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 12:05 -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 1196/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
messina 1.42.0 (landing page) Mark Pinese
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the messina package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/messina.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: messina |
Version: 1.42.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:messina.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings messina_1.42.0.tar.gz |
StartedAt: 2024-12-20 03:13:44 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:17:21 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 217.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: messina.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:messina.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings messina_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/messina.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 'messina/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'messina' version '1.42.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: 'doMC' * 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 'messina' can be installed ... WARNING Found the following significant warnings: crossval.cpp:229:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:230:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:231:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:238:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:239:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:240:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:246:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:247:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:248:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:254:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:255:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:256:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:268:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:269:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] crossval.cpp:270:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] messinaExtern.cpp:138:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] messinaExtern.cpp:139:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] messinaExtern.cpp:86:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] messinaExtern.cpp:92:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] See 'F:/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE messina: no visible binding for global variable 'Biobase' messinaSurv: no visible binding for global variable 'Biobase' Undefined global functions or variables: Biobase * 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/messina/libs/x64/messina.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (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 plot-MessinaSurvResult-missing-method 65.23 4.39 69.67 messinaSurv 48.91 4.56 53.50 * 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: 1 WARNING, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00check.log' for details.
messina.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL messina ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'messina' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Classifier.cpp -o Classifier.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Data.cpp -o Data.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c crossval.cpp -o crossval.o crossval.cpp: In function 'STATUS CrossVal::cv(int32_t, uint16_t, Classifier&, Result*, bool, bool)': crossval.cpp:229:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 229 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from 'void* operator new [](std::size_t)' 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:230:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 230 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from 'void* operator new [](std::size_t)' 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:231:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 231 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from 'void* operator new [](std::size_t)' 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:238:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 238 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from 'void* operator new [](std::size_t)' 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:239:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 239 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from 'void* operator new [](std::size_t)' 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:240:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 240 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from 'void* operator new [](std::size_t)' 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:246:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 246 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from 'void* operator new [](std::size_t)' 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:247:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 247 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from 'void* operator new [](std::size_t)' 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:248:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 248 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from 'void* operator new [](std::size_t)' 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:254:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 254 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from 'void* operator new [](std::size_t)' 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:255:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 255 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from 'void* operator new [](std::size_t)' 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:256:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 256 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from 'void* operator new [](std::size_t)' 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ crossval.cpp:268:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 268 | delete train_indices; | ^~~~~~~~~~~~~ crossval.cpp:184:52: note: returned from 'void* operator new [](std::size_t)' 184 | if ((train_indices = new int32_t[train_size]) == NULL) | ^ crossval.cpp:269:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 269 | delete test_indices; | ^~~~~~~~~~~~ crossval.cpp:187:50: note: returned from 'void* operator new [](std::size_t)' 187 | if ((test_indices = new int32_t[test_size]) == NULL) | ^ crossval.cpp:270:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 270 | delete in_test_set; | ^~~~~~~~~~~ crossval.cpp:193:44: note: returned from 'void* operator new [](std::size_t)' 193 | if ((in_test_set = new bool[n_samps]) == NULL) | ^ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c errors.cpp -o errors.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c messinaExtern.cpp -o messinaExtern.o messinaExtern.cpp: In function 'STATUS convertRMatrix2Data(Rcpp::NumericMatrix&, Rcpp::LogicalVector&, Data&)': messinaExtern.cpp:138:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 138 | delete exprs_array; | ^~~~~~~~~~~ messinaExtern.cpp:115:61: note: returned from 'void* operator new [](std::size_t)' 115 | if ((exprs_array = new uint16_t[n_probes * n_samples]) == NULL) | ^ messinaExtern.cpp:139:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 139 | delete class_array; | ^~~~~~~~~~~ messinaExtern.cpp:119:46: note: returned from 'void* operator new [](std::size_t)' 119 | if ((class_array = new bool[n_samples]) == NULL) | ^ messinaExtern.cpp: In function 'Rcpp::List messinaC(Rcpp::NumericMatrix, Rcpp::LogicalVector, uint32_t, uint32_t, float, float, bool, bool)': messinaExtern.cpp:86:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 86 | delete results; | ^~~~~~~ messinaExtern.cpp:78:51: note: returned from 'void* operator new [](std::size_t)' 78 | if ((results = new Result[data.getNGenes()]) == NULL) | ^ messinaExtern.cpp:92:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 92 | delete results; | ^~~~~~~ messinaExtern.cpp:78:51: note: returned from 'void* operator new [](std::size_t)' 78 | if ((results = new Result[data.getNGenes()]) == NULL) | ^ g++ -std=gnu++17 -shared -s -static-libgcc -o messina.dll tmp.def Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.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-messina/00new/messina/libs/x64 ** R ** data ** inst ** 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 (messina)
messina.Rcheck/messina-Ex.timings
name | user | system | elapsed | |
messina | 1.47 | 0.04 | 1.61 | |
messinaDE | 1.73 | 0.05 | 1.78 | |
messinaSurv | 48.91 | 4.56 | 53.50 | |
messinaTopResults | 0.95 | 0.07 | 1.01 | |
plot-MessinaClassResult-missing-method | 2.00 | 0.04 | 2.05 | |
plot-MessinaSurvResult-missing-method | 65.23 | 4.39 | 69.67 | |