Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-21 12:06 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4819 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4597 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4539 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1364/2318 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSnbase 2.35.2 (landing page) Laurent Gatto
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the MSnbase package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.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: MSnbase |
Version: 2.35.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSnbase |
StartedAt: 2025-08-20 17:05:52 -0400 (Wed, 20 Aug 2025) |
EndedAt: 2025-08-20 17:05:57 -0400 (Wed, 20 Aug 2025) |
EllapsedTime: 5.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MSnbase ### ############################################################################## ############################################################################## * checking for file ‘MSnbase/DESCRIPTION’ ... OK * preparing ‘MSnbase’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘MSnbase’ ... ** this is package ‘MSnbase’ version ‘2.35.2’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Spectrum1_class.c -o Spectrum1_class.o Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function] static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Spectrum2_class.c -o Spectrum2_class.o Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function] static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt, ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable] int i1, i2, ret; ^ utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable] double d1, d2, ret; ^ utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function] static int compar_double_asc_order(const void *p1, const void *p2) ^ utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function] static int compar_double_desc_order(const void *p1, const void *p2) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R installing to /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHl5AZ5/Rinst139235e78c007/00LOCK-MSnbase/00new/MSnbase/libs ** R ** data *** moving datasets to lazyload DB Warning: namespace ‘MSnbase’ is not available and has been replaced by .GlobalEnv when processing object ‘itraqdata’ Warning: namespace ‘MSnbase’ is not available and has been replaced by .GlobalEnv when processing object ‘itraqdata’ ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘PSMatch’ 1.13.2 is being loaded, but >= 1.13.3 is required Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted ERROR: lazy loading failed for package ‘MSnbase’ * removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHl5AZ5/Rinst139235e78c007/MSnbase’ ----------------------------------- ERROR: package installation failed