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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 220/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiRewire 3.39.0  (landing page)
Andrea Gobbi
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/BiRewire
git_branch: devel
git_last_commit: 8cf10d9
git_last_commit_date: 2024-10-29 09:48:11 -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 BiRewire on lconway

To the developers/maintainers of the BiRewire package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiRewire.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: BiRewire
Version: 3.39.0
Command: rm -rf BiRewire.buildbin-libdir && mkdir BiRewire.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiRewire_3.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiRewire.buildbin-libdir
StartedAt: 2024-12-24 00:15:35 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 00:15:50 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 15.0 seconds
RetCode: 0
Status:   OK  
PackageFile: BiRewire_3.39.0.tgz
PackageFileSize: 738.9 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiRewire.buildbin-libdir && mkdir BiRewire.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiRewire_3.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiRewire.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiRewire.buildbin-libdir BiRewire_3.39.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BiRewire’ ...
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BiRewire.c -o BiRewire.o
BiRewire.c:149:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:221:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:229:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:280:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:332:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:339:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:402:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:454:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:461:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:588:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:652:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:737:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:844:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:893:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:962:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:1096:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
BiRewire.c:1144:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                                 ~~             ^~~~~~~~~~~
                                                 %ld
BiRewire.c:1183:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
                Rprintf("DONE in %d seconds \n",-(tin-tfin));
                                 ~~             ^~~~~~~~~~~
                                 %ld
18 warnings generated.
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 interface.c -o interface.o
interface.c:105:68: warning: data argument not used by format string [-Wformat-extra-args]
                warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:900:20: note: expanded from macro 'asInteger'
#define asInteger               Rf_asInteger
                                ^
interface.c:147:68: warning: data argument not used by format string [-Wformat-extra-args]
                warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:900:20: note: expanded from macro 'asInteger'
#define asInteger               Rf_asInteger
                                ^
interface.c:252:68: warning: data argument not used by format string [-Wformat-extra-args]
                warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:900:20: note: expanded from macro 'asInteger'
#define asInteger               Rf_asInteger
                                ^
interface.c:296:68: warning: data argument not used by format string [-Wformat-extra-args]
                warning("Reached the maximum number admissible of iterations!\n",asInteger(MAXITER));
                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:900:20: note: expanded from macro 'asInteger'
#define asInteger               Rf_asInteger
                                ^
4 warnings generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BiRewire.so BiRewire.o interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/BiRewire.buildbin-libdir/00LOCK-BiRewire/00new/BiRewire/libs
** R
** data
** 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 (BiRewire)


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

>>>>>>> Paths before fix:
BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so:
	BiRewire.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/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" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.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" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.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" "BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so"

>>>>>>> Paths after fix:
BiRewire.buildbin-libdir/BiRewire/libs/BiRewire.so:
	BiRewire.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)