BioC 3.2: CHECK report for TCC on zin1

Package: TCC

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.10.0.tar.gz

StartedAt: 2016-04-23 06:01:27 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 06:10:43 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 556.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TCC.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TCC.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.10.0’
* 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 ... [16s/17s] 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'TCC,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [82s/83s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 12.922  0.016  12.999
TCC-class          10.823  0.020  10.848
calcNormFactors    10.250  0.004  10.303
calcAUCValue       10.122  0.048  10.239
plot.TCC            8.801  0.011   9.017
plotFCPseudocolor   8.293  0.008   8.379
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [321s/324s]
 [321s/324s] 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: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/TCC.Rcheck/00check.log’
for details.

* 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	0.027	0.004	0.030
TCC-class	10.823	0.020	10.848
TCC	0.009	0.000	0.009
WAD	0.184	0.000	0.184
arab	0.039	0.000	0.039
calcAUCValue	10.122	0.048	10.239
calcNormFactors	10.250	0.004	10.303
clusterSample	0.073	0.004	0.074
estimateDE	1.755	0.008	1.780
filterLowCountGenes	0.022	0.004	0.026
getNormalizedData	0.342	0.000	0.342
getResult	2.333	0.012	2.569
hypoData	4.002	0.000	4.030
hypoData_mg	4.159	0.000	4.168
hypoData_ts	0.002	0.000	0.002
makeFCMatrix	0.005	0.000	0.005
nakai	0.032	0.000	0.032
plot.TCC	8.801	0.011	9.017
plotFCPseudocolor	8.293	0.008	8.379
simulateReadCounts	12.922	0.016	12.999