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BioC 3.2: CHECK report for PGSEA on oaxaca

This page was generated on 2016-04-23 10:23:42 -0700 (Sat, 23 Apr 2016).

Package 768/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PGSEA 1.44.0
Karl Dykema
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/PGSEA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PGSEA
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PGSEA_1.44.0.tar.gz
StartedAt: 2016-04-23 03:00:15 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:02:34 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 139.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PGSEA_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PGSEA.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGSEA’ version ‘1.44.0’
* 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 ‘PGSEA’ can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘GO.db’ ‘KEGG.db’
  Please remove these calls from your code.
'library' or 'require' call to ‘org.Hs.eg.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GO.db’ ‘KEGG.db’ ‘annaffy’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
  partial argument match of 'env' to 'envir'
go2smc: no visible binding for global variable ‘GOTERM’
go2smc: no visible binding for global variable ‘org.Hs.egGO2ALLEGS’
kegg2smc: no visible binding for global variable ‘KEGGPATHNAME2ID’
kegg2smc: no visible binding for global variable ‘KEGGPATHID2EXTID’
* 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 ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
go2smc 44.687  1.447  46.163
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PGSEA.Rcheck/00check.log’
for details.


PGSEA.Rcheck/00install.out:

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

PGSEA.Rcheck/PGSEA-Ex.timings:

nameusersystemelapsed
GOLUBmcs0.0960.0080.104
PGSEA0.5230.0310.553
VAIgsc0.9450.0270.974
VAImcs0.3210.0170.338
aggregateExprs0.4040.0140.434
convertSmc0.0010.0000.001
editSmc0.0330.0020.035
go2smc44.687 1.44746.163
kegg2smc0.5220.0180.541
nbEset0.1110.0110.122
readGmt0.0460.0020.048
readSmc0.0490.0030.051
scanSmc0.0180.0010.020
smcPlot0.2870.0380.326
writeGmt0.0300.0020.032
writeSmc0.0830.0030.086