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BioC 3.2: CHECK report for DChIPRep on perceval

This page was generated on 2015-11-10 14:50:13 -0800 (Tue, 10 Nov 2015).

Package 253/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DChIPRep 1.0.3
Bernd Klaus
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DChIPRep
Last Changed Rev: 110308 / Revision: 110496
Last Changed Date: 2015-11-04 01:38:37 -0800 (Wed, 04 Nov 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK YES, new version is higher than in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DChIPRep
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.0.3.tar.gz
StartedAt: 2015-11-10 04:01:51 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 04:05:47 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 236.7 seconds
RetCode: 0
Status:  OK 
CheckDir: DChIPRep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DChIPRep.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DChIPRep/DESCRIPTION’ ... OK
* this is package ‘DChIPRep’ version ‘1.0.3’
* 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 ‘DChIPRep’ can be installed ... [16s/16s] 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 loading without being on the library search path ... 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 ... OK
* 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotProfiles     6.633  0.068   6.702
importData       6.078  0.018   6.096
plotSignificance 5.216  0.030   5.246
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [30s/30s]
 [30s/30s] 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: OK

DChIPRep.Rcheck/00install.out:

* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DChIPRep)

DChIPRep.Rcheck/DChIPRep-Ex.timings:

nameusersystemelapsed
DChIPRepResults0.0610.0030.065
DESeq2Data0.0470.0000.048
FDRresults3.1230.0453.177
getMATfromDataFrame2.3920.0182.410
importData6.0780.0186.096
importDataFromMatrices0.1050.0010.106
plotProfiles6.6330.0686.702
plotSignificance5.2160.0305.246
resultsDChIPRep2.3920.0012.394
runTesting2.7690.0242.792
show2.3860.0112.397
summarizeCountsPerPosition2.4870.0072.494