Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 271/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cancerclass 1.50.0 (landing page) Daniel Kosztyla
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: cancerclass |
Version: 1.50.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cancerclass.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cancerclass_1.50.0.tar.gz |
StartedAt: 2024-12-19 23:41:32 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:42:53 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 80.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cancerclass.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cancerclass.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cancerclass_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/cancerclass.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '1.50.0' * 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) 13.3.0' * 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 'F:/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 27.17 3.36 30.53 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/cancerclass.Rcheck/00check.log' for details.
cancerclass.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cancerclass ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'cancerclass' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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"F:/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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/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)
cancerclass.Rcheck/cancerclass-Ex.timings
name | user | system | elapsed | |
GOLUB | 27.17 | 3.36 | 30.53 | |
fit | 0 | 0 | 0 | |
loo | 0 | 0 | 0 | |
nvalidate | 0 | 0 | 0 | |
nvalidation-class | 0 | 0 | 0 | |
plot | 0 | 0 | 0 | |
predict.predictor-method | 0 | 0 | 0 | |
prediction-class | 0 | 0 | 0 | |
predictor-class | 0 | 0 | 0 | |
summary.prediction-method | 0 | 0 | 0 | |
validate | 0 | 0 | 0 | |
validation-class | 0 | 0 | 0 | |