Laurent Gatto
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/MSnbase |
| git_branch: devel |
| git_last_commit: 1d21d09 |
| git_last_commit_date: 2026-04-10 10:57:56 -0400 (Fri, 10 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1412/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSnbase 2.37.3 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for MSnbase in R Universe. | ||||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: MSnbase |
| Version: 2.37.3 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MSnbase |
| StartedAt: 2026-04-17 00:46:03 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 00:46:19 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 16.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MSnbase
###
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* 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 ‘2.37.3’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
8 | static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
9 | static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
92 | int i1, i2, ret;
| ^~~
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
107 | int i1, i2, ret;
| ^~~
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
123 | double d1, d2, ret;
| ^~~
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
133 | double d1, d2, ret;
| ^~~
utils.c: At top level:
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
131 | static int compar_double_desc_order(const void *p1, const void *p2)
| ^~~~~~~~~~~~~~~~~~~~~~~~
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
121 | static int compar_double_asc_order(const void *p1, const void *p2)
| ^~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpfSbSGP/Rinstdde631f01fe26/00LOCK-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: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
libnetcdf.so.19: cannot open shared object file: No such file or directory
Execution halted
ERROR: lazy loading failed for package ‘MSnbase’
* removing ‘/home/biocbuild/tmp/RtmpfSbSGP/Rinstdde631f01fe26/MSnbase’
-----------------------------------
ERROR: package installation failed