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BioC 3.4: CHECK report for INSPEcT on malbec1

This page was generated on 2017-04-15 16:13:06 -0400 (Sat, 15 Apr 2017).

Package 634/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.4.0
Stefano de Pretis
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/INSPEcT
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: INSPEcT
Version: 1.4.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.4.0.tar.gz
StartedAt: 2017-04-14 23:19:16 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:25:00 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 344.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: INSPEcT.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.4.0’
* 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 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         35.036  0.088  35.141
rocThresholds      21.596  0.016  21.625
makeSimDataset     15.640  0.244  20.818
makeSimModel       15.056  0.228  20.089
ratesFirstGuessVar 11.804  0.060  11.873
sfPlot             11.400  0.036  11.441
newINSPEcT         11.384  0.048  11.442
ratesFirstGuess    10.908  0.028  10.944
compareSteady       7.560  0.044   7.832
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck/00check.log’
for details.


INSPEcT.Rcheck/00install.out:

* 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)

INSPEcT.Rcheck/INSPEcT-Ex.timings:

nameusersystemelapsed
AIC-INSPEcT-method0.0080.0000.008
Extract0.0760.0080.083
INSPEcT_diffsteady-class1.7400.0081.747
chisqmodel0.0280.0000.026
chisqtest0.0080.0000.008
combine0.1200.0040.124
compareSteady7.5600.0447.832
geneClass0.0280.0040.035
getModel0.0040.0000.007
inHeatmap0.0280.0000.030
labeledSF0.0080.0000.006
logLik0.0080.0000.008
makeModelRates0.4840.0000.483
makeRPKMs4.7800.0484.833
makeSimDataset15.640 0.24420.818
makeSimModel15.056 0.22820.089
modelRates35.036 0.08835.141
modelingParams0.0080.0040.013
nGenes0.0040.0000.007
nTpts0.0080.0000.007
newINSPEcT11.384 0.04811.442
plotGene0.0280.0000.027
plotMA0.8880.0000.888
ratePvals0.0400.0040.041
ratesFirstGuess10.908 0.02810.944
ratesFirstGuessVar11.804 0.06011.873
removeModel0.0640.0000.061
rocCurve2.1600.0042.164
rocThresholds21.596 0.01621.625
sfPlot11.400 0.03611.441
split0.0600.0000.058
testingParams1.1600.0001.162
totalSF0.0120.0000.012
tpts0.0120.0000.012
viewModelRates0.0120.0000.013