Package: motifbreakR

Version: 1.8.0

Command: rm -rf motifbreakR.buildbin-libdir motifbreakR.Rcheck && mkdir motifbreakR.buildbin-libdir motifbreakR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifbreakR.buildbin-libdir motifbreakR_1.8.0.tar.gz >motifbreakR.Rcheck\00install.out 2>&1 && cp motifbreakR.Rcheck\00install.out motifbreakR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=motifbreakR.buildbin-libdir --install="check:motifbreakR-install.out" --force-multiarch --no-vignettes --timings motifbreakR_1.8.0.tar.gz

StartedAt: 2018-04-12 01:35:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:44:57 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 578.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: motifbreakR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf motifbreakR.buildbin-libdir motifbreakR.Rcheck && mkdir motifbreakR.buildbin-libdir motifbreakR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifbreakR.buildbin-libdir motifbreakR_1.8.0.tar.gz >motifbreakR.Rcheck\00install.out 2>&1 && cp motifbreakR.Rcheck\00install.out motifbreakR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=motifbreakR.buildbin-libdir --install="check:motifbreakR-install.out" --force-multiarch --no-vignettes --timings motifbreakR_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/motifbreakR.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 'motifbreakR/DESCRIPTION' ... OK
* this is package 'motifbreakR' version '1.8.0'
* 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 'motifbreakR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkFSBy2/R.INSTALL1524304851eb/motifbreakR/man/example.results.Rd:7: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkFSBy2/R.INSTALL1524304851eb/motifbreakR/man/example.results.Rd:12: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-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
** 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 ... 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
  'elementLengths'
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:
  elementLengths 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 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
snps.from.rsid 42.17   1.56   48.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
snps.from.rsid 47.71   1.85   49.55
* 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-3.6-bioc/meat/motifbreakR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'motifbreakR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** 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-3.6-bioc/tmpdir/RtmpkFSBy2/R.INSTALL1524304851eb/motifbreakR/man/example.results.Rd:7: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkFSBy2/R.INSTALL1524304851eb/motifbreakR/man/example.results.Rd:12: missing file link 'GRanges'
    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.
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.
* MD5 sums
packaged installation of 'motifbreakR' as motifbreakR_1.8.0.zip
* DONE (motifbreakR)
In R CMD INSTALL
In R CMD INSTALL