Problem installing S4Vectors on Mac Mini M1 Big Sur
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Richard • 0
@fa8790fc
Last seen 4 weeks 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 • 295 views
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I think it's still the case that Bioconductor doesn't support the native M1 version of R and it's recommended you run the Intel vesion via Rosetta (problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0)

Without an M1 Mac myself to test on I'll admit to being a bit behind with what the "default" R for M1 is and what the error messages look like if you end up mixing architectures, but "mach-o, but wrong architecture" makes me strongly suspect you're compiling S4Vectors for one architecture and running on the other. It might help if you provide the output of sessionInfo() which presumably says which architecture your R was built for.

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Thanks Mike. Here is the information you requested:

R.version _
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 1.1
year 2021
month 08
day 10
svn rev 80725
language R
version.string R version 4.1.1 (2021-08-10) nickname Kick Things
sessionInfo() R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.6

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

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_1.30.16 compiler_4.1.1 tools_4.1.1

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@herve-pages-1542
Last seen 3 days 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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Richard • 0
@fa8790fc
Last seen 4 weeks ago
United Kingdom

I should add things were fine until I upgraded to R 4.1

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You have not answered Hervé's question about whether there are also problems installing other packages from source. That information would definitely help identify whether this a general problem with your setup or S4Vectors specifically.

From what you've said it seems likely that installing the Intel version of R-4.1.1 from https://cran.r-project.org/bin/macosx/ and running that with Rosetta will help. Then you'll be able to use the binary packages provided by Bioconductor and avoid having to install things from source.

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I have found other package installation fail as well. Sorry - I had answered Herve's question but it disappeared ! I may have to do as you suggest and use Rosetta. Annoyingly, I can't downgrade the installation to 3.6

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