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CHECK report for maPredictDSC on tokay1

This page was generated on 2019-04-13 11:22:58 -0400 (Sat, 13 Apr 2019).

Package 875/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maPredictDSC 1.20.0
Adi Laurentiu Tarca
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/maPredictDSC
Branch: RELEASE_3_8
Last Commit: 845445c
Last Changed Date: 2018-10-30 11:41:51 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: maPredictDSC
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maPredictDSC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings maPredictDSC_1.20.0.tar.gz
StartedAt: 2019-04-13 03:29:59 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:40:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 612.5 seconds
RetCode: 0
Status:  OK  
CheckDir: maPredictDSC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maPredictDSC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings maPredictDSC_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/maPredictDSC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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
'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
  'installed.packages'
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
  'model.matrix'
maPredictDSC : mff: no visible global function definition for 'formula'
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 'pt'
maPredictDSC : mff : wf: no visible global function definition for
  'wilcox.test'
maPredictDSC : mff: no visible global function definition for 'predict'
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 'sd'
maPredictDSC: no visible global function definition for 'model.matrix'
maPredictDSC: no visible global function definition for 'formula'
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 'pt'
maPredictDSC : wf: no visible global function definition for
  'wilcox.test'
maPredictDSC: no visible global function definition for 'predict'
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 'na.omit'
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'
Undefined global functions or variables:
  AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs
  formula gcrma installed.packages knn lmFit makeContrasts mas5
  mas5calls mclapply model.matrix na.omit performance predict
  prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.omit", "predict",
             "pt", "sd", "wilcox.test")
  importFrom("utils", "installed.packages")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
predictDSC 183.56   4.52  220.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
predictDSC 172.67   3.68  176.44
* 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:/Users/biocbuild/bbs-3.8-bioc/meat/maPredictDSC.Rcheck/00check.log'
for details.



Installation output

maPredictDSC.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/maPredictDSC_1.20.0.tar.gz && rm -rf maPredictDSC.buildbin-libdir && mkdir maPredictDSC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maPredictDSC.buildbin-libdir maPredictDSC_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL maPredictDSC_1.20.0.zip && rm maPredictDSC_1.20.0.tar.gz maPredictDSC_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 10510  100 10510    0     0   272k      0 --:--:-- --:--:-- --:--:--  301k

install for i386

* installing *source* package 'maPredictDSC' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maPredictDSC'
    finding HTML links ... done
    aggregateDSC                            html  
    maPredictDSC-internal                   html  
    perfDSC                                 html  
    predictDSC                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'maPredictDSC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maPredictDSC' as maPredictDSC_1.20.0.zip
* DONE (maPredictDSC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'maPredictDSC' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

maPredictDSC.Rcheck/examples_i386/maPredictDSC-Ex.timings

nameusersystemelapsed
aggregateDSC000
perfDSC0.000.010.01
predictDSC183.56 4.52220.91

maPredictDSC.Rcheck/examples_x64/maPredictDSC-Ex.timings

nameusersystemelapsed
aggregateDSC000
perfDSC0.030.000.03
predictDSC172.67 3.68176.44