Question

install GenomicFeatures fail

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soda ▴ 80

@5b9023e7

Last seen 18 months ago

China

BiocManager::install('GenomicFeatures')

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

replacement repositories:
    CRAN: http://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'GenomicFeatures'
also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’

Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘Rhtslib’ ‘Rsamtools’ ‘GenomicAlignments’ ‘rtracklayer’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’, ‘GenomicFeatures’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rhtslib_1.25.1.tar.gz'
Content type 'application/x-gzip' length 1471726 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Rsamtools_2.9.1.tar.gz'
Content type 'application/x-gzip' length 2870908 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicAlignments_1.29.0.tar.gz'
Content type 'application/x-gzip' length 2301235 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/rtracklayer_1.53.1.tar.gz'
Content type 'application/x-gzip' length 4054820 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/GenomicFeatures_1.45.1.tar.gz'
Content type 'application/x-gzip' length 1375134 bytes (1.3 MB)
==================================================
downloaded 1.3 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:128: 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
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
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
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
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
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
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_encode.o cram/cram_encode.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_external.o cram/cram_external.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_index.o cram/cram_index.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_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/4.1-arm64/Resources/library/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘GenomicFeatures’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/GenomicFeatures’

The downloaded source packages are in
    ‘/private/var/folders/bt/t904ydv902d4lqg2_jxf_n600000gn/T/Rtmp4Q32an/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘Rhtslib’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘Rsamtools’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘GenomicAlignments’ had non-zero exit status
9: In .inet_warning(msg) :
  installation of package ‘rtracklayer’ had non-zero exit status
10: In .inet_warning(msg) :
  installation of package ‘GenomicFeatures’ had non-zero exit status

why?

GenomicFeatures install • 1.3k views

ADD COMMENT • link updated 3.2 years ago by James W. MacDonald 67k • written 3.2 years ago by soda ▴ 80

score 0 · Answer 1 · 2021-08-24

Is there a particular reason that you are using Bioc-devel? There is a binary package for Rhtslib for the release version. If you need to compile, do note this system requirement:

SystemRequirements  libbz2 & liblzma & libcurl (with header files), GNU make

And the error you get indicates liblzma is not available. I don't use MacOS, so I don't have any insight. Probably a search for 'macos liblzma' would give you the relevant information.