BioC 3.5: CHECK report for TCC on malbec2

Package: TCC

Version: 1.16.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.16.0.tar.gz

StartedAt: 2017-08-16 02:36:39 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:44:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 473.0 seconds

RetCode: 0

Status:  OK

CheckDir: TCC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.16.0’
* 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
simulateReadCounts 9.132  0.008   9.147
calcAUCValue       8.636  0.012   8.657
TCC-class          8.460  0.040   8.504
plot.TCC           6.984  0.008   6.999
calcNormFactors    6.736  0.008   6.751
plotFCPseudocolor  6.332  0.004   6.342
* 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

* 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)

name	user	system	elapsed
ROKU	0.412	0.000	0.410
TCC-class	8.460	0.040	8.504
TCC	0.008	0.000	0.009
WAD	0.156	0.004	0.161
arab	0.040	0.000	0.041
calcAUCValue	8.636	0.012	8.657
calcNormFactors	6.736	0.008	6.751
clusterSample	0.068	0.004	0.069
estimateDE	1.252	0.000	1.254
filterLowCountGenes	0.048	0.000	0.047
getNormalizedData	0.268	0.000	0.268
getResult	1.504	0.000	1.507
hypoData	3.724	0.000	3.728
hypoData_mg	3.452	0.000	3.456
hypoData_ts	0.004	0.000	0.002
makeFCMatrix	0.000	0.004	0.003
nakai	0.032	0.000	0.034
plot.TCC	6.984	0.008	6.999
plotFCPseudocolor	6.332	0.004	6.342
simulateReadCounts	9.132	0.008	9.147