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BioC 3.2: CHECK report for LMGene on oaxaca

This page was generated on 2016-04-23 10:23:09 -0700 (Sat, 23 Apr 2016).

Package 568/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LMGene 2.26.0
Blythe Durbin-Johnson
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/LMGene
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: LMGene
Version: 2.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LMGene_2.26.0.tar.gz
StartedAt: 2016-04-23 01:36:47 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:38:50 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 123.4 seconds
RetCode: 0
Status:  OK 
CheckDir: LMGene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LMGene_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/LMGene.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 ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.26.0’
* 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 ‘LMGene’ can be installed ... [6s/6s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘multtest’ ‘survival’
  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
GetLMObj: no visible global function definition for ‘exprs’
GetLMObj: no visible global function definition for ‘varLabels’
GetLMObj: no visible global function definition for ‘pData’
LMGene: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘pData’
genediff: no visible global function definition for ‘exprs’
genediff: no visible global function definition for ‘varLabels’
genediff : owaov: no visible global function definition for ‘pData’
lnormeS: no visible global function definition for ‘exprs’
lnormeS: no visible global function definition for ‘exprs<-’
msecalc: no visible global function definition for ‘exprs’
msecalcmult: no visible global function definition for ‘exprs’
neweS: no visible global function definition for ‘pData<-’
neweS: no visible global function definition for ‘varLabels<-’
plotMeanSD: no visible global function definition for ‘exprs’
psmeans: no visible global function definition for ‘exprs’
psmeans: no visible global function definition for ‘pData’
pvadjust: no visible global function definition for ‘mt.rawp2adjp’
rowaov: no visible global function definition for ‘exprs’
rowaov: no visible global function definition for ‘varLabels’
rowaov: no visible global function definition for ‘pData’
tranest: no visible global function definition for ‘exprs’
tranest: no visible global function definition for ‘phenoData’
tranest2: no visible global function definition for ‘exprs’
tranestAffyProbeLevel: no visible global function definition for
  ‘featureNames’
tranestAffyProbeLevel: no visible global function definition for ‘pm’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs<-’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs’
tranestmult: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs<-’
* 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 ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
tranestAffyProbeLevel 47.445  3.855  51.723
tranest                6.687  0.770   7.459
* 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/LMGene.Rcheck/00check.log’
for details.


LMGene.Rcheck/00install.out:

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

LMGene.Rcheck/LMGene-Ex.timings:

nameusersystemelapsed
LMGene1.4870.0191.506
genediff1.2000.0051.205
glog0.0030.0010.003
lnorm0.0640.0030.067
lnormeS0.0360.0020.038
neweS0.0440.0020.046
norm0.0370.0020.039
plotMeanSD0.1050.0030.109
psmeans0.0910.0030.095
pvadjust1.2380.0021.240
rowaov1.0730.0031.076
sample.eS0.0380.0020.040
sample.ind0.0580.0010.059
sample.mat0.0440.0020.047
tranest6.6870.7707.459
tranestAffyProbeLevel47.445 3.85551.723
transeS0.0050.0020.007
vlist0.0040.0010.005