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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 760/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
garfield 1.35.0  (landing page)
Valentina Iotchkova
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/garfield
git_branch: devel
git_last_commit: ff65122
git_last_commit_date: 2024-10-29 10:07:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


BUILD BIN results for garfield on lconway

To the developers/maintainers of the garfield package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/garfield.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: garfield
Version: 1.35.0
Command: rm -rf garfield.buildbin-libdir && mkdir garfield.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh garfield_1.35.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R garfield.buildbin-libdir
StartedAt: 2024-12-24 00:25:14 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 00:25:30 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 16.2 seconds
RetCode: 0
Status:   OK  
PackageFile: garfield_1.35.0.tgz
PackageFileSize: 391.5 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf garfield.buildbin-libdir && mkdir garfield.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh garfield_1.35.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R garfield.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=garfield.buildbin-libdir garfield_1.35.0.tar.gz'
>>>>>>> 

* installing *source* package ‘garfield’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c garfield_init.c -o garfield_init.o
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 garfield_perm.cpp -o garfield_perm.o
garfield_perm.cpp:306:74: warning: format specifies type 'char *' but the argument has type 'long' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                           ~~                                                          ^~~
                           %ld
garfield_perm.cpp:306:78: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                              ~~                                                           ^~~~~~
                              %d
garfield_perm.cpp:306:86: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                    ~~                                                             ^~~~~~~~~~~~~~~~~~~~~~
                                    %f
garfield_perm.cpp:306:27: warning: invalid conversion specifier '\x09' [-Wformat-invalid-specifier]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                      ~~^
garfield_perm.cpp:306:110: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                            ~~                                                                             ^~~~~~
                                            %d
garfield_perm.cpp:306:117: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat]
                Rprintf("\r%s/%s\t\t%s\%\t\t%s annotations/s\t\t Time remaining: %s s",j+1,nannot, 100.0 * (j+1) / nannot, nannot,1.0 * (nannot - (j+1)) / perms_per_sec   );
                                                                                 ~~                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                 %f
garfield_perm.cpp:356:16: warning: format specifies type 'char *' but the argument has type 'int' [-Wformat]
                Rprintf("%s",nannot);
                         ~~  ^~~~~~
                         %d
7 warnings 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 garfield_prep.cpp -o garfield_prep.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 garfield.so garfield_init.o garfield_perm.o garfield_prep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/garfield.buildbin-libdir/00LOCK-garfield/00new/garfield/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 (garfield)


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

>>>>>>> Paths before fix:
garfield.buildbin-libdir/garfield/libs/garfield.so:
	garfield.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)

>>>>>>> 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" "garfield.buildbin-libdir/garfield/libs/garfield.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" "garfield.buildbin-libdir/garfield/libs/garfield.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" "garfield.buildbin-libdir/garfield/libs/garfield.so"

>>>>>>> Paths after fix:
garfield.buildbin-libdir/garfield/libs/garfield.so:
	garfield.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)