BioC 3.3: CHECK report for INSPEcT on zin2

Package: INSPEcT

Version: 1.2.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.2.2.tar.gz

StartedAt: 2016-10-13 03:25:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:30:43 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 327.7 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.2’
* 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 ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         40.159  0.172  40.301
rocThresholds      24.502  0.008  24.491
makeSimModel       17.628  0.576  21.889
makeSimDataset     17.339  0.212  21.068
newINSPEcT         12.774  0.056  12.819
ratesFirstGuessVar 12.631  0.060  12.682
ratesFirstGuess    12.565  0.064  12.623
sfPlot             12.533  0.040  12.563
compareSteady       8.227  0.216   8.442
makeRPKMs           4.553  0.097   5.707
* 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 ‘INSPEcT’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘split’ from package ‘base’ in package ‘INSPEcT’
Creating a generic function for ‘AIC’ from package ‘stats’ in package ‘INSPEcT’
** 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	0.01	0.00	0.01
Extract	0.076	0.000	0.076
INSPEcT_diffsteady-class	1.740	0.304	2.043
chisqmodel	0.027	0.004	0.030
chisqtest	0.008	0.000	0.008
combine	0.123	0.004	0.135
compareSteady	8.227	0.216	8.442
geneClass	0.039	0.004	0.042
getModel	0.007	0.000	0.008
inHeatmap	0.039	0.000	0.038
labeledSF	0.007	0.000	0.008
logLik	0.009	0.000	0.008
makeModelRates	0.589	0.000	0.589
makeRPKMs	4.553	0.097	5.707
makeSimDataset	17.339	0.212	21.068
makeSimModel	17.628	0.576	21.889
modelRates	40.159	0.172	40.301
modelingParams	0.015	0.000	0.015
nGenes	0.007	0.000	0.007
nTpts	0.006	0.000	0.007
newINSPEcT	12.774	0.056	12.819
plotGene	0.03	0.00	0.03
plotMA	0.942	0.008	0.950
ratePvals	0.049	0.000	0.049
ratesFirstGuess	12.565	0.064	12.623
ratesFirstGuessVar	12.631	0.060	12.682
removeModel	0.043	0.000	0.044
rocCurve	2.403	0.008	2.409
rocThresholds	24.502	0.008	24.491
sfPlot	12.533	0.040	12.563
split	0.065	0.000	0.065
testingParams	1.172	0.000	1.172
totalSF	0.003	0.004	0.007
tpts	0.008	0.000	0.007
viewModelRates	0.008	0.000	0.008