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BioC 3.4: CHECK report for REDseq on moscato1

This page was generated on 2016-09-21 03:43:28 -0700 (Wed, 21 Sep 2016).

Package 1001/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.19.0
Lihua Julie Zhu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/REDseq
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REDseq
Version: 1.19.0
Command: rm -rf REDseq.buildbin-libdir REDseq.Rcheck && mkdir REDseq.buildbin-libdir REDseq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.19.0.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.19.0.tar.gz
StartedAt: 2016-09-20 15:04:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:10:49 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 359.9 seconds
RetCode: 0
Status:  OK  
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf REDseq.buildbin-libdir REDseq.Rcheck && mkdir REDseq.buildbin-libdir REDseq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=REDseq.buildbin-libdir REDseq_1.19.0.tar.gz >REDseq.Rcheck\00install.out 2>&1 && cp REDseq.Rcheck\00install.out REDseq-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=REDseq.buildbin-libdir --install="check:REDseq-install.out" --force-multiarch --no-vignettes --timings REDseq_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/REDseq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.19.0'
* 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    7.80   0.09   10.61
searchPattern 5.27   0.08    5.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
buildREmap    8.10   0.15    8.35
searchPattern 5.05   0.05    5.38
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/REDseq.Rcheck/00check.log'
for details.


REDseq.Rcheck/00install.out:


install for i386

* installing *source* package 'REDseq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%

install for x64

* installing *source* package 'REDseq' ...
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%
* MD5 sums
packaged installation of 'REDseq' as REDseq_1.19.0.zip
* DONE (REDseq)

REDseq.Rcheck/examples_i386/REDseq-Ex.timings:

nameusersystemelapsed
REDseq-package0.010.000.02
assignSeq2REsite0.880.000.87
binom.test.REDseq000
buildREmap 7.80 0.0910.61
compareREDseq0.020.000.01
distanceHistSeq2RE0.020.000.01
example.REDseq000
example.assignedREDseq0.000.020.02
example.map000
plotCutDistribution0.030.010.04
searchPattern5.270.085.36
summarizeByRE0.020.000.01
summarizeBySeq000
writeHits0.030.000.03

REDseq.Rcheck/examples_x64/REDseq-Ex.timings:

nameusersystemelapsed
REDseq-package000
assignSeq2REsite1.100.001.11
binom.test.REDseq0.020.000.01
buildREmap8.100.158.35
compareREDseq0.010.000.01
distanceHistSeq2RE0.020.000.02
example.REDseq000
example.assignedREDseq000
example.map000
plotCutDistribution0.030.000.03
searchPattern5.050.055.38
summarizeByRE0.020.000.02
summarizeBySeq000
writeHits0.010.000.03