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BioC 3.4: CHECK report for INSPEcT on zin1

This page was generated on 2016-09-21 03:40:01 -0700 (Wed, 21 Sep 2016).

Package 617/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
INSPEcT 1.3.2
Stefano de Pretis
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/INSPEcT
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.3.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings INSPEcT_1.3.2.tar.gz
StartedAt: 2016-09-20 08:11:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:17:16 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 349.9 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/INSPEcT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.3.2’
* 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 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
modelRates         39.148  0.128  39.277
rocThresholds      24.512  0.072  24.586
makeSimDataset     17.948  0.896  23.288
makeSimModel       17.236  0.288  21.682
ratesFirstGuess    12.584  0.072  12.655
newINSPEcT         12.320  0.060  12.379
ratesFirstGuessVar 12.248  0.036  12.285
sfPlot             12.220  0.040  12.264
compareSteady       9.044  0.716   9.769
* 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
Creating a generic function for ‘split’ from package ‘base’ in package ‘INSPEcT’
Creating a generic function for ‘AIC’ from package ‘stats’ in package ‘INSPEcT’
** 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-method0.0120.0000.011
Extract0.1400.0000.137
INSPEcT_diffsteady-class1.9240.8242.749
chisqmodel0.0280.0040.031
chisqtest0.0080.0000.008
combine0.1360.0160.151
compareSteady9.0440.7169.769
geneClass0.0440.0000.044
getModel0.0080.0000.008
inHeatmap0.0320.0040.036
labeledSF0.0040.0000.008
logLik0.0080.0000.008
makeModelRates0.6040.0000.606
makeRPKMs4.7040.0524.826
makeSimDataset17.948 0.89623.288
makeSimModel17.236 0.28821.682
modelRates39.148 0.12839.277
modelingParams0.0120.0000.014
nGenes0.0080.0000.007
nTpts0.0080.0000.006
newINSPEcT12.320 0.06012.379
plotGene0.0320.0000.030
plotMA0.9560.0481.012
ratePvals0.0440.0000.041
ratesFirstGuess12.584 0.07212.655
ratesFirstGuessVar12.248 0.03612.285
removeModel0.0400.0040.043
rocCurve2.0360.0402.077
rocThresholds24.512 0.07224.586
sfPlot12.220 0.04012.264
split0.0560.0040.060
testingParams1.140.001.14
totalSF0.0080.0000.007
tpts0.0080.0000.007
viewModelRates0.0080.0000.008