A. MacNamara
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CNORdt |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8b16c2d |
| git_last_commit_date: 2023-04-25 10:24:21 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 378/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNORdt 1.42.0 (landing page) A. MacNamara
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the CNORdt 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: CNORdt |
| Version: 1.42.0 |
| Command: rm -rf CNORdt.buildbin-libdir && mkdir CNORdt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORdt_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORdt.buildbin-libdir |
| StartedAt: 2023-10-19 12:13:04 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 12:13:25 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 21.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CNORdt_1.42.0.tgz |
| PackageFileSize: 325.5 KiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CNORdt.buildbin-libdir && mkdir CNORdt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNORdt_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CNORdt.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNORdt.buildbin-libdir CNORdt_1.42.0.tar.gz'
>>>>>>>
* installing *source* package ‘CNORdt’ ...
** 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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c simulatorDT.c -o simulatorDT.o
simulatorDT.c:243:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((track_cond == nCond)) {
~~~~~~~~~~~^~~~~~~~
simulatorDT.c:243:19: note: remove extraneous parentheses around the comparison to silence this warning
if((track_cond == nCond)) {
~ ^ ~
simulatorDT.c:243:19: note: use '=' to turn this equality comparison into an assignment
if((track_cond == nCond)) {
^~
=
simulatorDT.c:53:6: warning: unused variable 'nSignals' [-Wunused-variable]
int nSignals = INTEGER(nSignals_in)[0];
^
simulatorDT.c:55:6: warning: unused variable 'nTimes' [-Wunused-variable]
int nTimes = INTEGER(nTimes_in)[0];
^
3 warnings generated.
clang -arch arm64 -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 CNORdt.so simulatorDT.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CNORdt.buildbin-libdir/00LOCK-CNORdt/00new/CNORdt/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 (CNORdt)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so
>>>>>>>
>>>>>>> Paths before fix:
CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so:
CNORdt.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/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" "CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so"
>>>>>>> Paths after fix:
CNORdt.buildbin-libdir/CNORdt/libs/CNORdt.so:
CNORdt.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)