BioC 3.1: CHECK report for REDseq on moscato2

Package: REDseq

Version: 1.14.1

Command: rm -rf REDseq.buildbin-libdir REDseq.Rcheck && mkdir REDseq.buildbin-libdir REDseq.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.14.1.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.14.1.tar.gz

StartedAt: 2015-10-09 05:26:40 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:32:32 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 352.0 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.14.1.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.14.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/REDseq.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.14.1'
* 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' ... [30s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
buildREmap    8.86   0.14   10.02
searchPattern 5.85   0.07    5.92
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
buildREmap    10.88   0.13   11.00
searchPattern  5.29   0.11    5.46
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/REDseq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'REDseq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: %in%, paste
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: %in%, paste

install for x64

* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "IRanges" for requests: %in%, paste
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.14.1.zip
* DONE (REDseq)

name	user	system	elapsed
REDseq-package	0	0	0
assignSeq2REsite	0.61	0.02	0.63
binom.test.REDseq	0.01	0.00	0.01
buildREmap	8.86	0.14	10.02
compareREDseq	0.02	0.00	0.01
distanceHistSeq2RE	0.02	0.00	0.02
example.REDseq	0	0	0
example.assignedREDseq	0.00	0.02	0.01
example.map	0	0	0
plotCutDistribution	0.03	0.00	0.04
searchPattern	5.85	0.07	5.92
summarizeByRE	0	0	0
summarizeBySeq	0.01	0.00	0.02
writeHits	0.00	0.00	2.18

name	user	system	elapsed
REDseq-package	0	0	0
assignSeq2REsite	0.70	0.01	0.72
binom.test.REDseq	0.01	0.00	0.01
buildREmap	10.88	0.13	11.00
compareREDseq	0.01	0.00	0.02
distanceHistSeq2RE	0.02	0.01	0.03
example.REDseq	0	0	0
example.assignedREDseq	0	0	0
example.map	0	0	0
plotCutDistribution	0.05	0.00	0.05
searchPattern	5.29	0.11	5.46
summarizeByRE	0.00	0.02	0.01
summarizeBySeq	0	0	0
writeHits	0.00	0.00	0.06