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lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
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Installation failed on Apple Silicon Macbook & R 4.2.1 #579

Closed lingjuewang closed 1 year ago

lingjuewang commented 1 year ago

I encountered an error when installing MSnbase through BiocManager on my M1 Macbook. It seems that some of the dependent packages cannot be compiled on the arm64-based R 4.2.1, including affy, preprocessCore, vsn, impute.

Any comments would be greatly appreciated.

sessionInfo()

Platform: aarch64-apple-darwin20 (64-bit)` Running under: macOS Monterey 12.4 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager_1.30.18 compiler_4.2.1 tools_4.2.1

BiocManager::install("MSnbase")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Installing package(s) 'MSnbase' also installing the dependencies ‘preprocessCore’, ‘vsn’, ‘affy’, ‘impute’

Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘preprocessCore’ ‘vsn’ ‘affy’ ‘impute’ ‘MSnbase’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source packages ‘preprocessCore’, ‘vsn’, ‘affy’, ‘impute’, ‘MSnbase’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/preprocessCore_1.58.0.tar.gz' Content type 'application/x-gzip' length 123998 bytes (121 KB)

downloaded 121 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/vsn_3.64.0.tar.gz' Content type 'application/x-gzip' length 1837579 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/affy_1.74.0.tar.gz' Content type 'application/x-gzip' length 1214001 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/impute_1.70.0.tar.gz' Content type 'application/x-gzip' length 641570 bytes (626 KB)

downloaded 626 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/MSnbase_2.22.0.tar.gz' Content type 'application/x-gzip' length 5836500 bytes (5.6 MB)

downloaded 5.6 MB

  • installing source package ‘preprocessCore’ ... using staged installation 'config' variable 'CPP' is defunct checking for gcc... clang -arch arm64 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 arm64 accepts -g... yes checking for clang -arch arm64 option to accept ISO C89... none needed checking how to run the C preprocessor... clang -arch arm64 -E checking for library containing pthread_create... none required checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes checking if R is using flexiblas... flexiblas not found. preprocessCore threading will not be disabled configure: Enabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars libs clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_colSummarize.c -o R_colSummarize.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c:109:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:111:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:117:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:115:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:288:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:290:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:282:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:284:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:458:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:460:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:466:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:464:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:641:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:643:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:637:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:635:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:819:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:817:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:811:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:813:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:988:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:990:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:994:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:996:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1165:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:1169:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1171:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1163:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:1345:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1343:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1339:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:1337:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer; ^ R_subColSummarize.c:1518:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:1522:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1524:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1698:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subColSummarize.c:1696:30: warning: unused variable 'buffer2' [-Wunused-variable] double results, buffer, buffer2; ^ R_subColSummarize.c:1696:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer, buffer2; ^ R_subColSummarize.c:1702:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subColSummarize.c:1704:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subColSummarize.c:1660:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function] static void subColSummarize_medianpolish_group(void data){ ^ 41 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c:90:11: warning: unused variable 'weights' [-Wunused-variable] double weights; ^ R_subrcModel_interfaces.c:75:11: warning: unused variable 'buffer' [-Wunused-variable] double buffer, buffer2; ^ R_subrcModel_interfaces.c:75:20: warning: unused variable 'buffer2' [-Wunused-variable] double buffer, buffer2; ^ R_subrcModel_interfaces.c:91:11: warning: unused variable 'se' [-Wunused-variable] double se; ^ R_subrcModel_interfaces.c:171:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subrcModel_interfaces.c:167:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subrcModel_interfaces.c:165:30: warning: unused variable 'buffer2' [-Wunused-variable] double results, buffer, buffer2; ^ R_subrcModel_interfaces.c:165:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer, buffer2; ^ R_subrcModel_interfaces.c:165:11: warning: unused variable 'results' [-Wunused-variable] double results, buffer, buffer2; ^ R_subrcModel_interfaces.c:173:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subrcModel_interfaces.c:377:20: warning: unused variable 'buffer2' [-Wunused-variable] double buffer, buffer2; ^ R_subrcModel_interfaces.c:377:11: warning: unused variable 'buffer' [-Wunused-variable] double buffer, buffer2; ^ R_subrcModel_interfaces.c:398:10: warning: unused variable 'scale' [-Wunused-variable] double scale=-1.0; ^ R_subrcModel_interfaces.c:487:8: warning: unused variable 'cur_rows' [-Wunused-variable] int cur_rows; ^ R_subrcModel_interfaces.c:491:7: warning: unused variable 'ncur_rows' [-Wunused-variable] int ncur_rows; ^ R_subrcModel_interfaces.c:493:9: warning: unused variable 'j' [-Wunused-variable] int i,j; ^ R_subrcModel_interfaces.c:485:11: warning: unused variable 'results' [-Wunused-variable] double results, buffer, buffer2; ^ R_subrcModel_interfaces.c:485:21: warning: unused variable 'buffer' [-Wunused-variable] double results, buffer, buffer2; ^ R_subrcModel_interfaces.c:485:30: warning: unused variable 'buffer2' [-Wunused-variable] double results, buffer, buffer2; ^ 19 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c avg.c -o avg.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c avg_log.c -o avg_log.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c biweight.c -o biweight.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c lm.c -o lm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c log_avg.c -o log_avg.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c log_median.c -o log_median.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c median.c -o median.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c median_log.c -o median_log.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c medianpolish.c -o medianpolish.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c plmd.c -o plmd.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c plmr.c -o plmr.o plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function] static void XTWY_R(int rows, int cols, double out_weights, double y,double xtwy){ ^ plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function] static void XTWX_R(int rows, int cols, double out_weights, double xtwx){ ^ plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function] static void XTWX_R_inv(int rows, int cols, double xtwx){ ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c psi_fns.c -o psi_fns.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c qnorm.c -o qnorm.o qnorm.c:1905:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:1910:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2102:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (isMatrix(target)){ ^~~~ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:937:19: note: expanded from macro 'isMatrix'

