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BioC 3.2: CHECK report for mdgsa on zin1

This page was generated on 2015-08-24 10:50:20 -0700 (Mon, 24 Aug 2015).

Package 587/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdgsa 1.1.0
David Montaner
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mdgsa
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 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: mdgsa
Version: 1.1.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mdgsa_1.1.0.tar.gz
StartedAt: 2015-08-24 01:23:20 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:25:07 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 106.8 seconds
RetCode: 0
Status:  OK 
CheckDir: mdgsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mdgsa_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mdgsa.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 ‘mdgsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mdgsa’ 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 ‘mdgsa’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/13s]
 [13s/13s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/mdgsa.Rcheck/00check.log’
for details.


mdgsa.Rcheck/00install.out:

* installing *source* package ‘mdgsa’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mdgsa)

mdgsa.Rcheck/mdgsa-Ex.timings:

nameusersystemelapsed
annotFilter0.0060.0000.005
annotList2mat0.0010.0000.001
annotMat2list0.0010.0000.002
getGOnames0.550.020.57
getKEGGnames0.0030.0000.002
getOntology0.1090.0000.109
goLeaves2.2890.0362.324
indexTransform0.0070.0000.006
mdGsa0.030.000.03
mdPat0.0140.0000.014
plotMdGsa0.0000.0000.001
propagateGO3.6940.0083.699
pval2index0.0050.0040.008
revList0.0020.0000.001
splitOntologies0.2670.0000.267
transferIndex0.0450.0000.046
uvGsa0.0180.0000.018
uvPat0.0050.0000.005
uvSignif0.0050.0000.005