Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M [N] O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for nucleR on moscato2

This page was generated on 2014-10-08 08:54:07 -0700 (Wed, 08 Oct 2014).

Package 541/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 1.12.0
Oscar Flores
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/nucleR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: nucleR
Version: 1.12.0
Command: rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_1.12.0.tar.gz >nucleR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_1.12.0.tar.gz
StartedAt: 2014-10-08 03:27:11 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:31:53 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 282.9 seconds
RetCode: 0
Status:  OK  
CheckDir: nucleR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nucleR.buildbin-libdir nucleR_1.12.0.tar.gz >nucleR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=nucleR.buildbin-libdir --install="check:nucleR-install.out" --force-multiarch --no-vignettes --timings nucleR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/nucleR.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'htSeqTools'
* 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 'nucleR' 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:
  'methods' 'BiocGenerics' 'IRanges' 'Biobase' 'ShortRead'
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
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'ShortRead' 'parallel'
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... NOTE
Package unavailable to check Rd xrefs: 'Starr'
* 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' ... [14s] OK
** running examples for arch 'x64' ... [16s] 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

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/nucleR.Rcheck/00check.log'
for details.

nucleR.Rcheck/00install.out:


install for i386

* installing *source* package 'nucleR' ...
** 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 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_1.12.0.zip
* DONE (nucleR)

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

nameusersystemelapsed
controlCorrection0.030.000.03
coverage.rpm0.110.000.11
export.bed000
export.wig000
filterFFT0.20.00.2
fragmentLenDetect1.610.001.61
mergeCalls0.50.00.5
nucleR-package0.560.000.56
pcKeepCompDetect0.260.000.27
peakDetection0.600.010.60
peakScoring0.200.000.21
plotPeaks0.620.000.62
processReads0.170.000.17
processTilingArray000
syntheticNucMap0.380.000.38

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

nameusersystemelapsed
controlCorrection0.030.000.03
coverage.rpm0.130.000.13
export.bed000
export.wig000
filterFFT0.260.000.26
fragmentLenDetect1.780.001.78
mergeCalls0.770.000.77
nucleR-package0.540.000.54
pcKeepCompDetect0.250.020.27
peakDetection0.670.000.67
peakScoring0.20.00.2
plotPeaks0.550.000.55
processReads0.190.000.18
processTilingArray000
syntheticNucMap0.480.000.49