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BioC 3.2: CHECK report for stepwiseCM on moscato1

This page was generated on 2015-08-20 13:20:31 -0700 (Thu, 20 Aug 2015).

Package 993/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepwiseCM 1.15.0
Askar Obulkasim
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/stepwiseCM
Last Changed Rev: 102594 / Revision: 107602
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 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 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: stepwiseCM
Version: 1.15.0
Command: rm -rf stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && mkdir stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepwiseCM.buildbin-libdir stepwiseCM_1.15.0.tar.gz >stepwiseCM.Rcheck\00install.out 2>&1 && cp stepwiseCM.Rcheck\00install.out stepwiseCM-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=stepwiseCM.buildbin-libdir --install="check:stepwiseCM-install.out" --force-multiarch --no-vignettes --timings stepwiseCM_1.15.0.tar.gz
StartedAt: 2015-08-20 10:52:11 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 10:57:35 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 324.0 seconds
RetCode: 0
Status:  OK  
CheckDir: stepwiseCM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && mkdir stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepwiseCM.buildbin-libdir stepwiseCM_1.15.0.tar.gz >stepwiseCM.Rcheck\00install.out 2>&1 && cp stepwiseCM.Rcheck\00install.out stepwiseCM-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=stepwiseCM.buildbin-libdir --install="check:stepwiseCM-install.out" --force-multiarch --no-vignettes --timings stepwiseCM_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/stepwiseCM.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 'stepwiseCM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'stepwiseCM' version '1.15.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'randomForest' 'MAclinical' 'tspair' 'pamr' 'snowfall' 'glmpath'
  'penalized' 'e1071' 'Biobase'
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 'stepwiseCM' 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
Packages in Depends field not imported from:
  'Biobase' 'MAclinical' 'e1071' 'glmpath' 'pamr' 'penalized'
  'randomForest' 'snowfall' 'tspair'
  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
.Wrapper.Classifier: no visible global function definition for
  'tspcalc'
.Wrapper.Classifier: no visible global function definition for
  'cv.glmpath'
.Wrapper.Classifier: no visible global function definition for
  'glmpath'
.Wrapper.Classifier: no visible global function definition for
  'predict.glmpath'
.Wrapper.Classifier: no visible global function definition for 'optL1'
.Wrapper.Classifier: no visible global function definition for
  'penalized'
.Wrapper.Classifier: no visible global function definition for 'optL2'
.Wrapper.Classifier: no visible global function definition for
  'pamr.train'
.Wrapper.Classifier: no visible global function definition for
  'pamr.cv'
.Wrapper.Classifier: no visible global function definition for
  'pamr.predict'
.Wrapper.Classifier: no visible global function definition for
  'tune.svm'
.Wrapper.Classifier: no visible global function definition for
  'tune.control'
.Wrapper.Classifier: no visible global function definition for 'svm'
.Wrapper.Classifier: no visible global function definition for
  'plsrf_x'
.Wrapper.Classifier: no visible global function definition for
  'plsrf_x_pv'
.Wrapper.Classifier: no visible global function definition for
  'randomForest'
.Wrapper.Proximity: no visible global function definition for
  'randomForest'
Classifier: no visible global function definition for 'exprs'
Classifier: no visible global function definition for 'tspcalc'
Classifier: no visible global function definition for 'cv.glmpath'
Classifier: no visible global function definition for 'glmpath'
Classifier: no visible global function definition for 'predict.glmpath'
Classifier: no visible global function definition for 'optL1'
Classifier: no visible global function definition for 'penalized'
Classifier: no visible global function definition for 'optL2'
Classifier: no visible global function definition for 'pamr.train'
Classifier: no visible global function definition for 'pamr.cv'
Classifier: no visible global function definition for 'pamr.predict'
Classifier: no visible global function definition for 'pamr.listgenes'
Classifier: no visible global function definition for 'tune.svm'
Classifier: no visible global function definition for 'tune.control'
Classifier: no visible global function definition for 'svm'
Classifier: no visible global function definition for 'plsrf_x'
Classifier: no visible global function definition for 'plsrf_x_pv'
Classifier: no visible global function definition for 'randomForest'
Classifier.par: no visible global function definition for 'exprs'
Classifier.par: no visible global function definition for 'sfInit'
Classifier.par: no visible global function definition for 'sfLibrary'
Classifier.par: no visible binding for global variable 'stepwiseCM'
Classifier.par: no visible global function definition for 'sfExportAll'
Classifier.par: no visible global function definition for 'sfLapply'
Classifier.par: no visible global function definition for 'sfStop'
Proximity: no visible global function definition for 'exprs'
Proximity: no visible global function definition for 'randomForest'
Proximity: no visible global function definition for 'sfInit'
Proximity: no visible global function definition for 'sfLibrary'
Proximity: no visible binding for global variable 'randomForest'
Proximity: no visible binding for global variable 'stepwiseCM'
Proximity: no visible global function definition for 'sfExportAll'
Proximity: no visible global function definition for 'sfLapply'
Proximity: no visible global function definition for 'sfStop'
* 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' ... [117s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
stepwiseCM-package 27.95   0.36   28.33
Curve.generator    26.38   0.11   26.49
Step.pred          25.62   0.04   25.69
RS.generator       23.29   0.03   23.33
Classifier          9.22   0.12    9.35
** running examples for arch 'x64' ... [131s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
stepwiseCM-package 31.88   0.39   32.27
Step.pred          28.78   0.05   28.84
Curve.generator    28.67   0.13   28.82
RS.generator       26.02   0.04   26.07
Classifier         11.26   0.14   11.41
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/stepwiseCM.Rcheck/00check.log'
for details.


stepwiseCM.Rcheck/00install.out:


install for i386

* installing *source* package 'stepwiseCM' ...
** 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 'stepwiseCM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'stepwiseCM' as stepwiseCM_1.15.0.zip
* DONE (stepwiseCM)

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

nameusersystemelapsed
CNS0.400.000.41
Classifier9.220.129.35
Classifier.par0.250.020.26
Curve.generator26.38 0.1126.49
Proximity0.260.000.26
RS.generator23.29 0.0323.33
Step.pred25.62 0.0425.69
stepwiseCM-package27.95 0.3628.33

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

nameusersystemelapsed
CNS0.220.020.23
Classifier11.26 0.1411.41
Classifier.par0.170.010.18
Curve.generator28.67 0.1328.82
Proximity0.220.000.22
RS.generator26.02 0.0426.07
Step.pred28.78 0.0528.84
stepwiseCM-package31.88 0.3932.27