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BioC 3.4: CHECK report for TCC on tokay1

This page was generated on 2017-04-15 16:18:09 -0400 (Sat, 15 Apr 2017).

Package 1228/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCC 1.14.0
Jianqiang Sun
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TCC
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCC
Version: 1.14.0
Command: rm -rf TCC.buildbin-libdir TCC.Rcheck && mkdir TCC.buildbin-libdir TCC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCC.buildbin-libdir TCC_1.14.0.tar.gz >TCC.Rcheck\00install.out 2>&1 && cp TCC.Rcheck\00install.out TCC-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TCC.buildbin-libdir --install="check:TCC-install.out" --force-multiarch --no-vignettes --timings TCC_1.14.0.tar.gz
StartedAt: 2017-04-15 01:08:45 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:24:46 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 960.9 seconds
RetCode: 0
Status:  OK  
CheckDir: TCC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TCC.buildbin-libdir TCC.Rcheck && mkdir TCC.buildbin-libdir TCC.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCC.buildbin-libdir TCC_1.14.0.tar.gz >TCC.Rcheck\00install.out 2>&1 && cp TCC.Rcheck\00install.out TCC-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TCC.buildbin-libdir --install="check:TCC-install.out" --force-multiarch --no-vignettes --timings TCC_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/TCC.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCC' version '1.14.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
TCC-class          10.26   0.11   10.38
calcNormFactors     7.77   0.00    7.76
simulateReadCounts  7.49   0.02    7.50
plot.TCC            6.71   0.00    6.71
calcAUCValue        6.53   0.02    6.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
TCC-class          10.12   0.03   10.16
simulateReadCounts  9.49   0.02    9.50
calcAUCValue        9.37   0.07    9.44
calcNormFactors     8.71   0.01    8.72
plot.TCC            7.37   0.08    7.45
plotFCPseudocolor   5.72   0.00    5.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'TCC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCC' as TCC_1.14.0.zip
* DONE (TCC)

TCC.Rcheck/examples_i386/TCC-Ex.timings:

nameusersystemelapsed
ROKU0.020.000.01
TCC-class10.26 0.1110.38
TCC0.020.000.01
WAD0.160.000.16
arab0.060.000.06
calcAUCValue6.530.026.55
calcNormFactors7.770.007.76
clusterSample0.060.010.08
estimateDE1.590.021.61
filterLowCountGenes0.030.000.03
getNormalizedData0.380.000.38
getResult2.210.002.21
hypoData2.20.02.2
hypoData_mg2.520.022.53
hypoData_ts0.000.010.02
makeFCMatrix000
nakai0.040.000.04
plot.TCC6.710.006.71
plotFCPseudocolor4.750.004.75
simulateReadCounts7.490.027.50

TCC.Rcheck/examples_x64/TCC-Ex.timings:

nameusersystemelapsed
ROKU0.020.000.01
TCC-class10.12 0.0310.16
TCC000
WAD0.310.010.32
arab0.050.000.05
calcAUCValue9.370.079.44
calcNormFactors8.710.018.72
clusterSample0.060.000.06
estimateDE1.690.031.72
filterLowCountGenes0.030.000.03
getNormalizedData0.310.000.32
getResult1.950.011.97
hypoData2.940.002.93
hypoData_mg2.890.002.89
hypoData_ts000
makeFCMatrix0.020.000.02
nakai0.030.000.03
plot.TCC7.370.087.45
plotFCPseudocolor5.720.005.72
simulateReadCounts9.490.029.50