    define isMatrix Rf_isMatrix

                            ^

    qnorm.c:2115:55: note: uninitialized use occurs here qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); ^~~ qnorm.c:2102:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~ qnorm.c:2083:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 qnorm.c:2504:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,row_mean_ind; ^ qnorm.c:2509:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na; ^ qnorm.c:2823:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double sample_percentiles; ^ qnorm.c:2824:11: warning: unused variable 'datvec' [-Wunused-variable] double datvec; ^ qnorm.c:2957:12: warning: unused variable 'j' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2957:14: warning: unused variable 'ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2957:18: warning: unused variable 'target_ind' [-Wunused-variable] size_t i,j,ind,target_ind; ^ qnorm.c:2959:14: warning: unused variable 'dimat' [-Wunused-variable] dataitem *dimat; ^ qnorm.c:2961:11: warning: unused variable 'row_mean' [-Wunused-variable] double row_mean = target; ^ qnorm.c:2963:11: warning: unused variable 'ranks' [-Wunused-variable] double ranks = (double )Calloc((rows),double); ^ qnorm.c:2964:10: warning: unused variable 'samplepercentile' [-Wunused-variable] double samplepercentile; ^ qnorm.c:2965:10: warning: unused variable 'target_ind_double' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2965:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] double target_ind_double,target_ind_double_floor; ^ qnorm.c:2967:7: warning: unused variable 'targetnon_na' [-Wunused-variable] int targetnon_na = targetrows; ^ qnorm.c:2968:7: warning: unused variable 'non_na' [-Wunused-variable] int non_na = 0; ^ qnorm.c:2972:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] double sample_percentiles; ^ qnorm.c:2973:11: warning: unused variable 'datvec' [-Wunused-variable] double datvec; ^ qnorm.c:3228:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] } else if (isMatrix(target)){ ^~~~ /Library/Frameworks/R.framework/Resources/include/Rinternals.h:937:19: note: expanded from macro 'isMatrix'

    define isMatrix Rf_isMatrix

                            ^

    qnorm.c:3242:77: note: uninitialized use occurs here qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); ^~~ qnorm.c:3228:10: note: remove the 'if' if its condition is always true } else if (isMatrix(target)){ ^~~~~ qnorm.c:3209:21: note: initialize the variable 'target_rows' to silence this warning size_t target_rows, target_cols; ^ = 0 21 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm.c -o rlm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_anova.c -o rlm_anova.o rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable] double endprobe; ^ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] double scale=0.0; ^ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] double Kappa=0.0; / A correction factor / ^ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] double sumpsi2=0.0; / sum of psi(r_i)^2 / ^ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] double sumderivpsi=0.0; / sum of psi'(r_i) / ^ rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] double k1 = psi_k; / was 1.345; / ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] double vs=0.0,m,varderivpsi=0.0; ^ rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable] double endprobe; ^ 10 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_se.c -o rlm_se.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rma_background4.c -o rma_background4.o rma_background4.c:355:10: warning: unused variable 'param' [-Wunused-variable] double param[3]; ^ rma_background4.c:354:10: warning: unused variable 'j' [-Wunused-variable] size_t j; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -falign-functions=64 -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o 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 preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [preprocessCore.so] Error 1 ERROR: compilation failed for package ‘preprocessCore’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore’
  • installing source package ‘impute’ ... using staged installation libs /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c knnimpute.f -o knnimpute.o make: /opt/R/arm64/bin/gfortran: No such file or directory make: *** [knnimpute.o] Error 1 ERROR: compilation failed for package ‘impute’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/impute’ ERROR: dependency ‘preprocessCore’ is not available for package ‘affy’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/affy’ ERROR: dependency ‘affy’ is not available for package ‘vsn’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/vsn’ ERROR: dependencies ‘vsn’, ‘affy’, ‘impute’ are not available for package ‘MSnbase’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/MSnbase’

The downloaded source packages are in ‘/private/var/folders/r1/xp0tdv954nq3mvxlcy0p9cdh0000gn/T/RtmpeYyCbt/downloaded_packages’ Warning messages: 1: In install.packages(...) : installation of package ‘preprocessCore’ had non-zero exit status 2: In install.packages(...) : installation of package ‘impute’ had non-zero exit status 3: In install.packages(...) : installation of package ‘affy’ had non-zero exit status 4: In install.packages(...) : installation of package ‘vsn’ had non-zero exit status 5: In install.packages(...) : installation of package ‘MSnbase’ had non-zero exit status

lgatto commented 1 year ago

There have been discussions about the Apple M1 chip, but I haven't followed them closely as I don't have a Mac. May be @jorainer can help. Otherwise, you could also ask on bioc-devel or the support forum.

lingjuewang commented 1 year ago

Thank you @lgatto for prompt reply! On latest Bioconductor 3.15 release notes, I realized the arm64-based R version is not supported yet.

"We do not currently support arm64 so arm64 Mac users who wish to install Bioconductor Mac binary packages must install the Intel 64-bit build of R available on CRAN."

Bioconductor 3.15 released

After re-installing the intel-based version of R, the issue is fixed. It should be good now.