Install problems on centos 7 of TCGAbiolinks
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Entering edit mode
@jarod_v6liberoit-6654
Last seen 2.7 years ago
Italy

This is the error:
 

 source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
> biocLite("TCGAbiolinks")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘TCGAbiolinks’
also installing the dependencies ‘openssl’, ‘rvest’, ‘httr’

trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.5.tar.gz'
Content type 'unknown' length 1236042 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/rvest_0.3.2.tar.gz'
Content type 'unknown' length 1597137 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.2.1.tar.gz'
Content type 'unknown' length 133398 bytes (130 KB)
==================================================
downloaded 130 KB

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/TCGAbiolinks_2.0.13.tar.gz'
Content type 'unknown' length 27658403 bytes (26.4 MB)
==================================================
downloaded 26.4 MB

* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- 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 (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/maurizio/R/x86_64-redhat-linux-gnu-library/3.3/openssl’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/home/maurizio/R/x86_64-redhat-linux-gnu-library/3.3/httr’
ERROR: dependency ‘httr’ is not available for package ‘rvest’
* removing ‘/home/maurizio/R/x86_64-redhat-linux-gnu-library/3.3/rvest’
ERROR: dependencies ‘rvest’, ‘httr’ are not available for package ‘TCGAbiolinks’
* removing ‘/home/maurizio/R/x86_64-redhat-linux-gnu-library/3.3/TCGAbiolinks’

 

 

openssl version
OpenSSL 1.0.2j  26 Sep 2016

 

 

 

Could you please help me? how can set openssl.

tcgabiolinks centos7 • 1.3k views
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1
Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 4 hours ago
EMBL Heidelberg / de.NBI

I suspect you need to install the OpenSSL development libraries.  On CentOS that will be something like this at the command line:

yum install openssl-devel
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