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:
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> 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
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
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 containing
libcurl.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:ERROR: configuration failed for package ‘curl’
ERROR: configuration failed for package ‘openssl’
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 containing
libxml-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:ERROR: configuration failed for package ‘xml2’
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
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