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This page was generated on 2024-11-05 12:07 -0500 (Tue, 05 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4503
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1409/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NetPathMiner 1.42.0  (landing page)
Ahmed Mohamed
Snapshot Date: 2024-11-04 13:40 -0500 (Mon, 04 Nov 2024)
git_url: https://git.bioconductor.org/packages/NetPathMiner
git_branch: RELEASE_3_20
git_last_commit: 97bf773
git_last_commit_date: 2024-10-29 11:34:22 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


BUILD BIN results for NetPathMiner on lconway

To the developers/maintainers of the NetPathMiner package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetPathMiner.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: NetPathMiner
Version: 1.42.0
Command: rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NetPathMiner.buildbin-libdir
StartedAt: 2024-11-05 05:05:55 -0500 (Tue, 05 Nov 2024)
EndedAt: 2024-11-05 05:06:27 -0500 (Tue, 05 Nov 2024)
EllapsedTime: 32.0 seconds
RetCode: 0
Status:   OK  
PackageFile: NetPathMiner_1.42.0.tgz
PackageFileSize: 2.607 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf NetPathMiner.buildbin-libdir && mkdir NetPathMiner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh NetPathMiner_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R NetPathMiner.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=NetPathMiner.buildbin-libdir NetPathMiner_1.42.0.tar.gz'
>>>>>>> 

* installing *source* package ‘NetPathMiner’ ...
** using staged installation
restoring Makevars.in file...
mv: _Makevars.in_: No such file or directory
rm: Makevars: No such file or directory
removing compiled code...
rm: *.o: No such file or directory
'config' variable 'CPP' is defunct
checking for gcc... clang -arch x86_64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** 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 -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c kgml_interface.cpp -o kgml_interface.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c methods.cpp -o methods.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sbml_interface.cpp -o sbml_interface.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 NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.buildbin-libdir/00LOCK-NetPathMiner/00new/NetPathMiner/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 (NetPathMiner)


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

>>>>>>> Paths before fix:
NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so:
	NetPathMiner.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so"

>>>>>>> Paths after fix:
NetPathMiner.buildbin-libdir/NetPathMiner/libs/NetPathMiner.so:
	NetPathMiner.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 66.1.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)