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 #######################? 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'

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 > > #######################? > 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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

> 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 >> >> >> >> >>> >>> #######################? >>> 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@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@unito.it www: www.bioinformatica.unito.it