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BioC 3.1: CHECK report for LMGene on moscato2

This page was generated on 2015-10-09 09:27:30 -0700 (Fri, 09 Oct 2015).

Package 529/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LMGene 2.24.0
Blythe Durbin-Johnson
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/LMGene
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LMGene
Version: 2.24.0
Command: rm -rf LMGene.buildbin-libdir LMGene.Rcheck && mkdir LMGene.buildbin-libdir LMGene.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LMGene.buildbin-libdir LMGene_2.24.0.tar.gz >LMGene.Rcheck\00install.out 2>&1 && cp LMGene.Rcheck\00install.out LMGene-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=LMGene.buildbin-libdir --install="check:LMGene-install.out" --force-multiarch --no-vignettes --timings LMGene_2.24.0.tar.gz
StartedAt: 2015-10-09 03:16:43 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:19:44 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 181.3 seconds
RetCode: 0
Status:  OK  
CheckDir: LMGene.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf LMGene.buildbin-libdir LMGene.Rcheck && mkdir LMGene.buildbin-libdir LMGene.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LMGene.buildbin-libdir LMGene_2.24.0.tar.gz >LMGene.Rcheck\00install.out 2>&1 && cp LMGene.Rcheck\00install.out LMGene-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=LMGene.buildbin-libdir --install="check:LMGene-install.out" --force-multiarch --no-vignettes --timings LMGene_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/LMGene.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LMGene/DESCRIPTION' ... OK
* this is package 'LMGene' version '2.24.0'
* 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 whether package 'LMGene' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [64s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
tranestAffyProbeLevel 49.85   1.57   51.44
tranest                6.29   0.00    6.29
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
tranestAffyProbeLevel 46.78   3.68   50.53
tranest                8.38   0.00    8.38
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/LMGene.Rcheck/00check.log'
for details.


LMGene.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'LMGene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LMGene' as LMGene_2.24.0.zip
* DONE (LMGene)

LMGene.Rcheck/examples_i386/LMGene-Ex.timings:

nameusersystemelapsed
LMGene1.170.001.17
genediff1.010.001.01
glog000
lnorm0.130.000.13
lnormeS0.040.020.06
neweS0.050.000.05
norm0.030.000.03
plotMeanSD0.080.010.09
psmeans0.090.000.10
pvadjust1.170.001.17
rowaov1.020.021.03
sample.eS0.040.000.04
sample.ind0.080.000.08
sample.mat0.050.000.05
tranest6.290.006.29
tranestAffyProbeLevel49.85 1.5751.44
transeS0.000.020.02
vlist000

LMGene.Rcheck/examples_x64/LMGene-Ex.timings:

nameusersystemelapsed
LMGene1.430.011.45
genediff1.360.031.39
glog000
lnorm0.090.000.09
lnormeS0.050.000.05
neweS0.050.020.06
norm0.050.000.05
plotMeanSD0.100.000.11
psmeans0.100.000.09
pvadjust1.310.011.33
rowaov1.230.001.23
sample.eS0.030.020.05
sample.ind0.100.000.09
sample.mat0.040.000.05
tranest8.380.008.38
tranestAffyProbeLevel46.78 3.6850.53
transeS0.020.000.02
vlist000