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This page was generated on 2023-04-12 11:05:26 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD BIN results for biovizBase on palomino4


To the developers/maintainers of the biovizBase package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biovizBase.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 204/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.46.0  (landing page)
Michael Lawrence
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/biovizBase
git_branch: RELEASE_3_16
git_last_commit: a47060c
git_last_commit_date: 2022-11-01 11:06:19 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: biovizBase
Version: 1.46.0
Command: rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=biovizBase.buildbin-libdir biovizBase_1.46.0.tar.gz
StartedAt: 2023-04-11 07:38:37 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 07:39:41 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 63.8 seconds
RetCode: 0
Status:   OK  
PackageFile: biovizBase_1.46.0.zip
PackageFileSize: 2.569 MiB

Command output

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###
### Running command:
###
###   rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=biovizBase.buildbin-libdir biovizBase_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'biovizBase' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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 F:/biocbuild/bbs-3.16-bioc/R/include/R_ext/RS.h:34,
                 from F:/biocbuild/bbs-3.16-bioc/R/include/Rdefines.h:38,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
c:\rtools42\x86_64-w64-mingw32.static.posix\include\string.h:86:35: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'}
   86 |   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
      |                       ~~~~~~~~~~~~^~~~~
gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/biovizBase.buildbin-libdir/00LOCK-biovizBase/00new/biovizBase/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.46.0.zip
* DONE (biovizBase)