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BioC 3.4: CHECK report for GOTHiC on zin1

This page was generated on 2016-09-21 03:38:42 -0700 (Wed, 21 Sep 2016).

Package 533/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOTHiC 1.9.1
Borbala Mifsud
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOTHiC
Last Changed Rev: 119000 / Revision: 121152
Last Changed Date: 2016-06-28 09:09:39 -0700 (Tue, 28 Jun 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: GOTHiC
Version: 1.9.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOTHiC_1.9.1.tar.gz
StartedAt: 2016-09-20 07:30:34 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:34:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 210.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GOTHiC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOTHiC_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GOTHiC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.9.1’
* 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 ... 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
* 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
':::' call which should be '::': ‘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 : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiC : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiC: no visible binding for global variable ‘V1’
.binomialHiC: no visible binding for global variable ‘int1’
.binomialHiC: no visible binding for global variable ‘int2’
.binomialHiC: no visible binding for global variable ‘frequencies’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘binom.test’
.binomialHiC: no visible global function definition for ‘p.adjust’
.binomialHiC: no visible binding for global variable ‘pvalue’
.binomialHiC: no visible global function definition for ‘x11’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘pdf’
.binomialHiC : <anonymous>: no visible global function definition for
  ‘dev.off’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘frequencies’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int1’
.binomialHiChicup : <anonymous>: no visible binding for global variable
  ‘int2’
.binomialHiChicup: no visible binding for global variable ‘V1’
.binomialHiChicup: no visible binding for global variable ‘int1’
.binomialHiChicup: no visible binding for global variable ‘int2’
.binomialHiChicup: no visible binding for global variable ‘frequencies’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘binom.test’
.binomialHiChicup: no visible global function definition for ‘p.adjust’
.binomialHiChicup: no visible binding for global variable ‘pvalue’
.binomialHiChicup: no visible global function definition for ‘x11’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘pdf’
.binomialHiChicup : <anonymous>: no visible global function definition
  for ‘dev.off’
.findOverlaps.circle: no visible global function definition for
  ‘IntervalTree’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘isCircular’
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for ‘seqlengths’
.getHindIIIsitesFromHicup: no visible global function definition for
  ‘read.table’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘biocLite’
.getRestrictionSitesFromBSgenome: no visible global function definition
  for ‘seqlengths’
.importHicup: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘read.table’
.onlyPairing: no visible global function definition for ‘ScanBamParam’
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’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19 IntervalTree ScanBamParam V1 binom.test
  biocLite chr1 chr2 dev.off filtered frequencies int1 int2
  interactingLoci isCircular locus1 locus2 p.adjust pdf pvalue
  read.table resGR seqlengths x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "x11")
  importFrom("stats", "binom.test", "p.adjust")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOTHiC      39.952  4.452  46.143
GOTHiChicup  5.636  0.220   6.081
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.


GOTHiC.Rcheck/00install.out:

* 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
* DONE (GOTHiC)

GOTHiC.Rcheck/GOTHiC-Ex.timings:

nameusersystemelapsed
GOTHiC39.952 4.45246.143
GOTHiChicup5.6360.2206.081
filtered0.0800.0040.082
mapReadsToRestrictionSites0.6240.0200.645
pairReads2.2640.0322.294