Dario Strbenac
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_17 |
| git_last_commit: 528fd78 |
| git_last_commit_date: 2023-09-20 20:30:08 -0400 (Wed, 20 Sep 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -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 351/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 3.4.11 (landing page) Dario Strbenac
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the ClassifyR 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: ClassifyR |
| Version: 3.4.11 |
| Command: rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ClassifyR_3.4.11.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ClassifyR.buildbin-libdir |
| StartedAt: 2023-10-19 12:08:12 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 12:09:44 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 91.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: ClassifyR_3.4.11.tgz |
| PackageFileSize: 2.49 MiB |
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### Running command:
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### rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ClassifyR_3.4.11.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ClassifyR.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_3.4.11.tar.gz'
>>>>>>>
* installing *source* package ‘ClassifyR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable]
double sclback2=*sctest2;
^
coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable]
double sclback3=*sctest3;
^
coxformatrices.cpp:81:9: warning: suggest braces around initialization of subobject [-Wmissing-braces]
NULL
^~~~
{ }
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL'
# define NULL __null
^~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j;
^~~~~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j;
^~~~~~~~~
coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double temp;
^~~~~~~~~
coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double temp;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i;
^~~~~~~~~
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double **pointer;
^~~~~~~~~
12 warnings generated.
clang++ -arch arm64 -std=gnu++11 -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 ClassifyR.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ClassifyR.buildbin-libdir/00LOCK-ClassifyR/00new/ClassifyR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘ROCplot’ with signature ‘"ClassifyResult"’: no definition for class “ClassifyResult”
** help
*** installing help indices
*** copying figures
** 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 (ClassifyR)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so
>>>>>>>
>>>>>>> Paths before fix:
ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so:
ClassifyR.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" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
>>>>>>> Paths after fix:
ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so:
ClassifyR.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)