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BioC 2.14: CHECK report for GOTHiC on moscato2

This page was generated on 2014-10-08 08:56:17 -0700 (Wed, 08 Oct 2014).

Package 360/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOTHiC 1.1.2
Borbala Mifsud
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/GOTHiC
Last Changed Rev: 90696 / Revision: 95116
Last Changed Date: 2014-05-24 01:59:59 -0700 (Sat, 24 May 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: GOTHiC
Version: 1.1.2
Command: rm -rf GOTHiC.buildbin-libdir && mkdir GOTHiC.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOTHiC.buildbin-libdir GOTHiC_1.1.2.tar.gz >GOTHiC-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GOTHiC.buildbin-libdir --install="check:GOTHiC-install.out" --force-multiarch --no-vignettes --timings GOTHiC_1.1.2.tar.gz
StartedAt: 2014-10-08 01:46:38 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:54:05 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 446.6 seconds
RetCode: 0
Status:  OK  
CheckDir: GOTHiC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOTHiC.buildbin-libdir && mkdir GOTHiC.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOTHiC.buildbin-libdir GOTHiC_1.1.2.tar.gz >GOTHiC-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GOTHiC.buildbin-libdir --install="check:GOTHiC-install.out" --force-multiarch --no-vignettes --timings GOTHiC_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GOTHiC.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 'GOTHiC/DESCRIPTION' ... OK
* this is package 'GOTHiC' version '1.1.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'GOTHiC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'IRanges:::orderIntegerPairs'
  See the note in ?`:::` about the use of this operator.
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 ... NOTE
.binInteractions: no visible binding for global variable 'chr1'
.binInteractions: no visible binding for global variable 'chr2'
.binInteractions: no visible binding for global variable 'locus1'
.binInteractions: no visible binding for global variable 'locus2'
.binomialHiC: no visible binding for global variable 'resGR'
.binomialHiC: no visible binding for global variable 'frequencies'
.binomialHiC: no visible binding for global variable 'int1'
.binomialHiC: no visible binding for global variable 'int2'
.binomialHiC: no visible binding for global variable 'pvalue'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'biocLite'
GOTHiC: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
GOTHiC: no visible binding for global variable 'filtered'
GOTHiC: no visible binding for global variable 'interactingLoci'
mapReadsToRestrictionSites: no visible binding for global variable
  'resGR'
* 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' ... [84s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOTHiC 56.89   2.75   64.32
** running examples for arch 'x64' ... [76s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOTHiC 54.88   2.37   57.38
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/GOTHiC.Rcheck/00check.log'
for details.

GOTHiC.Rcheck/00install.out:


install for i386

* installing *source* package 'GOTHiC' ...
** 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 'GOTHiC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOTHiC' as GOTHiC_1.1.2.zip
* DONE (GOTHiC)

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

nameusersystemelapsed
GOTHiC56.89 2.7564.32
filtered0.140.010.15
mapReadsToRestrictionSites2.450.052.50
pairReads4.290.704.99

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

nameusersystemelapsed
GOTHiC54.88 2.3757.38
filtered0.100.000.09
mapReadsToRestrictionSites1.450.041.48
pairReads4.180.544.73