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BioC 3.3: CHECK report for cancerclass on oaxaca

This page was generated on 2016-10-13 12:58:20 -0700 (Thu, 13 Oct 2016).

Package 145/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cancerclass 1.16.0
Daniel Kosztyla
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/cancerclass
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  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: cancerclass
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cancerclass_1.16.0.tar.gz
StartedAt: 2016-10-12 23:51:29 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:52:52 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 82.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cancerclass.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cancerclass_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cancerclass.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cancerclass/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cancerclass’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cancerclass’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
* 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
* 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' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘binom’
  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
File ‘cancerclass/R/cancerclass-internal.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

calc.auc: no visible global function definition for ‘integrate’
calc.auc : <anonymous>: no visible global function definition for
  ‘approx’
calc.roc: no visible global function definition for ‘binom.confint’
fit: no visible global function definition for ‘pData’
fit: no visible global function definition for ‘featureData’
fit: no visible global function definition for ‘exprs’
fit: no visible binding for global variable ‘methods’
get.prop: no visible global function definition for ‘binom.confint’
loo: no visible global function definition for ‘pData’
nvalidate: no visible global function definition for ‘pData’
nvalidate: no visible global function definition for ‘featureData’
nvalidate: no visible global function definition for ‘exprs’
nvalidate: no visible binding for global variable ‘methods’
prepare: no visible global function definition for ‘pData’
prepare: no visible global function definition for ‘exprs’
prepare: no visible global function definition for ‘exprs<-’
validate: no visible global function definition for ‘pData’
validate: no visible global function definition for ‘featureData’
validate: no visible global function definition for ‘exprs’
validate: no visible binding for global variable ‘methods’
plot3d,nvalidation: no visible global function definition for ‘persp’
plot3d,validation: no visible global function definition for ‘persp’
plot,nvalidation: no visible global function definition for ‘grey’
plot,nvalidation: no visible global function definition for ‘par’
plot,nvalidation: no visible global function definition for ‘barplot’
plot,nvalidation: no visible global function definition for ‘legend’
plot,nvalidation : <anonymous>: no visible global function definition
  for ‘quantile’
plot,nvalidation: no visible global function definition for ‘abline’
plot,nvalidation: no visible global function definition for ‘lines’
plot,prediction: no visible global function definition for ‘t.test’
plot,prediction: no visible global function definition for ‘par’
plot,prediction: no visible global function definition for ‘hist’
plot,prediction: no visible global function definition for ‘legend’
plot,prediction: no visible global function definition for ‘barplot’
plot,prediction: no visible global function definition for ‘lines’
plot,prediction: no visible global function definition for ‘abline’
plot,prediction: no visible global function definition for ‘glm’
plot,prediction: no visible binding for global variable ‘binomial’
plot,prediction: no visible global function definition for ‘pchisq’
plot,prediction: no visible global function definition for ‘qnorm’
plot,prediction: no visible global function definition for ‘points’
plot,predictor: no visible global function definition for ‘barplot’
plot,validation: no visible global function definition for ‘grey’
plot,validation: no visible global function definition for ‘par’
plot,validation: no visible global function definition for ‘barplot’
plot,validation: no visible global function definition for ‘legend’
plot,validation : <anonymous>: no visible global function definition
  for ‘quantile’
plot,validation: no visible global function definition for ‘abline’
plot,validation: no visible global function definition for ‘lines’
predict,predictor: no visible global function definition for ‘pData’
predict,predictor: no visible global function definition for ‘exprs’
summary,prediction: no visible global function definition for
  ‘fisher.test’
Undefined global functions or variables:
  abline approx barplot binom.confint binomial exprs exprs<-
  featureData fisher.test glm grey hist integrate legend lines methods
  pData par pchisq persp points qnorm quantile t.test
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "barplot", "hist", "legend", "lines",
             "par", "persp", "points")
  importFrom("stats", "approx", "binomial", "fisher.test", "glm",
             "integrate", "pchisq", "qnorm", "quantile", "t.test")
  importFrom("utils", "methods")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOLUB 34.027  0.596  34.674
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/cancerclass.Rcheck/00check.log’
for details.


cancerclass.Rcheck/00install.out:

* installing *source* package ‘cancerclass’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c copa.c -o copa.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c cor.c -o cor.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c fc.c -o fc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c help.c -o help.o
help.c:335:7: warning: explicitly assigning a variable of type 'double' to itself [-Wself-assign]
   var=var; ///(to-from-1); R=var(N-1) => /(count-1)
   ˜˜˜^˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ort.c -o ort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c os.c -o os.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c shift.c -o shift.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c statistics.c -o statistics.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c student.c -o student.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c throw.c -o throw.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c welch.c -o welch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c wilcox.c -o wilcox.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cancerclass.so copa.o cor.o fc.o help.o ort.o os.o shift.o statistics.o student.o throw.o welch.o wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/cancerclass.Rcheck/cancerclass/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cancerclass)

cancerclass.Rcheck/cancerclass-Ex.timings:

nameusersystemelapsed
GOLUB34.027 0.59634.674
fit000
loo0.0000.0000.001
nvalidate0.0000.0000.001
nvalidation-class0.0020.0000.002
plot0.0010.0010.001
predict.predictor-method0.0010.0000.001
prediction-class0.0000.0000.001
predictor-class0.0010.0000.001
summary.prediction-method000
validate0.0010.0000.001
validation-class0.0010.0000.002