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BioC 3.5: CHECK report for cancerclass on tokay2

This page was generated on 2017-08-16 13:21:40 -0400 (Wed, 16 Aug 2017).

Package 167/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cancerclass 1.20.0
Daniel Kosztyla
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cancerclass
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cancerclass
Version: 1.20.0
Command: rm -rf cancerclass.buildbin-libdir cancerclass.Rcheck && mkdir cancerclass.buildbin-libdir cancerclass.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cancerclass.buildbin-libdir cancerclass_1.20.0.tar.gz >cancerclass.Rcheck\00install.out 2>&1 && cp cancerclass.Rcheck\00install.out cancerclass-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cancerclass.buildbin-libdir --install="check:cancerclass-install.out" --force-multiarch --no-vignettes --timings cancerclass_1.20.0.tar.gz
StartedAt: 2017-08-15 22:26:54 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:29:11 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 137.2 seconds
RetCode: 0
Status:  OK  
CheckDir: cancerclass.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cancerclass.buildbin-libdir cancerclass.Rcheck && mkdir cancerclass.buildbin-libdir cancerclass.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cancerclass.buildbin-libdir cancerclass_1.20.0.tar.gz >cancerclass.Rcheck\00install.out 2>&1 && cp cancerclass.Rcheck\00install.out cancerclass-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=cancerclass.buildbin-libdir --install="check:cancerclass-install.out" --force-multiarch --no-vignettes --timings cancerclass_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cancerclass.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cancerclass/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cancerclass' version '1.20.0'
* 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 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
* 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' 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/cancerclass.buildbin-libdir/cancerclass/libs/i386/cancerclass.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
GOLUB 22.18    0.5   22.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
GOLUB 33.56   0.37   33.94
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/cancerclass.Rcheck/00check.log'
for details.


cancerclass.Rcheck/00install.out:


install for i386

* installing *source* package 'cancerclass' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c copa.c -o copa.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cor.c -o cor.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fc.c -o fc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c help.c -o help.o
help.c: In function 'welch_df':
help.c:263:19: warning: variable 'mean2' set but not used [-Wunused-but-set-variable]
     double mean1, mean2, var1, var2 = 0.0;
                   ^
help.c:263:12: warning: variable 'mean1' set but not used [-Wunused-but-set-variable]
     double mean1, mean2, var1, var2 = 0.0;
            ^
help.c: In function 'bsortdesc':
help.c:344:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable]
     int i,k,anzahl=0;
             ^
help.c: In function 'bsort':
help.c:368:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable]
     int i,k,anzahl=0;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ort.c -o ort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c os.c -o os.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c shift.c -o shift.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c statistics.c -o statistics.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c student.c -o student.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c throw.c -o throw.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c welch.c -o welch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c wilcox.c -o wilcox.o
wilcox.c: In function 'wilcoxon':
wilcox.c:37:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable]
    int overall = 0;
        ^
wilcox.c: In function 'pwilcoxon':
wilcox.c:75:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable]
    int overall = 0;
        ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o cancerclass.dll tmp.def copa.o cor.o fc.o help.o ort.o os.o shift.o statistics.o student.o throw.o welch.o wilcox.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/cancerclass.buildbin-libdir/cancerclass/libs/i386
** 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 'cancerclass' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c copa.c -o copa.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cor.c -o cor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fc.c -o fc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c help.c -o help.o
help.c: In function 'welch_df':
help.c:263:19: warning: variable 'mean2' set but not used [-Wunused-but-set-variable]
     double mean1, mean2, var1, var2 = 0.0;
                   ^
help.c:263:12: warning: variable 'mean1' set but not used [-Wunused-but-set-variable]
     double mean1, mean2, var1, var2 = 0.0;
            ^
help.c: In function 'bsortdesc':
help.c:344:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable]
     int i,k,anzahl=0;
             ^
help.c: In function 'bsort':
help.c:368:13: warning: variable 'anzahl' set but not used [-Wunused-but-set-variable]
     int i,k,anzahl=0;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ort.c -o ort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c os.c -o os.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c shift.c -o shift.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c statistics.c -o statistics.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c student.c -o student.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c throw.c -o throw.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c welch.c -o welch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c wilcox.c -o wilcox.o
wilcox.c: In function 'wilcoxon':
wilcox.c:37:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable]
    int overall = 0;
        ^
wilcox.c: In function 'pwilcoxon':
wilcox.c:75:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable]
    int overall = 0;
        ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o cancerclass.dll tmp.def copa.o cor.o fc.o help.o ort.o os.o shift.o statistics.o student.o throw.o welch.o wilcox.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/cancerclass.buildbin-libdir/cancerclass/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cancerclass' as cancerclass_1.20.0.zip
* DONE (cancerclass)

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

nameusersystemelapsed
GOLUB22.18 0.5022.69
fit000
loo000
nvalidate000
nvalidation-class000
plot000
predict.predictor-method000
prediction-class0.020.000.01
predictor-class000
summary.prediction-method000
validate000
validation-class000

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

nameusersystemelapsed
GOLUB33.56 0.3733.94
fit000
loo000
nvalidate000
nvalidation-class000
plot000
predict.predictor-method000
prediction-class000
predictor-class000
summary.prediction-method000
validate000
validation-class000