Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 374/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cn.farms 1.48.0 (landing page) Andreas Mitterecker
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the cn.farms package: - 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. |
Package: cn.farms |
Version: 1.48.0 |
Command: rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cn.farms_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cn.farms.buildbin-libdir |
StartedAt: 2023-10-19 12:12:14 -0400 (Thu, 19 Oct 2023) |
EndedAt: 2023-10-19 12:13:40 -0400 (Thu, 19 Oct 2023) |
EllapsedTime: 86.7 seconds |
RetCode: 0 |
Status: OK |
PackageFile: cn.farms_1.48.0.tgz |
PackageFileSize: 2.466 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cn.farms_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cn.farms.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.48.0.tar.gz' >>>>>>> * installing *source* package ‘cn.farms’ ... ** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_cnfarms.c -o R_init_cnfarms.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c laplace.cpp -o laplace.o laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ laplace.cpp:364:36: note: uninitialized use occurs here double I2left=(-leftMy/leftSigma)*I1left+I0left; ^~~~~~ laplace.cpp:275:7: note: remove the 'if' if its condition is always true else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ laplace.cpp:275:10: warning: variable 'I1left' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~ laplace.cpp:364:36: note: uninitialized use occurs here double I2left=(-leftMy/leftSigma)*I1left+I0left; ^~~~~~ laplace.cpp:275:10: note: remove the '&&' if its condition is always true else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~ laplace.cpp:198:15: note: initialize the variable 'I1left' to silence this warning double I1left; ^ = 0.0 laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ laplace.cpp:365:39: note: uninitialized use occurs here double I2right=(-rightMy/rightSigma)*I1right+I0right; ^~~~~~~ laplace.cpp:275:7: note: remove the 'if' if its condition is always true else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ laplace.cpp:275:10: warning: variable 'I1right' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized] else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~ laplace.cpp:365:39: note: uninitialized use occurs here double I2right=(-rightMy/rightSigma)*I1right+I0right; ^~~~~~~ laplace.cpp:275:10: note: remove the '&&' if its condition is always true else if(argLeft >= 0.0 && argRight >= 0.0) { ^~~~~~~~~~~~~~~~~ laplace.cpp:199:16: note: initialize the variable 'I1right' to silence this warning double I1right; ^ = 0.0 laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable] int method=0; ^ laplace.cpp:23:11: warning: unused variable 'steps' [-Wunused-const-variable] const int steps=30; ^ laplace.cpp:26:14: warning: unused variable 'integrationFailureFactor' [-Wunused-const-variable] const double integrationFailureFactor=5.0; ^ laplace.cpp:27:14: warning: unused variable 'sigmaFactor' [-Wunused-const-variable] const double sigmaFactor=0.1; ^ laplace.cpp:30:14: warning: unused variable 'Pi' [-Wunused-const-variable] const double Pi=M_PI; ^ laplace.cpp:31:14: warning: unused variable 'E' [-Wunused-const-variable] const double E=M_E; ^ laplace.cpp:34:14: warning: unused variable 'sqrt3' [-Wunused-const-variable] const double sqrt3=1.7320508075688772935274463415058723669428052538104; ^ laplace.cpp:35:14: warning: unused variable 'sqrt2Pi' [-Wunused-const-variable] const double sqrt2Pi=2.5066282746310005024157652848110452530069867406099; ^ 12 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sparse_farms.c -o sparse_farms.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cn.farms.buildbin-libdir/00LOCK-cn.farms/00new/cn.farms/libs ** R ** demo ** 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 (cn.farms) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so >>>>>>> >>>>>>> Paths before fix: cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so: cn.farms.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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) /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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so" >>>>>>> Paths after fix: cn.farms.buildbin-libdir/cn.farms/libs/cn.farms.so: cn.farms.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)