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BioC 3.0: CHECK report for GSEAlm on moscato1

This page was generated on 2015-04-10 09:45:11 -0700 (Fri, 10 Apr 2015).

Package 409/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEAlm 1.26.0
Assaf Oron
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GSEAlm
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: GSEAlm
Version: 1.26.0
Command: rm -rf GSEAlm.buildbin-libdir GSEAlm.Rcheck && mkdir GSEAlm.buildbin-libdir GSEAlm.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSEAlm.buildbin-libdir GSEAlm_1.26.0.tar.gz >GSEAlm.Rcheck\00install.out 2>&1 && cp GSEAlm.Rcheck\00install.out GSEAlm-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GSEAlm.buildbin-libdir --install="check:GSEAlm-install.out" --force-multiarch --no-vignettes --timings GSEAlm_1.26.0.tar.gz
StartedAt: 2015-04-10 02:01:04 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:02:04 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 60.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GSEAlm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GSEAlm.buildbin-libdir GSEAlm.Rcheck && mkdir GSEAlm.buildbin-libdir GSEAlm.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GSEAlm.buildbin-libdir GSEAlm_1.26.0.tar.gz >GSEAlm.Rcheck\00install.out 2>&1 && cp GSEAlm.Rcheck\00install.out GSEAlm-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GSEAlm.buildbin-libdir --install="check:GSEAlm-install.out" --force-multiarch --no-vignettes --timings GSEAlm_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GSEAlm.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSEAlm/DESCRIPTION' ... OK
* this is package 'GSEAlm' version '1.26.0'
* 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 whether package 'GSEAlm' can be installed ... 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
* 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
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'Biobase'
  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
pvalFromPermMat: warning in matrix(as.double(NA), nr = nrow(perms),
  ncol = 2): partial argument match of 'nr' to 'nrow'
CooksDPerGene: no visible global function definition for 'exprs'
dfbetasPerGene: no visible global function definition for 'exprs'
dfbetasPerGene: no visible global function definition for
  'featureNames'
dfbetasPerGene: no visible global function definition for 'sampleNames'
dffitsPerGene: no visible global function definition for 'exprs'
dffitsPerGene: no visible global function definition for 'featureNames'
dffitsPerGene : <anonymous>: no visible global function definition for
  'exprs'
getResidPerGene: no visible global function definition for 'exprs'
getResidPerGene: no visible global function definition for 'phenoData'
gsealmPerm: no visible global function definition for 'pData'
gsealmPerm: no visible global function definition for 'pData<-'
lmPerGene: no visible global function definition for 'varLabels'
lmPerGene: no visible global function definition for 'pData'
lmPerGene: no visible global function definition for 'exprs'
* checking Rd files ... NOTE
prepare_Rd: gsealmPerm.Rd:62: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'GlobalAncova'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files contain a license that requires
distribution of original sources:
  'crop.sty'
Please ensure that you have complied with it.
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [8s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
gsealmPerm 5.28      0    5.29
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'graph' 'lattice'
* 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

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GSEAlm.Rcheck/00check.log'
for details.

GSEAlm.Rcheck/00install.out:


install for i386

* installing *source* package 'GSEAlm' ...
** R
** 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 'GSEAlm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSEAlm' as GSEAlm_1.26.0.zip
* DONE (GSEAlm)

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

nameusersystemelapsed
GSNormalize0.110.020.12
dfbetasPerGene0.280.030.31
getResidPerGene0.160.000.16
gsealmPerm3.220.013.23
lmPerGene0.050.000.05
resplot0.150.020.17

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

nameusersystemelapsed
GSNormalize0.230.000.24
dfbetasPerGene0.550.000.54
getResidPerGene0.270.000.27
gsealmPerm5.280.005.29
lmPerGene0.070.000.06
resplot0.20.00.2