Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for maPredictDSC on windows1.bioconductor.org

This page was generated on 2015-10-27 17:30:37 -0400 (Tue, 27 Oct 2015).

Package 591/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maPredictDSC 1.8.0
Adi Laurentiu Tarca
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/maPredictDSC
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ 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: maPredictDSC
Version: 1.8.0
Command: rm -rf maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && mkdir maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maPredictDSC.buildbin-libdir maPredictDSC_1.8.0.tar.gz >maPredictDSC.Rcheck\00install.out 2>&1 && cp maPredictDSC.Rcheck\00install.out maPredictDSC-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=maPredictDSC.buildbin-libdir --install="check:maPredictDSC-install.out" --force-multiarch --no-vignettes --timings maPredictDSC_1.8.0.tar.gz
StartedAt: 2015-10-27 03:10:24 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:22:11 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 707.1 seconds
RetCode: 0
Status:  OK  
CheckDir: maPredictDSC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && mkdir maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maPredictDSC.buildbin-libdir maPredictDSC_1.8.0.tar.gz >maPredictDSC.Rcheck\00install.out 2>&1 && cp maPredictDSC.Rcheck\00install.out maPredictDSC-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=maPredictDSC.buildbin-libdir --install="check:maPredictDSC-install.out" --force-multiarch --no-vignettes --timings maPredictDSC_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/maPredictDSC.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maPredictDSC/DESCRIPTION' ... OK
* this is package 'maPredictDSC' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'MASS' 'affy' 'limma' 'gcrma' 'ROC' 'class' 'e1071' 'caret'
  'hgu133plus2.db' 'ROCR' 'AnnotationDbi' 'LungCancerACvsSCCGEO'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'maPredictDSC' 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
** 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' calls to packages already attached by Depends:
  'ROC' 'ROCR' 'affy' 'caret' 'class' 'e1071' 'gcrma' 'limma'
  Please remove these calls from your code.
'library' or 'require' call to 'parallel' 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:
  'LungCancerACvsSCCGEO' 'ROC' 'ROCR' 'affy' 'caret' 'class' 'e1071'
  'gcrma' 'hgu133plus2.db' 'limma'
  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
maPredictDSC: no visible global function definition for 'ReadAffy'
maPredictDSC: no visible global function definition for 'rma'
maPredictDSC: no visible global function definition for 'mas5'
maPredictDSC: no visible global function definition for 'gcrma'
maPredictDSC: no visible global function definition for 'exprs'
maPredictDSC: no visible global function definition for 'mas5calls'
maPredictDSC: no visible global function definition for 'createFolds'
maPredictDSC : mff: no visible global function definition for 'lmFit'
maPredictDSC : mff: no visible global function definition for
  'makeContrasts'
maPredictDSC : mff: no visible global function definition for
  'contrasts.fit'
maPredictDSC : mff: no visible global function definition for 'eBayes'
maPredictDSC : mff: no visible global function definition for
  'topTable'
maPredictDSC : mff: no visible global function definition for 'knn'
maPredictDSC : mff: no visible global function definition for 'svm'
maPredictDSC : mff: no visible global function definition for
  'rocdemo.sca'
maPredictDSC : mff: no visible binding for global variable 'dxrule.sca'
maPredictDSC : mff: no visible global function definition for 'AUC'
maPredictDSC: no visible global function definition for 'mclapply'
maPredictDSC: no visible global function definition for 'lmFit'
maPredictDSC: no visible global function definition for 'makeContrasts'
maPredictDSC: no visible global function definition for 'contrasts.fit'
maPredictDSC: no visible global function definition for 'eBayes'
maPredictDSC: no visible global function definition for 'topTable'
maPredictDSC: no visible global function definition for 'knn'
maPredictDSC: no visible global function definition for 'svm'
perfDSC: no visible global function definition for 'prediction'
perfDSC: no visible global function definition for 'performance'
perfDSC: no visible global function definition for 'trapezint'
perfDSC: no visible global function definition for 'rocdemo.sca'
perfDSC: no visible binding for global variable 'dxrule.sca'
perfDSC: no visible global function definition for 'AUC'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [254s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
predictDSC 239.72   4.02  247.95
** running examples for arch 'x64' ... [290s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
predictDSC 280.1   2.12  282.22
* 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
  'C:/biocbld/bbs-3.2-bioc/meat/maPredictDSC.Rcheck/00check.log'
for details.


maPredictDSC.Rcheck/00install.out:


install for i386

* installing *source* package 'maPredictDSC' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'maPredictDSC' ...
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'maPredictDSC' as maPredictDSC_1.8.0.zip
* DONE (maPredictDSC)

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

nameusersystemelapsed
aggregateDSC000
perfDSC0.030.000.03
predictDSC239.72 4.02247.95

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

nameusersystemelapsed
aggregateDSC000
perfDSC0.30.00.3
predictDSC280.10 2.12282.22