I am on a computer with Ubuntu 12.04 (64-bit), R 3.3.0 and Bioconductor 3.3.
When I try to install the Bioconductor package mygene. I keep getting the error 'dereferencing pointer to incomplete type' when R installs mygene's dependent package openssl and httr. Below is the full output from R.
Would anyone know how to solve this? Many thanks for the help in advance!
> biocLite('mygene')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) ‘mygene’
also installing the dependencies ‘openssl’, ‘httr’
trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.4.tar.gz'
Content type 'application/x-gzip' length 1165388 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/httr_1.1.0.tar.gz'
Content type 'application/x-gzip' length 118882 bytes (116 KB)
==================================================
downloaded 116 KB
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/mygene_1.8.0.tar.gz'
Content type 'application/x-gzip' length 121213 bytes (118 KB)
==================================================
downloaded 118 KB
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/opt/R-3.3.0/openssl-1.1.0/include
Using PKG_LIBS=-L/opt/R-3.3.0/openssl-1.1.0/lib -lssl -lcrypto
** libs
gcc -std=gnu99 -I/exeh/exe3/ccarlos/bin/R-3.3.0/include -DNDEBUG -I/opt/R-3.3.0/openssl-1.1.0/include -I/usr/local/include -fpic -g -O2 -c aes.c -o aes.o
gcc -std=gnu99 -I/exeh/exe3/ccarlos/bin/R-3.3.0/include -DNDEBUG -I/opt/R-3.3.0/openssl-1.1.0/include -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o
gcc -std=gnu99 -I/exeh/exe3/ccarlos/bin/R-3.3.0/include -DNDEBUG -I/opt/R-3.3.0/openssl-1.1.0/include -I/usr/local/include -fpic -g -O2 -c bignum.c -o bignum.o
gcc -std=gnu99 -I/exeh/exe3/ccarlos/bin/R-3.3.0/include -DNDEBUG -I/opt/R-3.3.0/openssl-1.1.0/include -I/usr/local/include -fpic -g -O2 -c cert.c -o cert.o
cert.c: In function ‘R_cert_info’:
cert.c:45:37: error: dereferencing pointer to incomplete type
cert.c:49:50: error: dereferencing pointer to incomplete type
cert.c:50:39: error: dereferencing pointer to incomplete type
cert.c:50:62: error: dereferencing pointer to incomplete type
cert.c:55:31: error: dereferencing pointer to incomplete type
cert.c:62:31: error: dereferencing pointer to incomplete type
make: *** [cert.o] Error 1
ERROR: compilation failed for package ‘openssl’
* removing ‘/exeh/exe3/ccarlos/bin/R-3.3.0/library/openssl’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/exeh/exe3/ccarlos/bin/R-3.3.0/library/httr’
ERROR: dependency ‘httr’ is not available for package ‘mygene’
* removing ‘/exeh/exe3/ccarlos/bin/R-3.3.0/library/mygene’
The downloaded source packages are in
‘/tmp/RtmpgW4oJW/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Waing messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘openssl’ 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 ‘mygene’ had non-zero exit status