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BioC 3.1: CHECK report for GOTHiC on morelia

This page was generated on 2015-10-09 09:41:24 -0700 (Fri, 09 Oct 2015).

Package 428/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOTHiC 1.4.2
Borbala Mifsud
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GOTHiC
Last Changed Rev: 105075 / Revision: 109384
Last Changed Date: 2015-06-17 06:42:53 -0700 (Wed, 17 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GOTHiC
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOTHiC_1.4.2.tar.gz
StartedAt: 2015-10-09 02:37:35 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:41:43 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 248.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GOTHiC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOTHiC_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GOTHiC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.4.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GOTHiC’ can be installed ... [18s/18s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘IRanges::shift’ when loading ‘GOTHiC’
See ‘/Users/biocbuild/bbs-3.1-bioc/meat/GOTHiC.Rcheck/00install.out’ for details.
* 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
* 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' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
* 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 global function definition for ‘mclapply’
.binomialHiC: no visible binding for global variable ‘pvalue’
.findOverlaps.parallel: no visible global function definition for
  ‘mclapply’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘isCircular’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘seqlengths’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘biocLite’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘seqlengths’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/63s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GOTHiC    37.942  3.862  46.101
pairReads  5.636  0.167   5.805
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.


GOTHiC.Rcheck/00install.out:

* installing *source* package ‘GOTHiC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘IRanges::shift’ when loading ‘GOTHiC’
** 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’
Warning: replacing previous import by ‘IRanges::shift’ when loading ‘GOTHiC’
* DONE (GOTHiC)

GOTHiC.Rcheck/GOTHiC-Ex.timings:

nameusersystemelapsed
GOTHiC37.942 3.86246.101
filtered0.0680.0050.074
mapReadsToRestrictionSites1.2000.1371.338
pairReads5.6360.1675.805