Steffen Neumann
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/xcms |
| git_branch: devel |
| git_last_commit: 24473768 |
| git_last_commit_date: 2025-06-10 04:50:21 -0400 (Tue, 10 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 2299/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 4.7.2 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the xcms package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/xcms.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: xcms |
| Version: 4.7.2 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL xcms |
| StartedAt: 2025-08-14 16:28:15 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 16:33:10 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 294.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL xcms
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'xcms' ...
** this is package 'xcms' version '4.7.2'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
obiwarp/xcms_dynprog.cpp: In member function 'void DynProg::find_path(VEC::MatF&, VEC::VecF&, int, float, float, int, float)':
obiwarp/xcms_dynprog.cpp:1113:9: warning: variable 'bestscore' set but not used [-Wunused-but-set-variable]
1113 | float bestscore;
| ^~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c fastMatch.c -o fastMatch.o
fastMatch.c: In function 'fastMatch':
fastMatch.c:32:72: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
32 | Rf_error("fastMatch/calloc: memory could not be allocated ! (%lu bytes)\n", nx * sizeof(struct idxStruct) );
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llu
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c mzROI.c -o mzROI.o
mzROI.c: In function 'checkmzROIBufSize':
mzROI.c:79:80: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
79 | Rf_error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct) );
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int long long unsigned int
| %llu
mzROI.c: In function 'checkmzvalBufSize':
mzROI.c:102:78: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
102 | Rf_error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int long long unsigned int
| %llu
mzROI.c: In function 'cleanup':
mzROI.c:331:78: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
331 | Rf_error("findmzROI/cleanup: buffer memory could not be allocated ! (%lu bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int long long unsigned int
| %llu
mzROI.c: In function 'findmzROI':
mzROI.c:629:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
629 | Rf_error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",ROI_INIT_LENGTH * sizeof(struct mzROIStruct) );
| ~~^
| |
| long unsigned int
| %llu
mzROI.c:633:77: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
633 | Rf_error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",MZVAL_INIT_LENGTH * sizeof(struct mzROIStruct) );
| ~~^
| |
| long unsigned int
| %llu
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c util.c -o util.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c xcms.c -o xcms.o
gcc -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign -fno-inline -c binners.c -o binners.o
binners.c: In function '_breaks_on_binSize':
binners.c:357:7: warning: unused variable 'idx' [-Wunused-variable]
357 | int idx = 0;
| ^~~
g++ -std=gnu++17 -shared -s -static-libgcc -o xcms.dll tmp.def massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o binners.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-xcms/00new/xcms/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'group' in package 'xcms'
Creating a new generic function for 'sigma' in package 'xcms'
** help
*** installing help indices
*** copying figures
** 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 (xcms)