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CHECK report for gcapc on tokay2

This page was generated on 2018-10-17 08:43:15 -0400 (Wed, 17 Oct 2018).

Package 546/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gcapc 1.4.0
Mingxiang Teng
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gcapc
Branch: RELEASE_3_7
Last Commit: 1f1a329
Last Changed Date: 2018-04-30 10:35:44 -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 [ WARNINGS ] 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: gcapc
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gcapc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gcapc_1.4.0.tar.gz
StartedAt: 2018-10-17 02:07:00 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:19:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 752.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: gcapc.Rcheck
Warnings: 1

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:gcapc.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gcapc_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/gcapc.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 'gcapc/DESCRIPTION' ... OK
* this is package 'gcapc' version '1.4.0'
* 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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-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 or elapsed time > 5s
             user system elapsed
peaksCAT    97.98   2.88  100.88
gcapcPeaks  56.67   1.34   58.05
refinePeaks 52.85   1.20   54.05
gcEffects   46.65   2.92   49.58
bindWidth    8.39   0.42    9.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peaksCAT    90.78   2.71   93.50
gcEffects   45.42   2.31   47.75
refinePeaks 45.95   1.25   47.20
gcapcPeaks  43.58   1.70   45.30
bindWidth    7.95   0.19    8.14
* 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-3.7-bioc/meat/gcapc.Rcheck/00check.log'
for details.



Installation output

gcapc.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/gcapc_1.4.0.tar.gz && rm -rf gcapc.buildbin-libdir && mkdir gcapc.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gcapc.buildbin-libdir gcapc_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL gcapc_1.4.0.zip && rm gcapc_1.4.0.tar.gz gcapc_1.4.0.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 3420k  100 3420k    0     0  38.7M      0 --:--:-- --:--:-- --:--:-- 42.2M

install for i386

* installing *source* package 'gcapc' ...
** 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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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-3.7-bioc/tmpdir/RtmpOoWOFb/R.INSTALL1bdc27b71494/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
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_1.4.0.zip
* DONE (gcapc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'gcapc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

gcapc.Rcheck/examples_i386/gcapc-Ex.timings

nameusersystemelapsed
bindWidth8.390.429.22
gcEffects46.65 2.9249.58
gcapcPeaks56.67 1.3458.05
peaksCAT 97.98 2.88100.88
read5endCoverage0.310.000.31
refinePeaks52.85 1.2054.05

gcapc.Rcheck/examples_x64/gcapc-Ex.timings

nameusersystemelapsed
bindWidth7.950.198.14
gcEffects45.42 2.3147.75
gcapcPeaks43.58 1.7045.30
peaksCAT90.78 2.7193.50
read5endCoverage0.320.000.31
refinePeaks45.95 1.2547.20