Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages

This page was generated on 2024-03-08 16:41:47 -0500 (Fri, 08 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 655
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Package 28/118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.50.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-03-08 15:25:35 -0500 (Fri, 08 Mar 2024)
git_url: https://git.bioconductor.org/packages/biovizBase
git_branch: RELEASE_3_18
git_last_commit: c961633
git_last_commit_date: 2023-10-24 09:48:08 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  

INSTALL results for biovizBase on nebbiolo2


To the developers/maintainers of the biovizBase package:
- 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.

raw results


Summary

Package: biovizBase
Version: 1.50.0
Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL biovizBase
StartedAt: 2024-03-08 15:35:14 -0500 (Fri, 08 Mar 2024)
EndedAt: 2024-03-08 15:35:58 -0500 (Fri, 08 Mar 2024)
EllapsedTime: 44.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL biovizBase
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘biovizBase’ ...
** using staged installation
** libs
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
   57 |   if (strncmp(b, "BAI\1", 4))
      |               ^
      |               |
      |               Rbyte * {aka unsigned char *}
In file included from /home/hpages/bbs-3.18-bioc-R41/R/include/R_ext/RS.h:34,
                 from /home/hpages/bbs-3.18-bioc-R41/R/include/Rdefines.h:39,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:159:33: note: expected ‘const char *’ but argument is of type ‘Rbyte *’ {aka ‘unsigned char *’}
  159 | extern int strncmp (const char *__s1, const char *__s2, size_t __n)
      |                     ~~~~~~~~~~~~^~~~
gcc -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-biovizBase/00new/biovizBase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (biovizBase)