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BioC 3.0: CHECK report for TCC on perceval

This page was generated on 2015-04-10 09:58:37 -0700 (Fri, 10 Apr 2015).

Package 882/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.6.5
Jianqiang Sun , Tomoaki Nishiyama
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/TCC
Last Changed Rev: 97975 / Revision: 102249
Last Changed Date: 2015-01-03 18:50:59 -0800 (Sat, 03 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: TCC
Version: 1.6.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TCC_1.6.5.tar.gz
StartedAt: 2015-04-10 06:56:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 07:10:20 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 805.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TCC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TCC_1.6.5.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/TCC.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.6.5’
* 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 ‘TCC’ can be installed ... [31s/32s] 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 ... 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 ... [126s/127s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 20.916  0.125  21.049
TCC-class          16.388  0.301  16.691
calcAUCValue       15.187  0.065  15.268
calcNormFactors    13.485  0.068  13.556
plotFCPseudocolor  13.000  0.064  13.102
plot.TCC           12.620  0.182  13.041
hypoData_mg         6.918  0.045   7.008
hypoData            6.193  0.030   6.227
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [402s/403s]
 [403s/403s] 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

TCC.Rcheck/00install.out:

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

TCC.Rcheck/TCC-Ex.timings:

nameusersystemelapsed
ROKU0.0170.0010.019
TCC-class16.388 0.30116.691
TCC0.0120.0010.013
WAD0.3460.0100.356
arab0.0450.0060.052
calcAUCValue15.187 0.06515.268
calcNormFactors13.485 0.06813.556
clusterSample0.1120.0070.324
estimateDE1.8120.0071.821
filterLowCountGenes0.0300.0020.032
getNormalizedData0.4060.0020.408
getResult2.8810.0142.897
hypoData6.1930.0306.227
hypoData_mg6.9180.0457.008
hypoData_ts0.0020.0010.003
nakai0.0440.0040.047
plot.TCC12.620 0.18213.041
plotFCPseudocolor13.000 0.06413.102
simulateReadCounts20.916 0.12521.049