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BioC 3.4: CHECK report for stepwiseCM on moscato1

This page was generated on 2016-09-21 03:43:54 -0700 (Wed, 21 Sep 2016).

Package 1171/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stepwiseCM 1.19.0
Askar Obulkasim
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/stepwiseCM
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: stepwiseCM
Version: 1.19.0
Command: rm -rf stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && mkdir stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepwiseCM.buildbin-libdir stepwiseCM_1.19.0.tar.gz >stepwiseCM.Rcheck\00install.out 2>&1 && cp stepwiseCM.Rcheck\00install.out stepwiseCM-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=stepwiseCM.buildbin-libdir --install="check:stepwiseCM-install.out" --force-multiarch --no-vignettes --timings stepwiseCM_1.19.0.tar.gz
StartedAt: 2016-09-20 17:13:55 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 17:18:31 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 276.2 seconds
RetCode: 0
Status:  OK  
CheckDir: stepwiseCM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && mkdir stepwiseCM.buildbin-libdir stepwiseCM.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=stepwiseCM.buildbin-libdir stepwiseCM_1.19.0.tar.gz >stepwiseCM.Rcheck\00install.out 2>&1 && cp stepwiseCM.Rcheck\00install.out stepwiseCM-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=stepwiseCM.buildbin-libdir --install="check:stepwiseCM-install.out" --force-multiarch --no-vignettes --timings stepwiseCM_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/stepwiseCM.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.19.0'
* 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
  'predict'
.Wrapper.Classifier: no visible global function definition for
  'cv.glmpath'
.Wrapper.Classifier: no visible binding for global variable 'binomial'
.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 'predict'
Classifier: no visible global function definition for 'cv.glmpath'
Classifier: no visible binding for global variable 'binomial'
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'
Curve.generator: no visible global function definition for 'plot'
Curve.generator: no visible global function definition for 'points'
Curve.generator: no visible global function definition for 'legend'
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'
Undefined global functions or variables:
  binomial cv.glmpath exprs glmpath legend optL1 optL2 pamr.cv
  pamr.listgenes pamr.predict pamr.train penalized plot plsrf_x
  plsrf_x_pv points predict predict.glmpath randomForest sfExportAll
  sfInit sfLapply sfLibrary sfStop stepwiseCM svm tspcalc tune.control
  tune.svm
Consider adding
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "binomial", "predict")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
stepwiseCM-package 23.35   0.03   23.40
Curve.generator    22.56   0.05   22.61
Step.pred          22.11   0.03   22.14
RS.generator       20.23   0.01   20.25
Classifier          7.12   0.11    7.24
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
stepwiseCM-package 23.61   0.11   23.72
Curve.generator    21.68   0.05   21.73
Step.pred          21.72   0.01   21.73
RS.generator       19.75   0.03   19.78
Classifier          7.26   0.09    7.35
* 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-3.4-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_1.19.0.zip
* DONE (stepwiseCM)

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

nameusersystemelapsed
CNS0.190.020.21
Classifier7.120.117.24
Classifier.par0.180.010.20
Curve.generator22.56 0.0522.61
Proximity0.250.020.26
RS.generator20.23 0.0120.25
Step.pred22.11 0.0322.14
stepwiseCM-package23.35 0.0323.40

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

nameusersystemelapsed
CNS0.150.030.19
Classifier7.260.097.35
Classifier.par0.170.000.17
Curve.generator21.68 0.0521.73
Proximity0.220.020.24
RS.generator19.75 0.0319.78
Step.pred21.72 0.0121.73
stepwiseCM-package23.61 0.1123.72