[BioC] Trouble building Bioconductor

[Atro Tossavainen]

Hi,

I have successfully built R 2.2.1 for x86 Linux, PPC Linux, Solaris 7
and IRIX 6.5.  I am now trying to add Bioconductor to all of these
using

source("http://www.bioconductor.org/getBioC.R")
getBioC()

On x86 Linux (what I'm using is essentially FC1), I have no problems.

On Solaris 7, building gcrma fails.  Replacing my R path with "..."
in the following error messages.  I am using Sun WorkShop 6 update 2
C 5.3 2001/05/15.

* Installing *source* package 'gcrma' ...
** libs
cc -I/.../R/2.2.1/lib/R/include  -I/another/include   -KPIC  -g -c baseProfile.c -o baseProfile.o
cc -I/.../R/2.2.1/lib/R/include  -I/another/include   -KPIC  -g -c computeAffinities.c -o computeAffinities.o
cc -I/.../R/2.2.1/lib/R/include  -I/another/include   -KPIC  -g -c postmean.c -o postmean.o
"postmean.c", line 26: syntax error before or at: double
"postmean.c", line 27: undefined symbol: pnorms
"postmean.c", line 27: cannot dereference non-pointer type
"postmean.c", line 32: cannot dereference non-pointer type
"postmean.c", line 33: undefined symbol: diff_pnorms
"postmean.c", line 33: cannot dereference non-pointer type
"postmean.c", line 33: cannot dereference non-pointer type
cc: acomp failed for postmean.c
*** Error code 2
make: Fatal error: Command failed for target `postmean.o'
ERROR: compilation failed for package 'gcrma'
** Removing '/.../R/2.2.1/lib.sun4x_57/R/library/gcrma'

and everything else fails after that, of course, due to gcrma not having
been built.

On IRIX 6.5.28, with MIPSpro 7.3 compilers, it fails too:

        cc -I/.../R/2.2.1/lib/R/include  -I/another/include -OPT:IEEE_NaN_inf=ON    -g -c postmean.c -o postmean.o
cc-1241 cc: ERROR File = postmean.c, Line = 26
  A declaration cannot appear after an executable statement in a block.

    double pnorms[K+1],g[K+2],diff_pnorms;
    ^

1 error detected in the compilation of "postmean.c".
*** Error code 2 (bu21)
ERROR: compilation failed for package 'gcrma'
** Removing '/.../R/2.2.1/lib. at sys/R/library/gcrma'

On Yellow Dog Linux 2.3 (PPC, with gcc 2.95.4), it fails too:

gcc -I/.../R/2.2.1/lib/R/include  -I/usr/local/include   -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -g -O2 -c postmean.c -o postmean.o
postmean.c: In function `posty':
postmean.c:26: parse error before `double'
postmean.c:27: `pnorms' undeclared (first use in this function)
postmean.c:27: (Each undeclared identifier is reported only once
postmean.c:27: for each function it appears in.)
postmean.c:33: `diff_pnorms' undeclared (first use in this function)
make: *** [postmean.o] Error 1
ERROR: compilation failed for package 'gcrma'
** Removing '/.../R/2.2.1/lib. at sys/R/library/gcrma'

Help would be appreciated.

-- 
Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS