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This page was generated on 2025-01-28 11:43 -0500 (Tue, 28 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4659
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4454
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4465
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4419
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4409
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 270/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CardinalIO 1.5.0  (landing page)
Kylie Ariel Bemis
Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025)
git_url: https://git.bioconductor.org/packages/CardinalIO
git_branch: devel
git_last_commit: 60442d0
git_last_commit_date: 2024-10-29 11:22:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

BUILD BIN results for CardinalIO on lconway

To the developers/maintainers of the CardinalIO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CardinalIO.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.

raw results


Summary

Package: CardinalIO
Version: 1.5.0
Command: rm -rf CardinalIO.buildbin-libdir && mkdir CardinalIO.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CardinalIO_1.5.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CardinalIO.buildbin-libdir
StartedAt: 2025-01-28 00:00:35 -0500 (Tue, 28 Jan 2025)
EndedAt: 2025-01-28 00:00:59 -0500 (Tue, 28 Jan 2025)
EllapsedTime: 24.3 seconds
RetCode: 0
Status:   OK  
PackageFile: CardinalIO_1.5.0.tgz
PackageFileSize: 1.247 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CardinalIO.buildbin-libdir && mkdir CardinalIO.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CardinalIO_1.5.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CardinalIO.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CardinalIO.buildbin-libdir CardinalIO_1.5.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CardinalIO’ ...
** this is package ‘CardinalIO’ version ‘1.5.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c CardinalIO.cpp -o CardinalIO.o
In file included from CardinalIO.cpp:2:
In file included from ./CardinalIO.h:5:
./imzML.h:5:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c init.cpp -o init.o
In file included from init.cpp:3:
In file included from ./CardinalIO.h:5:
./imzML.h:5:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c pugixml.cpp -o pugixml.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CardinalIO.so CardinalIO.o init.o pugixml.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/CardinalIO.buildbin-libdir/00LOCK-CardinalIO/00new/CardinalIO/libs
** R
** 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 (CardinalIO)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so
>>>>>>> 

>>>>>>> Paths before fix:
CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so:
	CardinalIO.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so"

>>>>>>> Paths after fix:
CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so:
	CardinalIO.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)