BioC 3.3: CHECK report for INSPEcT on linux2.bioconductor.org

Package: INSPEcT

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.1.0.tar.gz

StartedAt: 2015-10-27 05:02:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:07:39 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 314.1 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_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.0’
* 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 ... [16s/16s] 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘INSPEcT’ for: ‘AIC’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [311s/154s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         47.970 11.017  37.834
makeSimModel       29.028 17.471  21.971
makeSimDataset     25.775 14.159  14.477
newINSPEcT         19.008 11.990   8.589
ratesFirstGuessVar 19.002 11.343   8.786
ratesFirstGuess    18.798 10.698   8.426
sfPlot             18.790 10.590   8.405
rocThresholds      29.283  0.011  29.306
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-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	0.000	0.008
Extract	0.068	0.000	0.068
chisqmodel	0.033	0.000	0.034
chisqtest	0.008	0.000	0.007
combine	0.103	0.000	0.103
geneClass	0.039	0.000	0.040
getModel	0.007	0.000	0.006
inHeatmap	0.030	0.000	0.031
labeledSF	0.007	0.000	0.007
logLik	0.007	0.000	0.007
makeGtfFromDb	3.565	0.044	3.611
makeModelRates	0.766	0.004	0.775
makeRPKMs	0.002	0.000	0.002
makeSimDataset	25.775	14.159	14.477
makeSimModel	29.028	17.471	21.971
modelRates	47.970	11.017	37.834
modelingParams	0.013	0.000	0.013
nCores	0.014	0.038	0.052
nGenes	0.01	0.00	0.01
nTpts	0.010	0.000	0.011
newINSPEcT	19.008	11.990	8.589
plotGene	0.032	0.000	0.032
ratePvals	0.046	0.003	0.050
ratesFirstGuess	18.798	10.698	8.426
ratesFirstGuessVar	19.002	11.343	8.786
removeModel	0.044	0.001	0.046
rocCurve	2.946	0.054	3.002
rocThresholds	29.283	0.011	29.306
sfPlot	18.790	10.590	8.405
split	0.059	0.003	0.063
testingParams	1.181	0.000	1.180
totalSF	0.011	0.000	0.011
tpts	0.011	0.000	0.011
viewModelRates	0.012	0.000	0.012