Paul Theodor Pyl
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/h5vc |
| git_branch: devel |
| git_last_commit: 1ae9c98 |
| git_last_commit_date: 2025-04-15 10:27:35 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 955/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| h5vc 2.43.0 (landing page) Paul Theodor Pyl
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the h5vc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/h5vc.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: h5vc |
| Version: 2.43.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL h5vc |
| StartedAt: 2025-10-23 15:16:22 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 15:16:41 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 19.2 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL h5vc
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘h5vc’ ...
** this is package ‘h5vc’ version ‘2.43.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c bam_plbuf.c -o bam_plbuf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function ‘int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:47:7: warning: unused variable ‘len’ [-Wunused-variable]
47 | int len = nttable->end - nttable->beg;
| ^~~
tallyBAM.cpp: In function ‘int pileup_func(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’:
tallyBAM.cpp:96:7: warning: unused variable ‘len’ [-Wunused-variable]
96 | int len = nttable->end - nttable->beg;
| ^~~
tallyBAM.cpp: In function ‘int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)’:
tallyBAM.cpp:140:13: warning: unused variable ‘c’ [-Wunused-variable]
140 | int c = 0;
| ^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: ‘int pileup_func_old(uint32_t, hts_pos_t, int, const bam_pileup1_t*, void*)’ defined but not used [-Wunused-function]
43 | static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
| ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o h5vc.so bam_plbuf.o tallyBAM.o /home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-h5vc/00new/h5vc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘h5vc’
** testing if installed package keeps a record of temporary installation path
* DONE (h5vc)