersystemelapsed
bindWidth7.590.508.21
gcEffects35.77 2.0837.88
gcapcPeaks47.14 1.3748.87
peaksCAT87.06 3.3590.55
read5endCoverage0.480.000.49
refinePeaks48.93 1.1650.13

gcapc.Rcheck/examples_x64/gcapc-Ex.timings

nameusersystemelapsed
bindWidth9.200.179.38
gcEffects35.33 2.3837.70
gcapcPeaks43.69 1.5645.87
peaksCAT85.84 2.5088.36
read5endCoverage0.390.000.39
refinePeaks64.73 1.3666.43