Problems Installing biomaRt
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@christophermcfall-15612
Last seen 3.3 years ago

I've tried to install biomaRt using the code below (arch linux OS) but it doesn't appear to be working:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

If anyone can lend a had, I'd appreciate it.

#Console:

###############################################################3

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("biomaRt")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘biomaRt’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/biomaRt_2.34.2.tar.gz'
Content type 'application/x-gzip' length 281204 bytes (274 KB)
==================================================
downloaded 274 KB

* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/arch/R/x86_64-pc-linux-gnu-library/3.4/stringi/libs/stringi.so':
  libicui18n.so.60: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘biomaRt’
* removing ‘/home/arch/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’

The downloaded source packages are in
    ‘/tmp/Rtmp0FccLg/downloaded_packages’
installation path not writeable, unable to update packages: cluster, Matrix, nlme, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status

biomart linux • 1.5k views
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Mike Smith ★ 5.0k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg / de.NBI

It looks like this problem really lies with the stringi package.  It'd suggest reinstalling that as a first try, and then re-running the biomaRt installation:

install.packages('stringi')

It looks like that has a system dependency on ICU4C, so if you still encounter error it may be that you need to install that via the Arch package manager. My Arch is pretty rusty, but I guess it's this you need.

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I am facing problem in installing biomaRt even after using "install.packages('stringi')" The problems is written below. I think I have some path problem please help

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager")

BiocManager::install("biomaRt") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'biomaRt' also installing the dependencies ‘curl’, ‘XML’, ‘httr’, ‘openssl’, ‘BiocFileCache’, ‘xml2’



  • installing source package ‘curl’ ... package ‘curl’ successfully unpacked and MD5 sums checked using staged installation Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containinglibcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libcurl was not found. Try installing:
    • deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
    • rpm: libcurl-devel (Fedora, CentOS, RHEL)
    • csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘curl’

  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/curl’
  • 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/sujata/R/x86_64-pc-linux-gnu-library/4.0/XML’
  • installing source package ‘openssl’ ... package ‘openssl’ successfully unpacked and MD5 sums checked using staged installation Using PKG_CFLAGS= --------------------------- [ANTICONF] -------------------------------- Configuration failed because openssl was not found. Try installing:
    • deb: libssl-dev (Debian, Ubuntu, etc)
    • rpm: openssl-devel (Fedora, CentOS, RHEL)
    • csw: libssl_dev (Solaris)
    • brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------- [ERROR MESSAGE] --------------------------- tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory #include <openssl/opensslv.h>
        ^~~~~~~~~~~~~~~~~~~~
      
      compilation terminated.

ERROR: configuration failed for package ‘openssl’

  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/openssl’
  • installing source package ‘xml2’ ... package ‘xml2’ successfully unpacked and MD5 sums checked using staged installation Package libxml-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing libxml-2.0.pc' to the PKG_CONFIG_PATH environment variable No package 'libxml-2.0' found Package libxml-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containinglibxml-2.0.pc' to the PKG_CONFIG_PATH environment variable No package 'libxml-2.0' found Using PKG_CFLAGS= Using PKG_LIBS=-lxml2 ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing:
    • deb: libxml2-dev (Debian, Ubuntu, etc)
    • rpm: libxml2-devel (Fedora, CentOS, RHEL)
    • csw: libxml2_dev (Solaris) If libxml-2.0 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘xml2’

  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/xml2’ ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/httr’ ERROR: dependencies ‘curl’, ‘httr’ are not available for package ‘BiocFileCache’
  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/BiocFileCache’ ERROR: dependencies ‘XML’, ‘httr’, ‘openssl’, ‘BiocFileCache’, ‘xml2’ are not available for package ‘biomaRt’
  • removing ‘/home/sujata/R/x86_64-pc-linux-gnu-library/4.0/biomaRt’

The downloaded source packages are in ‘/tmp/RtmpJOiY6N/downloaded_packages’ Installation path not writeable, unable to update packages: foreign, nlme, spatial Warning messages: 1: In install.packages(...) : installation of package ‘curl’ 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 ‘openssl’ had non-zero exit status 4: In install.packages(...) : installation of package ‘xml2’ had non-zero exit status 5: In install.packages(...) : installation of package ‘httr’ had non-zero exit status 6: In install.packages(...) : installation of package ‘BiocFileCache’ had non-zero exit status 7: In install.packages(...) : installation of package ‘biomaRt’ had non-zero exit status

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Tackle the first problem first by updating (or getting your system administrator) to update your system (not R) to have libcurl-devl, libssl-dev and libxml2-dev installed

------- Configuration failed because libcurl was not found. Try installing:
deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
rpm: libcurl-devel (Fedora, CentOS, RHEL)
csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------------- Configuration failed because openssl was not found. Try installing:
deb: libssl-dev (Debian, Ubuntu, etc)
rpm: openssl-devel (Fedora, CentOS, RHEL)
csw: libssl_dev (Solaris)
brew: openssl@1.1 (Mac OSX)
--------------------------- Configuration failed because libxml-2.0 was not found. Try installing:
deb: libxml2-dev (Debian, Ubuntu, etc)
rpm: libxml2-devel (Fedora, CentOS, RHEL)
csw: libxml2_dev (Solaris) If libxml-2.0 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
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@christophermcfall-15612
Last seen 3.3 years ago

Hi Mike. Nicely done. Thank you for your help on this. That seems to have fixed everything. 

Best,

Christopher

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