Multiple platform build/check report for BioC 3.8 - CHECK report for INSPEcT on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:INSPEcT.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings INSPEcT_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/INSPEcT.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.2’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
modelRates                      175.564  0.436 176.266
makeSimDataset                   72.224  2.652  69.693
rocThresholds                    50.404  0.032  50.652
INSPEcT_diffsteady-class         38.000 11.184  26.793
plotMA                           37.032 11.692  26.277
makeSimModel                     46.860  0.168  47.118
compareSteady                    35.204 10.124  23.429
rocCurve                         42.012  0.004  42.073
quantifyExpressionsFromBAMs      37.880  0.180  39.001
newINSPEcT                       21.088  3.844  13.111
processingDelay                  17.012  3.024  16.560
quantifyExpressionsFromTrCounts  16.316  0.008  16.347
compareSteadyNoNascent            7.576  0.140   7.552
* 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

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL INSPEcT
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘INSPEcT’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (INSPEcT)

Tests output

Example timings

name	user	system	elapsed
AIC-INSPEcT-method	0.304	0.000	0.314
Extract	0.512	0.004	0.522
INSPEcT-shinyApps	0	0	0
INSPEcT_diffsteady-class	38.000	11.184	26.793
chisqmodel	0.324	0.004	0.325
chisqtest	0.268	0.004	0.272
combine	0.696	0.044	0.740
compareSteady	35.204	10.124	23.429
compareSteadyNoNascent	7.576	0.140	7.552
geneClass	0.188	0.008	0.197
getModel	0.196	0.000	0.196
inHeatmap	0.184	0.004	0.187
labeledSF	0.192	0.000	0.191
logLik	0.276	0.000	0.277
makeModelRates	1.204	0.004	1.273
makeSimDataset	72.224	2.652	69.693
makeSimModel	46.860	0.168	47.118
modelRates	175.564	0.436	176.266
modelSelection	0.74	0.00	0.74
modelingParams	0.38	0.00	0.38
nGenes	0.144	0.004	0.148
nTpts	0.148	0.004	0.151
newINSPEcT	21.088	3.844	13.111
plotGene	0.34	0.00	0.34
plotMA	37.032	11.692	26.277
processingDelay	17.012	3.024	16.560
quantifyExpressionsFromBAMs	37.880	0.180	39.001
quantifyExpressionsFromTrCounts	16.316	0.008	16.347
ratePvals	0.196	0.000	0.195
ratesFirstGuess	0.152	0.000	0.153
ratesFirstGuessVar	0.156	0.000	0.153
removeModel	0.344	0.000	0.343
rocCurve	42.012	0.004	42.073
rocThresholds	50.404	0.032	50.652
split	0.368	0.000	0.386
tpts	0.296	0.000	0.297
viewModelRates	0.256	0.000	0.293

CHECK report for INSPEcT on malbec1

Summary

Command output

Installation output

Tests output

Example timings