Problem installing S4Vectors on Mac Mini M1 Big Sur

Problem installing S4Vectors on Mac Mini M1 Big Sur

1

@fa8790fc

Last seen 1 day ago

United Kingdom

Enter the body of text here

When I try to install S4Vectors on R version 4.1.1 on a Mac M1 Mini I get the following errors.
Any thoughts as to what I am ding wrong?

Thanks

Richard


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

> BiocManager::install("S4Vectors")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.ma.imperial.ac.uk

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'S4Vectors'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘S4Vectors’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘S4Vectors’

trying URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/S4Vectors_0.30.2.tar.gz'
Content type 'application/x-gzip' length 666602 bytes (650 KB)
==================================================
downloaded 650 KB

gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c AEbufs.c -o AEbufs.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c DataFrame_class.c -o DataFrame_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Hits_class.c -o Hits_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c LLint_class.c -o LLint_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c List_class.c -o List_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Rle_class.c -o Rle_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Rle_utils.c -o Rle_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c SEXP_utils.c -o SEXP_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c SimpleList_class.c -o SimpleList_class.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c anyMissing.c -o anyMissing.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c character_utils.c -o character_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c eval_utils.c -o eval_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hash_utils.c -o hash_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c integer_utils.c -o integer_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c logical_utils.c -o logical_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c raw_utils.c -o raw_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c safe_arithm.c -o safe_arithm.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sort_utils.c -o sort_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c subsetting_utils.c -o subsetting_utils.o
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c vector_utils.c -o vector_utils.o
gcc-8 -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 S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Error: package or namespace load failed for ‘S4Vectors’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/richardfmott/Library/R/4.1/library/00LOCK-S4Vectors/00new/S4Vectors/libs/S4Vectors.so':
  dlopen(/Users/richardfmott/Library/R/4.1/library/00LOCK-S4Vectors/00new/S4Vectors/libs/S4Vectors.so, 6): no suitable image found.  Did find:
    /Users/richardfmott/Library/R/4.1/library/00LOCK-S4Vectors/00new/S4Vectors/libs/S4Vectors.so: mach-o, but wrong architecture
    /Users/richardfmott/Library/R/4.1/library/00LOCK-S4Vectors/00new/S4Vectors/libs/S4Vectors.so: mach-o, but wrong architecture
Error: loading failed
Execution halted


S4Vectors

• 81 views

@herve-pages-1542

Last seen 3 hours ago

Seattle, WA, United States

The question is: can you install any package at all that requires compilation? For example what happens if you do:

install.packages("tibble", type="source")

If that fails, then it’s more likely that your current setup is broken and maybe you will have more luck by asking on the R-SIG-Mac mailing list.

Cheers,

H.


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