BioC 3.5: CHECK report for INSPEcT on oaxaca

Package: INSPEcT

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.5.0.tar.gz

StartedAt: 2017-03-04 04:34:25 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:41:46 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 440.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: INSPEcT.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.5.0’
* 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 ‘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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'INSPEcT,ANY,ANY,ANY'
  generic '[' and siglist 'INSPEcT_model,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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
makeSimModel       42.195  8.477  25.593
modelRates         43.965  0.228  44.208
rocThresholds      27.228  0.079  27.353
makeSimDataset     19.169  0.555  25.951
sfPlot             14.989  0.085  15.085
ratesFirstGuessVar 13.665  0.071  13.742
ratesFirstGuess    13.466  0.077  13.546
newINSPEcT         12.908  0.054  12.967
compareSteady      10.294  0.089  10.427
makeRPKMs           7.056  0.432  18.134
* 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
  ‘/Users/biocbuild/bbs-3.5-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	0.008	0.002	0.010
Extract	0.117	0.003	0.119
INSPEcT_diffsteady-class	2.222	0.064	2.288
chisqmodel	0.134	0.019	0.152
chisqtest	0.012	0.012	0.025
combine	0.455	0.065	0.521
compareSteady	10.294	0.089	10.427
geneClass	0.139	0.008	0.149
getModel	0.010	0.011	0.022
inHeatmap	0.177	0.013	0.190
labeledSF	0.010	0.012	0.022
logLik	0.011	0.012	0.023
makeModelRates	0.837	0.026	0.863
makeRPKMs	7.056	0.432	18.134
makeSimDataset	19.169	0.555	25.951
makeSimModel	42.195	8.477	25.593
modelRates	43.965	0.228	44.208
modelingParams	0.020	0.006	0.026
nGenes	0.010	0.004	0.014
nTpts	0.009	0.003	0.014
newINSPEcT	12.908	0.054	12.967
plotGene	0.027	0.003	0.029
plotMA	1.047	0.046	1.093
ratePvals	0.065	0.010	0.076
ratesFirstGuess	13.466	0.077	13.546
ratesFirstGuessVar	13.665	0.071	13.742
removeModel	0.092	0.002	0.093
rocCurve	2.033	0.039	2.071
rocThresholds	27.228	0.079	27.353
sfPlot	14.989	0.085	15.085
split	0.079	0.007	0.087
testingParams	1.340	0.008	1.348
totalSF	0.010	0.008	0.018
tpts	0.010	0.007	0.017
viewModelRates	0.010	0.008	0.018