Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (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 1308/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.26.0  (landing page)
Laurent Gatto
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: RELEASE_3_17
git_last_commit: 3e6268a
git_last_commit_date: 2023-04-25 10:19:06 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

BUILD BIN results for MSnbase on kjohnson2


To the developers/maintainers of the MSnbase 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.

raw results


Summary

Package: MSnbase
Version: 2.26.0
Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MSnbase_2.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R MSnbase.buildbin-libdir
StartedAt: 2023-10-19 15:12:26 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 15:14:40 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 134.0 seconds
RetCode: 0
Status:   OK  
PackageFile: MSnbase_2.26.0.tgz
PackageFileSize: 8.197 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MSnbase_2.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R MSnbase.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MSnbase.buildbin-libdir MSnbase_2.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘MSnbase’ ...
** 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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: unused function '_new_Spectrum1' [-Wunused-function]
static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: unused function '_new_Spectrum2' [-Wunused-function]
static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
utils.c:92:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:107:15: warning: unused variable 'ret' [-Wunused-variable]
  int i1, i2, ret;
              ^
utils.c:123:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:133:18: warning: unused variable 'ret' [-Wunused-variable]
  double d1, d2, ret;
                 ^
utils.c:121:12: warning: unused function 'compar_double_asc_order' [-Wunused-function]
static int compar_double_asc_order(const void *p1, const void *p2)
           ^
utils.c:131:12: warning: unused function 'compar_double_desc_order' [-Wunused-function]
static int compar_double_desc_order(const void *p1, const void *p2)
           ^
6 warnings generated.
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 MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSnbase.buildbin-libdir/00LOCK-MSnbase/00new/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp”
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
in method for ‘plotMzDelta’ with signature ‘"mzRramp"’: no definition for class “mzRramp”
** 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 (MSnbase)


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

>>>>>>> Paths before fix:
MSnbase.buildbin-libdir/MSnbase/libs/MSnbase.so:
	MSnbase.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" "MSnbase.buildbin-libdir/MSnbase/libs/MSnbase.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "MSnbase.buildbin-libdir/MSnbase/libs/MSnbase.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "MSnbase.buildbin-libdir/MSnbase/libs/MSnbase.so"

>>>>>>> Paths after fix:

MSnbase.buildbin-libdir/MSnbase/libs/MSnbase.so:
	MSnbase.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)