Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 266/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cancerclass 1.49.0  (landing page)
Daniel Kosztyla
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/cancerclass
git_branch: devel
git_last_commit: e945e63
git_last_commit_date: 2024-04-30 10:27:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for cancerclass on palomino6

To the developers/maintainers of the cancerclass package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cancerclass.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cancerclass
Version: 1.49.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cancerclass.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cancerclass_1.49.0.tar.gz
StartedAt: 2024-07-15 22:23:55 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:24:59 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 64.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cancerclass.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cancerclass.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cancerclass_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/cancerclass.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cancerclass/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cancerclass' version '1.49.0'
* 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
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) predictor-class.Rd:25: Lost braces
    25 |   \code{plot}{A plot method is only avaiable for the score "zeta" that is a linear combination of features.} 
       |              ^
* 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 ... NOTE
Objects in \usage without \alias in Rd file 'cancerclass-internal.Rd':
  '.onLoad' '.initFoo'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/cancerclass/libs/x64/cancerclass.dll':
  Found '_exit', possibly from '_exit' (C)
  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 use Fortran I/O
nor system RNGs nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
GOLUB 21.87   2.92   24.69
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/cancerclass.Rcheck/00check.log'
for details.


Installation output

cancerclass.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cancerclass
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'cancerclass' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c copa.c -o copa.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cor.c -o cor.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fc.c -o fc.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
  263 |     double mean1, mean2, var1, var2 = 0.0;
      |                   ^~~~~
help.c:263:12: warning: variable 'mean1' set but not used [-Wunused-but-set-variable]
  263 |     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]
  344 |     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]
  368 |     int i,k,anzahl=0;
      |             ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ort.c -o ort.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c os.c -o os.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c shift.c -o shift.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c statistics.c -o statistics.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c student.c -o student.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c throw.c -o throw.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c welch.c -o welch.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   37 |    int overall = 0;
      |        ^~~~~~~
wilcox.c: In function 'pwilcoxon':
wilcox.c:75:8: warning: variable 'overall' set but not used [-Wunused-but-set-variable]
   75 |    int overall = 0;
      |        ^~~~~~~
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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-cancerclass/00new/cancerclass/libs/x64
** 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
** 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
GOLUB21.87 2.9224.69
fit000
loo000
nvalidate000
nvalidation-class000
plot000
predict.predictor-method000
prediction-class000
predictor-class000
summary.prediction-method000
validate000
validation-class000