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BioC experimental data: CHECK report for harbChIP on moscato1

This page was generated on 2016-04-20 20:26:21 -0700 (Wed, 20 Apr 2016).

Package 117/257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
harbChIP 1.8.0
VJ Carey
Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/harbChIP
Last Changed Rev: 3460 / Revision: 3730
Last Changed Date: 2015-10-13 13:14:23 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 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 

Summary

Package: harbChIP
Version: 1.8.0
Command: rm -rf harbChIP.buildbin-libdir harbChIP.Rcheck && mkdir harbChIP.buildbin-libdir harbChIP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=harbChIP.buildbin-libdir harbChIP_1.8.0.tar.gz >harbChIP.Rcheck\00install.out 2>&1 && cp harbChIP.Rcheck\00install.out harbChIP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=harbChIP.buildbin-libdir --install="check:harbChIP-install.out" --force-multiarch --no-vignettes --timings harbChIP_1.8.0.tar.gz
StartedAt: 2016-04-20 14:12:29 -0700 (Wed, 20 Apr 2016)
EndedAt: 2016-04-20 14:16:54 -0700 (Wed, 20 Apr 2016)
EllapsedTime: 265.0 seconds
RetCode: 0
Status:  OK  
CheckDir: harbChIP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf harbChIP.buildbin-libdir harbChIP.Rcheck && mkdir harbChIP.buildbin-libdir harbChIP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=harbChIP.buildbin-libdir harbChIP_1.8.0.tar.gz >harbChIP.Rcheck\00install.out 2>&1 && cp harbChIP.Rcheck\00install.out harbChIP-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=harbChIP.buildbin-libdir --install="check:harbChIP-install.out" --force-multiarch --no-vignettes --timings harbChIP_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-data-experiment/meat/harbChIP.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'harbChIP/DESCRIPTION' ... OK
* this is package 'harbChIP' 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 'harbChIP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
  'Biobase' 'Biostrings' 'IRanges' 'tools'
  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
chkAllUS: no visible binding for global variable 'sceUpstr'
chkAllUS : <anonymous>: no visible global function definition for
  'countPattern'
chkMotif4TF: no visible global function definition for 'sampleNames'
chkMotif4TF: no visible global function definition for 'exprs'
Nmers,numeric-character-upstreamSeqs: no visible global function
  definition for 'Views'
* 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' ... [38s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
allhex 0.59      0   24.26
** running examples for arch 'x64' ... [7s] OK
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-data-experiment/meat/harbChIP.Rcheck/00check.log'
for details.


harbChIP.Rcheck/00install.out:


install for i386

* installing *source* package 'harbChIP' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'harbChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'harbChIP' as harbChIP_1.8.0.zip
* DONE (harbChIP)

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

nameusersystemelapsed
allhex 0.59 0.0024.26
buildUpstreamSeqs2000
chkMotif4TF000
harbChIP1.280.031.85
sceUpstream0.310.000.31
upstreamSeqs-class0.310.000.31

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

nameusersystemelapsed
allhex0.610.020.76
buildUpstreamSeqs2000
chkMotif4TF000
harbChIP1.420.011.43
sceUpstream0.270.000.27
upstreamSeqs-class0.300.000.29