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BioC 3.5: CHECK report for consensusSeekeR on oaxaca

This page was generated on 2017-03-04 16:51:00 -0500 (Sat, 04 Mar 2017).

Package 259/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
consensusSeekeR 1.3.0
Astrid Louise Deschenes
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/consensusSeekeR
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: consensusSeekeR
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.3.0.tar.gz
StartedAt: 2017-03-04 01:08:49 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:12:25 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 215.9 seconds
RetCode: 0
Status:  OK 
CheckDir: consensusSeekeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings consensusSeekeR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/consensusSeekeR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘consensusSeekeR/DESCRIPTION’ ... OK
* this is package ‘consensusSeekeR’ version ‘1.3.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘consensusSeekeR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
findConsensusPeakRegionsValidation: no visible global function
  definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/consensusSeekeR.Rcheck/00check.log’
for details.


consensusSeekeR.Rcheck/00install.out:

* installing *source* package ‘consensusSeekeR’ ...
** 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 (consensusSeekeR)

consensusSeekeR.Rcheck/consensusSeekeR-Ex.timings:

nameusersystemelapsed
A549_CTCF_MYJ_NarrowPeaks_partial1.5770.0451.622
A549_CTCF_MYJ_Peaks_partial0.7400.0230.763
A549_CTCF_MYN_NarrowPeaks_partial0.3560.0180.375
A549_CTCF_MYN_Peaks_partial0.5340.0230.557
A549_FOSL2_01_NarrowPeaks_partial0.3750.0210.396
A549_FOSL2_01_Peaks_partial0.3800.0160.396
A549_FOXA1_01_NarrowPeaks_partial0.4480.0200.468
A549_FOXA1_01_Peaks_partial0.7050.0200.727
A549_NR3C1_CFQ_NarrowPeaks_partial0.3790.0220.401
A549_NR3C1_CFQ_Peaks_partial0.4300.0250.456
A549_NR3C1_CFR_NarrowPeaks_partial0.3160.0150.332
A549_NR3C1_CFR_Peaks_partial0.3750.0200.395
A549_NR3C1_CFS_NarrowPeaks_partial1.0030.0191.020
A549_NR3C1_CFS_Peaks_partial0.9370.0230.960
NOrMAL_nucleosome_positions0.6140.0250.640
NOrMAL_nucleosome_ranges0.8910.0240.915
NucPosSimulator_nucleosome_positions0.5920.0440.636
NucPosSimulator_nucleosome_ranges0.6820.0220.706
PING_nucleosome_positions0.3630.0170.381
PING_nucleosome_ranges0.3400.0170.357
findConsensusPeakRegions0.7090.0150.723
findConsensusPeakRegionsValidation0.0340.0090.043
readNarrowPeakFile0.1400.0010.141