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BioC 3.6: CHECK report for TCC on malbec1

This page was generated on 2017-08-16 13:21:15 -0400 (Wed, 16 Aug 2017).

Package 1332/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.17.0
Jianqiang Sun
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TCC
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.17.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.17.0.tar.gz
StartedAt: 2017-08-16 02:44:24 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:52:05 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 461.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TCC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TCC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.17.0’
* 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 ‘TCC’ 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
TCC-class          8.856  0.044   8.905
simulateReadCounts 8.396  0.016   8.417
calcAUCValue       7.280  0.012   7.300
calcNormFactors    6.352  0.004   6.362
plot.TCC           5.572  0.012   5.590
plotFCPseudocolor  5.420  0.008   5.431
* 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: OK

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
ROKU0.0560.0000.056
TCC-class8.8560.0448.905
TCC0.0080.0000.008
WAD0.1360.0000.133
arab0.0360.0000.038
calcAUCValue7.2800.0127.300
calcNormFactors6.3520.0046.362
clusterSample0.0680.0000.067
estimateDE1.1320.0041.139
filterLowCountGenes0.0400.0040.043
getNormalizedData0.2520.0000.250
getResult1.5480.0001.549
hypoData2.5520.0002.555
hypoData_mg2.7640.0082.777
hypoData_ts0.0000.0000.001
makeFCMatrix0.0040.0000.003
nakai0.0360.0000.036
plot.TCC5.5720.0125.590
plotFCPseudocolor5.4200.0085.431
simulateReadCounts8.3960.0168.417