Steffen Neumann
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/xcms |
| git_branch: RELEASE_3_19 |
| git_last_commit: c84c34c |
| git_last_commit_date: 2024-04-30 10:13:53 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:35 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 2284/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| xcms 4.2.0 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | NA | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: xcms |
| Version: 4.2.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL xcms |
| StartedAt: 2024-05-08 20:42:26 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:44:40 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 134.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL xcms
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘xcms’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
rm -f 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
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/Tracker.cpp -o massifquant/Tracker.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/SegProc.cpp -o massifquant/SegProc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c obiwarp/mat.cpp -o obiwarp/mat.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c obiwarp/vec.cpp -o obiwarp/vec.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -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"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c xcms_obiwarp.cpp -o xcms_obiwarp.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fastMatch.c -o fastMatch.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mzClust_hclust.c -o mzClust_hclust.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c mzROI.c -o mzROI.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c xcms.c -o xcms.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -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 -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o xcms.so 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 -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-xcms/00new/xcms/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xcms)