BioC 3.2: CHECK report for INSPEcT on zin1

Package: INSPEcT

Version: 0.99.8

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_0.99.8.tar.gz

StartedAt: 2015-08-24 00:56:10 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:01:25 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 315.5 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_0.99.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘INSPEcT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INSPEcT’ version ‘0.99.8’
* 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 ‘INSPEcT’ can be installed ... [14s/14s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
* 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 loading without being on the library search path ... 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 ... [258s/150s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         45.299  7.921  38.760
makeSimModel       23.920 12.153  19.342
makeSimDataset     22.187  8.943  15.594
rocThresholds      26.202  0.167  26.436
sfPlot             16.222  9.268   9.534
ratesFirstGuessVar 16.085  8.084   8.719
ratesFirstGuess    15.620  8.228   8.639
newINSPEcT         15.868  7.965   8.827
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.

* installing *source* package ‘INSPEcT’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (INSPEcT)

name	user	system	elapsed
AIC-INSPEcT-method	0.012	0.000	0.011
Extract	0.097	0.000	0.097
chisqmodel	0.043	0.000	0.043
chisqtest	0.009	0.000	0.009
combine	0.139	0.004	0.143
geneClass	0.054	0.000	0.054
getModel	0.008	0.000	0.008
inHeatmap	0.036	0.004	0.040
labeledSF	0.008	0.000	0.008
logLik	0.01	0.00	0.01
makeGtfFromDb	0.944	0.036	0.981
makeModelRates	0.906	0.020	0.928
makeRPKMs	0.002	0.000	0.002
makeSimDataset	22.187	8.943	15.594
makeSimModel	23.920	12.153	19.342
modelRates	45.299	7.921	38.760
modelingParams	0.014	0.000	0.015
nCores	0.015	0.037	0.051
nGenes	0.008	0.000	0.008
nTpts	0.008	0.000	0.007
newINSPEcT	15.868	7.965	8.827
plotGene	0.042	0.000	0.042
ratePvals	0.050	0.015	0.065
ratesFirstGuess	15.620	8.228	8.639
ratesFirstGuessVar	16.085	8.084	8.719
removeModel	0.058	0.004	0.062
rocCurve	2.306	0.052	2.367
rocThresholds	26.202	0.167	26.436
sfPlot	16.222	9.268	9.534
split	0.091	0.000	0.091
testingParams	1.226	0.017	1.241
totalSF	0.007	0.000	0.007
tpts	0.003	0.004	0.007
viewModelRates	0.008	0.000	0.008