Re: [R] Problem with vegan package instalation on linux

From: Ronaldo Reis Junior <chrysopa_at_gmail.com>
Date: Wed, 09 Mar 2011 12:46:14 -0300

Gavin,

yes, I have GCC, Gfortran,

[root_at_amandix ~]# gcc --version

gcc (Debian 4.5.2-5) 4.5.2

[root_at_amandix ~]# gfortran --version

GNU Fortran (Debian 4.5.2-5) 4.5.2

[root_at_amandix ~]# make --version

GNU Make 3.81

I have another linux installed that I dont have any problem, the installations are similar. In this specific installation I cant install several packages that have the same error (ex. vegan and mapproj). I try to install several dev packages from gnome-dev, but without success. I dont find were is the problem. I try to install the mapproj from debian source to get dependencies but the error is the same.

Look

[root_at_amandix ~]# apt-get build-dep r-cran-mapproj
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
[root_at_amandix ~]# apt-get source r-cran-mapproj -b
Reading package lists... Done
Building dependency tree
Reading state information... Done
Need to get 31.5 kB of source archives.
Get:1 http://http.us.debian.org/debian/ unstable/main r-cran-mapproj 1.1-8.3-1 (dsc) [1069 B]
Get:2 http://http.us.debian.org/debian/ unstable/main r-cran-mapproj 1.1-8.3-1 (tar) [24.0 kB]
Get:3 http://http.us.debian.org/debian/ unstable/main r-cran-mapproj 1.1-8.3-1 (diff) [6455 B]
Fetched 31.5 kB in 1s (24.4 kB/s)

dpkg-source: info: extracting r-cran-mapproj in r-cran-mapproj-1.1-8.3
dpkg-source: info: unpacking r-cran-mapproj_1.1-8.3.orig.tar.gz
dpkg-source: info: applying r-cran-mapproj_1.1-8.3-1.diff.gz
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): 
-g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package r-cran-mapproj
dpkg-buildpackage: source version 1.1-8.3-1
dpkg-buildpackage: source changed by Chris Lawrence <lawrencc_at_debian.org>
dpkg-buildpackage: host architecture i386
  dpkg-source --before-build r-cran-mapproj-1.1-8.3   debian/rules clean
test -x debian/rules
dh_testroot
dh_clean
  debian/rules build
test -x debian/rules
mkdir -p "."
  debian/rules binary
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs        usr/lib/R/site-library
R CMD INSTALL -l
/root/r-cran-mapproj-1.1-8.3/debian/r-cran-mapproj/usr/lib/R/site-library --clean .
* installing *source* package 'mapproj' ... ** libs
make[1]: Entering directory `/root/r-cran-mapproj-1.1-8.3' make[1]: *** No rule to make target `aitoff.o', needed by `mapproj.so'. Stop.
make[1]: Leaving directory `/root/r-cran-mapproj-1.1-8.3'
make[1]: Entering directory `/root/r-cran-mapproj-1.1-8.3'
make[1]: Leaving directory `/root/r-cran-mapproj-1.1-8.3'
*** arch - Rgnome
Warning in file(con, "r") :

   cannot open file '/usr/lib/R/etc/Rgnome/Makeconf': No such file or directory
Error in file(con, "r") : cannot open the connection * removing
'/root/r-cran-mapproj-1.1-8.3/debian/r-cran-mapproj/usr/lib/R/site-library/mapproj' make: *** [R_any_arch] Error 1
dpkg-buildpackage: error: debian/rules binary gave error exit status 2 Build command 'cd r-cran-mapproj-1.1-8.3 && dpkg-buildpackage -b -uc' failed.
E: Child process failed

I try also in a debian list.

Any more help are welcome

Thanks
Ronaldo

Em 09-03-2011 12:28, Gavin Simpson escreveu:

> On Wed, 2011-03-09 at 11:41 -0300, Ronaldo Reis-Jr. wrote:
>    
>> Hi,
>>
>> I try to install vegan package on debian linux and I give this error:
>>      
> Have you got a fortran compiler installed on your system? gcc-gfortran
> is the package on my Fedora laptop.
>
> G
>
>    
>> =================================================
>> * installing *source* package 'vegan' ...
>> ** libs
>> make: *** No rule to make target `cepin.o', needed by `vegan.so'.  Stop.
>> *** arch - Rgnome
>> Warning in file(con, "r") :
>>    cannot open file '/usr/lib/R/etc/Rgnome/Makeconf': No such file or
>> directory
>> Error in file(con, "r") : cannot open the connection
>> * removing '/usr/local/lib/R/site-library/vegan'
>>
>> The downloaded packages are in
>>          '/tmp/RtmpYgJz5c/downloaded_packages'
>> Warning message:
>> In install.packages("vegan") :
>>    installation of package 'vegan' had non-zero exit status
>> ==============================================
>>
>> I try to find the problem without success.
>>
>> Anybody can help-me?
>>
>> Thanks
>> Ronaldo
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>      
>    

-- 
2ª lei - Na pesquisa, o que importa é o que está correto,
          e não quem está correto.

       --Herman, I. P. 2007. Following the law. NATURE, Vol 445, p. 228.

>  Prof. Ronaldo Reis Júnior
|  .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional
| : :'  : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia
| `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil
|   `- Fone: (38) 3229-8192 | ronaldo.reis_at_unimontes.br
| http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366


	[[alternative HTML version deleted]]



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