[BioC] Ruuid installation problems
Raffaele Calogero
raffaele.calogero at unito.it
Tue Feb 22 13:09:48 CET 2005
> Dear Robert.
> Thank you for your kind answer.
> This is what I have done:
> /opt/gnome/bin/glib-config --cflags
> -I/opt/gnome/include/glib-1.2 -I/opt/gnome/lib/glib/include
> I tryied to set the path in my .bashrc adding the line:
> PATH=$PATH:/opt/gnome/include/glib-1.2:/opt/gnome/lib/glib/include
> export PATH
>
> but I did not succeded and I got always the same error.
> Then I modified the configure file in the Ruuid installation at line:
> PKG_CPPFLAGS="-I/usr/local/include/glib12"
> in
> PKG_CPPFLAGS="-I/opt/gnome/include/glib-1.2"
> I tarred and gzipped the Ruuid dir and I installed it
> It seems to work although I got a warning:
> Warning message:
> Undefined slot classes in definition of "Ruuid": uuid(class "uuidt")
> in: .completeClassSlots(ClassDef, where)
>
>
> Yours sincerely
> Raffaele
>
> ###############################
> creating cache ./config.cache
> checking for glib-config... no
> checking how to run the C preprocessor... cc -E
> checking for /usr/include/unistd.h... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c clear.c -o clear.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c compare.c -o compare.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c copy.c -o copy.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c gen_uuid.c -ogen_uuid.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c isnull.c -o isnull.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c pack.c -o pack.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c parse.c -o parse.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c Rinit.c -o Rinit.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c Ruuid.c -o Ruuid.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c unpack.c -o unpack.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c unparse.c -o unparse.o
> gcc -I/usr/lib/R/include -I/opt/gnome/include/glib-1.2
> -DHAVE_UNISTD_H=1 -I/usr/local/include -I/opt/gnome/include -fPIC
> -c uuid_time.c -o uuid_time.o
> gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o Ruuid.so clear.o
> compare.o copy.o gen_uuid.o isnull.o pack.o parse.o Rinit.o Ruuid.o
> unpack.o unparse.o uuid_time.o -L/usr/lib/R/lib -lR
> ** R
> ** inst
> ** save image
> [1] TRUE
> [1] "Ruuid"
> Warning message:
> Undefined slot classes in definition of "Ruuid": uuid(class "uuidt")
> in: .completeClassSlots(ClassDef, where)
> [1] "uuid"
> [1] "uuid"
> [1] "uuidt"
> [1] "uuidt"
> [1] "uuid"
>
> ** help
> >>> Building/Updating help pages for package 'Ruuid'
> Formats: text html latex example
> Ruuid-class text html latex example
> getuuid text html latex example
> uuidt-class text html latex example
> * DONE (Ruuid)
>
>
> Robert Gentleman wrote:
>
>>
>> On Feb 22, 2005, at 1:45 AM, Raffaele Calogero wrote:
>>
>>> Dear All,
>>> I have the following configuration:
>>> Centrino 2GHz, 756MB Ram, Suse linux 9.2, Bioconductor 1.5
>>> I got problem in installing the Ruuid package (see error below).
>>> The error seems related to the lack of glib library, as I have
>>> seen from the Bioconductor mail archive.
>>> However, the problem is that after installing:
>>> glib-1.2.10-589.i586.rpm glib2-2.4.6-5.1.i586.rpm
>>> glib2-devel-2.4.6-5.1.i586.rpm
>>> glib-devel-1.2.10-589.i586.rpm
>>> I continue to be unable to install Ruuid
>>
>>
>>
>>
>>> Does anybody have some suggestions?
>>> Raffaele
>>>
>>>
>>>
>>
>>
>> Yes, and the lines below tell you the problem (or at least some of it)
>>
>> most of these libraries have a little helper function, in the case
>> of glib, it is called
>> glib-config
>> find it, make sure it is on you path, so that if you go (in the shell)
>>
>> glib-config --cflags
>>
>> you see something like:
>> -I/usr/local/include/glib-1.2 -I/usr/local/lib/glib/include
>>
>> where the location, will of course be different - unless your
>> computer looks a lot like mine,
>> but do make sure that the file glib.h is in one of those
>> directories named here
>> (installing from rpms sometimes does odd things -). Once that is
>> true, then you should have
>> not problems...
>>
>>
>> Robert
>>
>>
>>
>>
>>>
>>> #######################à
>>> In file included from clear.c:14:
>>> uuidP.h:33:18: glib.h: No such file or directory
>>> In file included from clear.c:14:
>>> uuidP.h:47: error: parse error before "guint32"
>>> uuidP.h:47: warning: no semicolon at end of struct or union
>>> uuidP.h:48: warning: data definition has no type or storage class
>>> uuidP.h:49: error: parse error before "time_hi_and_version"
>>> uuidP.h:49: warning: data definition has no type or storage class
>>> uuidP.h:50: error: parse error before "clock_seq"
>>> uuidP.h:50: warning: data definition has no type or storage class
>>> uuidP.h:51: error: parse error before "node"
>>> uuidP.h:51: warning: data definition has no type or storage class
>>> uuidP.h:52: error: parse error before '}' token
>>> make: *** [clear.o] Error 1
>>> ERROR: compilation failed for package 'Ruuid'
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel. ++39 0116705420
Lab. ++39 0116705408
Fax ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www: www.bioinformatica.unito.it
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