bigguscodus commented 5 years ago

I have a problem with installation BSgenome. What am i supposed to do ? Here is the log:

BiocManager::install("BSgenome") Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05) Installing package(s) 'BSgenome' also installing the dependencies ‘SummarizedExperiment’, ‘RCurl’, ‘XML’, ‘GenomicAlignments’, ‘Rhtslib’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘rtracklayer’, ‘Rsamtools’

x-gzip' length 1517919 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.95-4.12.tar.gz' Content type 'application/x-gzip' length 916763 bytes (895 KB)

downloaded 895 KB

trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.20.tar.gz' Content type 'application/x-gzip' length 1600829 bytes (1.5 MB)

downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicAlignments_1.22.0.tar.gz' Content type 'application/x-gzip' length 2315848 bytes (2.2 MB)

downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rhtslib_1.18.0.tar.gz' Content type 'application/x-gzip' length 1471164 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.0.tar.gz' Content type 'application/x-gzip' length 3409309 bytes (3.3 MB)

downloaded 3.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz' Content type 'application/x-gzip' length 1169872 bytes (1.1 MB)

downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/rtracklayer_1.46.0.tar.gz' Content type 'application/x-gzip' length 1541921 bytes (1.5 MB)

downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rsamtools_2.2.0.tar.gz' Content type 'application/x-gzip' length 3033552 bytes (2.9 MB)

downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BSgenome_1.54.0.tar.gz' Content type 'application/x-gzip' length 6067030 bytes (5.8 MB)

downloaded 5.8 MB

installing source package ‘RCurl’ ... package ‘RCurl’ successfully unpacked and MD5 sums checked using staged installation checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
installing source package ‘XML’ ... package ‘XML’ successfully unpacked and MD5 sums checked using staged installation checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/XML’
installing source package ‘Rhtslib’ ... using non-staged installation via StagedInstall field libs cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[1]: Entering directory '/tmp/Rtmpr6Dmy1/R.INSTALL4f1c631f2b98/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o' /usr/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o' gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fpic -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c hfile_libcurl.c:45:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
```
  ^~~~~~~~~~~~~
```
compilation terminated. Makefile.Rhtslib:128: recipe for target 'hfile_libcurl.o' failed make[1]: Leaving directory '/tmp/Rtmpr6Dmy1/R.INSTALL4f1c631f2b98/Rhtslib/src/htslib-1.7' make[1]: [hfile_libcurl.o] Error 1 Makevars.common:24: recipe for target 'htslib' failed make: [htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib’ ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’ ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’ ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’ ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘Rhtslib’ are not available for package ‘Rsamtools’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’ ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/GenomicAlignments’ ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/rtracklayer’ ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘rtracklayer’, ‘Rsamtools’ are not available for package ‘BSgenome’
removing ‘/home/mikka/R/x86_64-pc-linux-gnu-library/3.6/BSgenome’

The downloaded source packages are in ‘/tmp/RtmpEFa6gM/downloaded_packages’ Installation path not writeable, unable to update packages: mgcv, survival Warning messages: 1: In install.packages(...) : installation of package ‘RCurl’ had non-zero exit status 2: In install.packages(...) : installation of package ‘XML’ had non-zero exit status 3: In install.packages(...) : installation of package ‘Rhtslib’ had non-zero exit status 4: In install.packages(...) : installation of package ‘GenomeInfoDb’ had non-zero exit status 5: In install.packages(...) : installation of package ‘GenomicRanges’ had non-zero exit status 6: In install.packages(...) : installation of package ‘SummarizedExperiment’ had non-zero exit status 7: In install.packages(...) : installation of package ‘Rsamtools’ had non-zero exit status 8: In install.packages(...) : installation of package ‘GenomicAlignments’ had non-zero exit status 9: In install.packages(...) : installation of package ‘rtracklayer’ had non-zero exit status 10: In install.packages(...) : installation of package ‘BSgenome’ had non-zero exit status

hpages commented 5 years ago

This does not look like a BSgenome issue. As you can see, many packages couldn't be installed, not just BSgenome. The fact that BSgenome failed to install is just the consequence of other packages required (directly or indirectly) by BSgenome failing to install.

At the root of the problem, it seems that installation of CRAN packages RCurl and XML failed, thus preventing many Bioconductor packages from installing. Please consult on general purpose forums / mailing lists, or directly with the authors / maintainers of these packages for advice. As always people will ask you to provide the output of your sessionInfo() so they can help you.

Best, H.

bigguscodus commented 5 years ago

Thank you!

hpages commented 5 years ago

I hope you were able to sort this out. Closing this now.

jdblischak commented 4 years ago

Both RCurl

checking for curl-config... no
Cannot find curl-config

and Rhtslib

hfile_libcurl.c:45:10: fatal error: curl/curl.h: No such file or directory

failed to install because the libcurl development files aren't available. This can be fixed on Debian/Ubuntu by running the following:

sudo apt install libcurl4-openssl-dev

hpages commented 4 years ago

Please don't post in a closed issue, especially if your post has nothing to do with BSgenome. Thx!

Bioconductor / BSgenome

Failed to install #4