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CHECK report for motifbreakR on tokay1

This page was generated on 2019-04-13 11:25:53 -0400 (Sat, 13 Apr 2019).

Package 993/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 1.12.0
Simon Gert Coetzee
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/motifbreakR
Branch: RELEASE_3_8
Last Commit: c35ebfb
Last Changed Date: 2018-10-30 11:41:58 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifbreakR
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifbreakR_1.12.0.tar.gz
StartedAt: 2019-04-13 03:57:46 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:08:15 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 629.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: motifbreakR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifbreakR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings motifbreakR_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifbreakR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifbreakR/DESCRIPTION' ... OK
* this is package 'motifbreakR' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'motifbreakR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifbreakR.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 ... NOTE
Packages in Depends field not imported from:
  'MotifDb' 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMotifLogoStack.2: no visible global function definition for 'par'
snps.from.file: no visible global function definition for 'info'
snps.from.file: no visible global function definition for 'rowRanges'
snps.from.rsid: no visible global function definition for 'snpsById'
Undefined global functions or variables:
  info par rowRanges snpsById
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* 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
snps.from.rsid 47.58   1.40   59.74
motifbreakR     5.71   0.34    6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
snps.from.rsid 52.91   1.72   54.65
motifbreakR     5.50   0.15    5.66
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.



Installation output

motifbreakR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/motifbreakR_1.12.0.tar.gz && rm -rf motifbreakR.buildbin-libdir && mkdir motifbreakR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifbreakR.buildbin-libdir motifbreakR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifbreakR_1.12.0.zip && rm motifbreakR_1.12.0.tar.gz motifbreakR_1.12.0.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 1356k  100 1356k    0     0  26.4M      0 --:--:-- --:--:-- --:--:-- 28.7M

install for i386

* installing *source* package 'motifbreakR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
** help
*** installing help indices
  converting help for package 'motifbreakR'
    finding HTML links ... done
    calculatePvalue                         html  
    finding level-2 HTML links ... done

    encodemotif                             html  
    example.results                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpUTBeQu/R.INSTALL2480110a278f/motifbreakR/man/example.results.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    factorbook                              html  
    hocomoco                                html  
    homer                                   html  
    motifbreakR                             html  
    motifbreakR_motif                       html  
    plotMB                                  html  
    snps.from.file                          html  
    snps.from.rsid                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
In R CMD INSTALL

install for x64

* installing *source* package 'motifbreakR' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'motifbreakR'
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_1.12.0.zip
* DONE (motifbreakR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'motifbreakR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

motifbreakR.Rcheck/examples_i386/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue0.310.000.32
encodemotif0.030.000.03
example.results0.060.020.08
factorbook0.000.010.02
hocomoco0.020.000.01
homer0.010.000.02
motifbreakR5.710.346.06
motifbreakR_motif0.030.020.05
plotMB0.040.000.05
snps.from.file0.460.051.06
snps.from.rsid47.58 1.4059.74

motifbreakR.Rcheck/examples_x64/motifbreakR-Ex.timings

nameusersystemelapsed
calculatePvalue0.150.030.19
encodemotif0.030.000.03
example.results0.090.000.09
factorbook0.000.020.02
hocomoco0.050.000.05
homer0.020.000.01
motifbreakR5.500.155.66
motifbreakR_motif0.030.000.03
plotMB0.050.000.05
snps.from.file0.560.030.59
snps.from.rsid52.91 1.7254.65