BioC 3.3: CHECK report for INSPEcT on morelia

Package: INSPEcT

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings INSPEcT_1.1.0.tar.gz

StartedAt: 2015-10-22 07:23:51 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:28:33 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 281.9 seconds

RetCode: 0

Status:  OK

CheckDir: INSPEcT.Rcheck

Warnings: 0

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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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/INSPEcT.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [12s/12s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [322s/143s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
modelRates         51.885  9.308  35.549
makeSimModel       30.913 12.452  14.371
makeSimDataset     29.808 11.685  12.995
ratesFirstGuessVar 24.705 12.811   7.580
newINSPEcT         23.897 10.302   6.950
ratesFirstGuess    23.449  9.323   7.238
sfPlot             22.933  9.832   6.191
rocThresholds      24.327  0.079  24.426
makeGtfFromDb       2.901  0.315  16.119
* 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
  ‘/Users/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	0.004	0.012
Extract	0.116	0.007	0.123
chisqmodel	0.025	0.005	0.030
chisqtest	0.007	0.004	0.011
combine	0.112	0.004	0.116
geneClass	0.041	0.004	0.046
getModel	0.007	0.004	0.010
inHeatmap	0.032	0.005	0.063
labeledSF	0.006	0.003	0.010
logLik	0.006	0.004	0.010
makeGtfFromDb	2.901	0.315	16.119
makeModelRates	0.509	0.021	0.577
makeRPKMs	0.003	0.000	0.003
makeSimDataset	29.808	11.685	12.995
makeSimModel	30.913	12.452	14.371
modelRates	51.885	9.308	35.549
modelingParams	0.012	0.017	0.030
nCores	0.019	0.022	0.041
nGenes	0.010	0.012	0.022
nTpts	0.010	0.013	0.024
newINSPEcT	23.897	10.302	6.950
plotGene	0.050	0.017	0.067
ratePvals	0.067	0.022	0.088
ratesFirstGuess	23.449	9.323	7.238
ratesFirstGuessVar	24.705	12.811	7.580
removeModel	0.051	0.008	0.058
rocCurve	2.584	0.137	2.723
rocThresholds	24.327	0.079	24.426
sfPlot	22.933	9.832	6.191
split	0.082	0.017	0.100
testingParams	0.975	0.037	1.012
totalSF	0.006	0.008	0.014
tpts	0.006	0.008	0.014
viewModelRates	0.006	0.008	0.014