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BioC 3.2: CHECK report for TarSeqQC on perceval

This page was generated on 2015-10-27 17:37:36 -0400 (Tue, 27 Oct 2015).

Package 1044/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.0.0
Gabriela Merino
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TarSeqQC
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists 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: TarSeqQC
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.0.0.tar.gz
StartedAt: 2015-10-27 12:49:10 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 12:53:34 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 264.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TarSeqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TarSeqQC.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 ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.0.0’
* 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 ‘TarSeqQC’ can be installed ... [14s/14s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [453s/60s] OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
TargetExperiment-initialize        50.534 24.244  14.489
TargetExperiment-setters           37.342 19.797  14.553
TargetExperiment-buildFeaturePanel 25.067  8.669  11.667
pileupCounts                       20.439  6.582   9.326
TargetExperiment-buildReport        4.360  2.659   0.783
TargetExperiment-summarizePanel     4.010  2.899   2.030
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [270s/56s]
 [270s/56s] 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

TarSeqQC.Rcheck/00install.out:

* installing *source* package ‘TarSeqQC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘TarSeqQC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TarSeqQC)

TarSeqQC.Rcheck/TarSeqQC-Ex.timings:

nameusersystemelapsed
TargetExperiment-buildFeaturePanel25.067 8.66911.667
TargetExperiment-buildReport4.3602.6590.783
TargetExperiment-constructor0.0030.0000.004
TargetExperiment-getters0.1910.0050.196
TargetExperiment-initialize50.53424.24414.489
TargetExperiment-plot0.0020.0000.002
TargetExperiment-plotAttrExpl0.0020.0000.001
TargetExperiment-plotFeatPerform0.0020.0000.002
TargetExperiment-plotFeature0.0020.0010.003
TargetExperiment-plotGeneAttrPerFeat0.0020.0000.002
TargetExperiment-plotNtdPercentage0.0030.0000.004
TargetExperiment-plotRegion0.0040.0010.005
TargetExperiment-print0.0590.0140.073
TargetExperiment-setters37.34219.79714.553
TargetExperiment-show0.0640.0160.079
TargetExperiment-statistics0.0390.0090.047
TargetExperiment-summarizePanel4.0102.8992.030
pileupCounts20.439 6.582 9.326