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BioC 3.2: CHECK report for InPAS on zin1

This page was generated on 2015-08-24 10:50:29 -0700 (Mon, 24 Aug 2015).

Package 511/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InPAS 1.1.7
Jianhong Ou
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/InPAS
Last Changed Rev: 107392 / Revision: 107696
Last Changed Date: 2015-08-13 14:24:25 -0700 (Thu, 13 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: InPAS
Version: 1.1.7
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings InPAS_1.1.7.tar.gz
StartedAt: 2015-08-24 00:54:16 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:58:33 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 256.5 seconds
RetCode: 0
Status:  OK 
CheckDir: InPAS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings InPAS_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/InPAS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘InPAS’ version ‘1.1.7’
* 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 ‘InPAS’ can be installed ... [20s/21s] 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 ... 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
filterRes 5.15   0.04   5.196
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [19s/19s] OK
* 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: OK

InPAS.Rcheck/00install.out:

* installing *source* package ‘InPAS’ ...
** 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 (InPAS)

InPAS.Rcheck/InPAS-Ex.timings:

nameusersystemelapsed
CPsites0.0010.0000.001
coverageFromBedGraph0.0010.0000.001
filterRes5.1500.0405.196
fisher.exact.test0.0530.0000.053
getUTR3eSet4.5200.0204.552
inPAS0.0010.0000.002
limmaAnalyze0.0390.0040.043
prepare4GSEA0.0790.0000.079
singleGroupAnalyze0.0130.0000.013
singleSampleAnalyze0.0010.0040.003
testUsage4.5570.0124.636
usage4plot1.7450.0161.761
utr3.hg190.5180.0080.526
utr3.mm100.5100.0080.518
utr3Annotation0.0010.0000.000
utr3UsageEstimation0.0010.0000.002