Question: alao can not install DIffBind on R studio in linux
0
gravatar for mikysyc2016
5 weeks ago by
mikysyc201610
mikysyc201610 wrote:

When I try to install "DiffBind" on R studio, I get the erro below. I use R 3.4 and BIoconductor 3.6.

ERROR: configuration failed for package ‘curl’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/curl’ * installing source package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked Using PKG_CFLAGS= ------------------------- ANTICONF ERROR --------------------------- 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: configuration failed for package ‘openssl’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/openssl’ * installing source package ‘RMySQL’ ... ** package ‘RMySQL’ successfully unpacked and MD5 sums checked Using PKG_CFLAGS= Using PKG_LIBS=-lmysqlclient ------------------------- ANTICONF ERROR --------------------------- Configuration failed because no mysql client library was found. Try installing: * deb: libmariadbclient-dev | libmariadb-client-lgpl-dev (Debian, Ubuntu) * rpm: mariadb-connector-c-devel | mariadb-devel | mysql-devel (Fedora, CentOS, RHEL) * csw: mysql56_dev (Solaris) * brew: mariadb-connector-c (OSX) If you already have a mysql client library installed, verify that either mariadb_config or mysql_config is on your PATH. If these are unavailable you can also set INCLUDE_DIR and LIB_DIR manually via:

R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

ERROR: configuration failed for package ‘RMySQL’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/RMySQL’ ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/httr’ ERROR: dependency ‘httr’ is not available for package ‘biomaRt’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’ ERROR: dependencies ‘RMySQL’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/GenomicFeatures’ ERROR: dependency ‘GenomicFeatures’ is not available for package ‘VariantAnnotation’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/VariantAnnotation’ ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’ are not available for package ‘systemPipeR’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/systemPipeR’ ERROR: dependency ‘systemPipeR’ is not available for package ‘DiffBind’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/DiffBind’

The downloaded source packages are in ‘/tmp/Rtmp7Ysenv/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘curl’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘openssl’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RMySQL’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘httr’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘biomaRt’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status 7: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘VariantAnnotation’ had non-zero exit status 8: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘systemPipeR’ had non-zero exit status 9: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DiffBind’ had non-zero exit status

install.packages("zilb") Installing package into ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified)

R • 131 views
ADD COMMENTlink modified 5 weeks ago by cpad01127.6k • written 5 weeks ago by mikysyc201610
0
gravatar for cpad0112
5 weeks ago by
cpad01127.6k
India
cpad01127.6k wrote:

Address these issues first (install libssl-dev and libmariadbclient-dev on your system and try again):

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) I

because no mysql client library was found. Try installing: * deb: libmariadbclient-dev | libmariadb-client-lgpl-dev (Debian, Ubuntu) * rpm: mariadb-connector-c-devel | mariadb-devel | mysql-devel (Fedora, CentOS, RHEL) * csw: mysql56_dev (Solaris) * brew: mariadb-connector-c (OSX) 

dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’ 

ERROR: dependency ‘httr’ is not available for package ‘biomaR
ADD COMMENTlink written 5 weeks ago by cpad01127.6k

install the "libssl-dev and libmariadbclient-dev" still have error as below:

ERROR: configuration failed for package ‘curl’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/curl’ ERROR: dependency ‘curl’ is not available for package ‘httr’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/httr’ ERROR: dependency ‘httr’ is not available for package ‘biomaRt’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’ ERROR: dependency ‘biomaRt’ is not available for package ‘GenomicFeatures’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/GenomicFeatures’ ERROR: dependency ‘GenomicFeatures’ is not available for package ‘VariantAnnotation’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/VariantAnnotation’ ERROR: dependencies ‘GenomicFeatures’, ‘VariantAnnotation’ are not available for package ‘systemPipeR’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/systemPipeR’ ERROR: dependency ‘systemPipeR’ is not available for package ‘DiffBind’ * removing ‘/home/yachen/R/x86_64-pc-linux-gnu-library/3.4/DiffBind’

The downloaded source packages are in ‘/tmp/Rtmp7Ysenv/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘curl’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘httr’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘biomaRt’ had non-zero exit status 4: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GenomicFeatures’ had non-zero exit status 5: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘VariantAnnotation’ had non-zero exit status 6: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘systemPipeR’ had non-zero exit status 7: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘DiffBind’ had non-zero exit status

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by mikysyc201610

My suggestion is to resolve the earliest failure. In this case curl package. First try to install curl package (only) in R and if it fails, please post the error logs here.Then install rest of the packages one by one.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by cpad01127.6k

I try your sugeestion and install others. It works now! Thanks.

ADD REPLYlink written 5 weeks ago by mikysyc201610
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 995 users visited in the last hour