Unable to install "scruff" with BiocManager::install()
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Jackson • 0
@1d0e347e
Last seen 18 months ago
United States

I am running into an error trying to install "scruff" with BiocManager::install(). I have a new M1 Max Macbook running macOS Monterey. Perhaps this is the source of the problem? I know others have encountered challenges installing packages with BiocManager on M1 chip machines.

Please see error below (I needed to remove some of the output due to character limits). Any help would be appreciated.

# TRY TO INSTRALL SCRUFF
> BiocManager::install('scruff')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'scruff'
also installing the dependencies ‘Rhtslib’, ‘biovizBase’, ‘BSgenome’, ‘VariantAnnotation’, ‘OrganismDbi’, ‘ensembldb’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘Rsamtools’, ‘ShortRead’, ‘ggbio’, ‘rtracklayer’, ‘Rsubread’

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: ‘Rhtslib’ ‘biovizBase’
  ‘VariantAnnotation’ ‘GenomicAlignments’ ‘Rsamtools’ ‘ShortRead’ ‘rtracklayer’ ‘Rsubread’
Do you want to attempt to install these from sources? (Yes/no/cancel) 
installing the source packages ‘Rhtslib’, ‘biovizBase’, ‘BSgenome’, ‘VariantAnnotation’, ‘OrganismDbi’, ‘ensembldb’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘Rsamtools’, ‘ShortRead’, ‘ggbio’, ‘rtracklayer’, ‘Rsubread’, ‘scruff’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Rhtslib_1.28.0.tar.gz'
Content type 'application/x-gzip' length 1470492 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

# other "trying URL ..." lines removed

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/scruff_1.14.0.tar.gz'
Content type 'application/x-gzip' length 1597192 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib"
Makefile.Rhtslib:131: warning: overriding commands for target `.c.o'
/Library/Frameworks/R.framework/Resources/etc/Makeconf:168: warning: ignoring old commands for target `.c.o'
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
bgzf.c:1026:16: warning: variable 'size' set but not used [-Wunused-but-set-variable]
    int count, size = 0, block_length, remaining;
               ^
1 warning generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c

# other "clang - arch arm64 ..." lines removed

clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
vcf.c:641:14: warning: variable 'needs_sync' set but not used [-Wunused-but-set-variable]
    int len, needs_sync = 0, done = 0;
             ^
vcf.c:2826:50: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0;
                                                 ^
2 warnings generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
cram/cram_codecs.c:1268:19: warning: variable 'ntot' set but not used [-Wunused-but-set-variable]
    int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k;
                  ^
1 warning generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c

# other "clang - arch arm64 ..." lines removed

clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
#include <lzma.h>
         ^~~~~~~~
1 error generated.
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
LRMbase-index.c:146:40: warning: variable 'all_mismatched' set but not used [-Wunused-but-set-variable]
        int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
                                              ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
LRMseek-zlib.c:194:15: warning: variable 'this_chunk_size' set but not used [-Wunused-but-set-variable]
        unsigned int this_chunk_size = 0;
                     ^
1 warning generated.

# other "clang - arch arm64 ..." lines removed

SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
                int window_no = 0;
                    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.10.5\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c aligner.c -o aligner.o

# other "clang - arch arm64 ..." lines removed

cell-counts.c:1249:29: error: implicit declaration of function 'warning_array_hash_numbers' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                        int all_chro_unmatched = warning_array_hash_numbers(annot_chros, cct_context-> chromosome_table.read_name_to_index, & anno_index_matched);
                                                 ^
cell-counts.c:1249:29: note: did you mean 'warning_hash_hash_numbers'?
./input-files.h:336:5: note: 'warning_hash_hash_numbers' declared here
int warning_hash_hash_numbers(HashTable * t1, HashTable * t2, int * matched);
    ^
cell-counts.c:3129:20: warning: incompatible pointer types passing 'gene_sc_vote_t *' to parameter of type 'gene_vote_t *' [-Wincompatible-pointer-types]
                                                        print_votes(vote_me, cct_context -> index_prefix);
                                                                    ^~~~~~~
./gene-algorithms.h:116:32: note: passing argument to parameter 'vote' here
void print_votes(gene_vote_t * vote, char *index_prefix);
                               ^
cell-counts.c:4219:10: warning: unused variable 'tv2' [-Wunused-variable]
        void ** tv2 = me->appendix3;
                ^
cell-counts.c:4503:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(&section1_items,1, 8, input_fps[xk1]);
                               ^
cell-counts.c:4528:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
                               ^
cell-counts.c:4602:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
                               ^
cell-counts.c:4649:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                size_t frret = fread(&binlen, 1, 4, notmapped_fp);
                       ^
cell-counts.c:4469:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
        srInt_64 removed_umis = 0;
                 ^
7 warnings and 1 error generated.
make: *** [cell-counts.o] Error 1
ERROR: compilation failed for package ‘Rsubread’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rsubread’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘Rhtslib’ are not available for package ‘ShortRead’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ShortRead’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BSgenome’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/GenomicFeatures’
ERROR: dependencies ‘Rsamtools’, ‘rtracklayer’, ‘BSgenome’, ‘GenomicFeatures’, ‘Rhtslib’ are not available for package ‘VariantAnnotation’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/VariantAnnotation’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘OrganismDbi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/OrganismDbi’
ERROR: dependencies ‘GenomicFeatures’, ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘ensembldb’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ensembldb’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’ are not available for package ‘biovizBase’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/biovizBase’
ERROR: dependencies ‘biovizBase’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, ‘ensembldb’ are not available for package ‘ggbio’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ggbio’
ERROR: dependencies ‘GenomicAlignments’, ‘GenomicFeatures’, ‘Rsamtools’, ‘ShortRead’, ‘ggbio’, ‘rtracklayer’, ‘Rsubread’ are not available for package ‘scruff’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/scruff’

The downloaded source packages are in
    ‘/private/var/folders/hq/jb16fbcd5h10rw3fx08h8g940000gq/T/RtmpT3gf8L/downloaded_packages’
There were 14 warnings (use warnings() to see them)


# SESSION INFO
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5
scruff Install ShortRead • 788 views
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Entering edit mode

We are not providing M1 mac binaries at this time. We have begun process of generation and expect to be providing them in the very near future. If you search and read some of the relevant posts there are some work arounds. Here are some related posts

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