Package: REDseq

Version: 1.24.0

Command: rm -rf REDseq.buildbin-libdir REDseq.Rcheck && mkdir REDseq.buildbin-libdir REDseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.24.0.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.24.0.tar.gz

StartedAt: 2018-04-12 02:34:17 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:40:49 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 391.8 seconds

RetCode: 0

Status:  OK

CheckDir: REDseq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf REDseq.buildbin-libdir REDseq.Rcheck && mkdir REDseq.buildbin-libdir REDseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.24.0.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/REDseq.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 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'BSgenome.Celegans.UCSC.ce2' 'multtest' 'Biostrings'
  'BSgenome' 'ChIPpeakAnno'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'REDseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'Biostrings' 'ChIPpeakAnno' 'multtest'
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2'
  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 ... 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 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
buildREmap 7.42   0.17    14.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
buildREmap 10.06    0.2   10.26
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/REDseq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'REDseq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
  converting help for package 'REDseq'
    finding HTML links ... done
    REDseq-package                          html  
    assignSeq2REsite                        html  
    binom.test.REDseq                       html  
    buildREmap                              html  
    compareREDseq                           html  
    distanceHistSeq2RE                      html  
    example.REDseq                          html  
    example.assignedREDseq                  html  
    example.map                             html  
    plotCutDistribution                     html  
    searchPattern                           html  
    summarizeByRE                           html  
    summarizeBySeq                          html  
    writeHits                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
In R CMD INSTALL

install for x64

* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.24.0.zip
* DONE (REDseq)
In R CMD INSTALL
In R CMD INSTALL