On 10/06/16 12:15, martin.dyrba(a)dzne.de wrote:
> Dear R package developers,
> Since the upgrade from R 3.2.x to 3.3.0 I was confronted with several problems updating/installing some R packages.
>
> Here for instance:
> # R
>
> R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
> Copyright (C) 2016 The R Foundation for Statistical Computing
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>> install.packages("slam")
> Installing package into ‘/usr/lib64/R/library’
> (as ‘lib’ is unspecified)
> trying URL 'https://cran.uni-muenster.de/src/contrib/slam_0.1-34.tar.gz'
> Content type 'application/x-gzip' length 46766 bytes (45 KB)
> ==================================================
> downloaded 45 KB
>
> * installing *source* package ‘slam’ ...
> ** package ‘slam’ successfully unpacked and MD5 sums checked
> ** libs
> ...
> gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -o slam.so apply.o grouped.o sparse.o util.o -L/usr/lib64/R/lib -lRblas -ldl -lpthread -lrt /builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a /builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a /builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a /builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a /builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a -lcurl -lidn -lssh2 -lssl -lcrypto -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lldap -lz -lgfortran -lm -L/usr/lib64/R/lib -lR
> gcc: /builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a: No such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a: No such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a: No such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a: No such file or directory
> gcc: /builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a: No such file or directory
> make: *** [slam.so] Error 1
> ERROR: compilation failed for package ‘slam’
> ...
>
> The same errors occur if I try to install other packages. It seems as newer libraries are needed as CentOS 6 can provide. My kernel version is 2.6.32-642.1.1.el6.x86_64. My R-core version is 3.3.0-5.el6.
>
> Could somebody give me a hint how to solve this issue?
> Thx, Martin
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Hi Martin,
If you want a quick win, the following got R 3.3.0-5.el6 working for me
on Scientific Linux 6.7:
yum install libssh2-devel openldap-devel
Then edit the FLIBS line in /usr/lib64/R/etc/Makeconf and remove all the
references to the static libraries /builddir/..../lib*.a (as per the
errors above).
This file will likely be overwritten when R is next updated.
Regards,
Rob
--
Rob O'Neale
Research Computing Support Officer
College of Engineering, Mathematics and Physical Sciences
University of Exeter
r.oneale(a)exeter.ac.uk
01392 726342
