Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 932/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
h5vc 2.40.0 (landing page) Paul Theodor Pyl
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 2.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL h5vc |
StartedAt: 2024-12-19 15:24:10 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 15:24:28 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 17.9 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL h5vc ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘h5vc’ ... ** 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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -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-3.20-bioc/R/lib -L/usr/local/lib -o h5vc.so bam_plbuf.o tallyBAM.o /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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)