From istazahn at gmail.com  Mon Nov  4 04:40:59 2013
From: istazahn at gmail.com (Ista Zahn)
Date: Sun, 3 Nov 2013 22:40:59 -0500
Subject: [Rd] Failed to install kernlab package
In-Reply-To: <1383513331455-4679652.post@n4.nabble.com>
References: <1383513331455-4679652.post@n4.nabble.com>
Message-ID: <CA+vqiLGdx3_xxrLgK69gTXv8Uw94=sr93XdsM62xk8-9-hosGw@mail.gmail.com>

Hi,

I can't reproduce the error with a fully updated CentOS 6 with R-core
and R-devel installed from
http://www.nic.funet.fi/pub/mirrors/fedora.redhat.com/pub/epel/6/x86_64/.
Here is the sessionInfo from my CentOS 6 system where installation of
kernlab was successful:

sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=C                LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_3.0.1 tools_3.0.1

Best,
Ista

On Sun, Nov 3, 2013 at 4:15 PM, Lizkitty <lizhen.peng at stonybrook.edu> wrote:
> Hi everyone,
>
> I am trying to install kernlab package, but failed many times by now on
> CentOS 6 operating system. FYI, I have no problem with this package
> installation on windows platform.
>
> Here is the error message:
>
> trying URL 'http://cran.wustl.edu/src/contrib/kernlab_0.9-18.tar.gz'
> Content type 'application/x-gzip' length 1069148 bytes (1.0 Mb)
> opened URL
> ==================================================
> downloaded 1.0 Mb
>
> * installing *source* package ?kernlab? ...
> ** package ?kernlab? successfully unpacked and MD5 sums checked
> ** libs
> g++ -I/n/sw/R-3.0.1_gcc-4.7.2/lib64/R/include -DNDEBUG  -I/usr/local/include
> -fpic  -g -O2  -c brweight.cpp -o brweight.o
> In file included from
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/bits/localefwd.h:42:0,
>                  from
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/ios:42,
>                  from
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/ostream:40,
>                  from
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/iostream:40,
>                  from errorcode.h:43,
>                  from brweight.h:43,
>                  from brweight.cpp:42:
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/x86_64-unknown-linux-gnu/bits/c++locale.h:53:23:
> error: ?uselocale? was not declared in this scope
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/x86_64-unknown-linux-gnu/bits/c++locale.h:53:45:
> error: invalid type in declaration before ?;? token
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/x86_64-unknown-linux-gnu/bits/c++locale.h:
> In function ?int std::__convert_from_v(__locale_struct* const&, char*, int,
> const char*, ...)?:
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/x86_64-unknown-linux-gnu/bits/c++locale.h:76:53:
> error: ?__gnu_cxx::__uselocale? cannot be used as a function
> /n/sw/gcc-4.7.2/lib/gcc/x86_64-unknown-linux-gnu/4.7.2/../../../../include/c++/4.7.2/x86_64-unknown-linux-gnu/bits/c++locale.h:101:33:
> error: ?__gnu_cxx::__uselocale? cannot be used as a function
> make: *** [brweight.o] Error 1
> ERROR: compilation failed for package ?kernlab?
> * removing ?/n/home09/wang/R/x86_64-unknown-linux-gnu-library/3.0/kernlab?
>
> The downloaded source packages are in
>         ?/scratch/tmp/Rtmpt52VjR/downloaded_packages?
> Warning message:
> In install.packages("kernlab") :
>   installation of package ?kernlab? had non-zero exit status
>
>
> I found out online that many others also failed installing kernlab on linux,
> but no explicit unique solutions for this problem.
> What I have tried so far are:
> 1) change cran mirrors
> 2) using command line directly: R CMD INSTALL kernlab_0.9-18.tar.gz, after
> downloading the package
> 3) reset working directory
> Unfortunately, none of these solved my problem...
>
> Any suggestions are highly appreciated!
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Failed-to-install-kernlab-package-tp4679652.html
> Sent from the R devel mailing list archive at Nabble.com.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Failed to install kernlab package
Ista Zahn