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CHECK report for cancerclass on malbec1

This page was generated on 2020-08-07 11:18:41 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cancerclass PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 218/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cancerclass 1.33.0
Daniel Kosztyla
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/cancerclass
Branch: master
Last Commit: 9510177
Last Changed Date: 2020-04-27 14:29:45 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cancerclass
Version: 1.33.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cancerclass.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cancerclass_1.33.0.tar.gz
StartedAt: 2020-08-06 23:38:44 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:39:42 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 58.0 seconds
RetCode: 0
Status:  OK 
CheckDir: cancerclass.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cancerclass.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cancerclass_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/cancerclass.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.33.0’
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
GOLUB 23.46  0.232  23.758
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/cancerclass.Rcheck/00check.log’
for details.



Installation output

cancerclass.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL cancerclass
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘cancerclass’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c copa.c -o copa.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cor.c -o cor.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fc.c -o fc.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
             ^~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ort.c -o ort.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c os.c -o os.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c shift.c -o shift.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c statistics.c -o statistics.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c student.c -o student.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c throw.c -o throw.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c welch.c -o welch.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
        ^~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/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 -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-cancerclass/00new/cancerclass/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cancerclass)

Tests output


Example timings

cancerclass.Rcheck/cancerclass-Ex.timings

nameusersystemelapsed
GOLUB23.460 0.23223.758
fit000
loo000
nvalidate0.0000.0000.001
nvalidation-class0.0000.0000.001
plot000
predict.predictor-method000
prediction-class0.0000.0000.001
predictor-class0.0000.0000.001
summary.prediction-method000
validate000
validation-class0.0000.0000.001