Re: reviewers needed for some pkgsrc-wip packages

[georg.schwarz%freenet.de@localhost (Georg Schwarz)]

I tried to build a few packages from WIP on on IRIX 5.3. Here is my feedback.


wip/biopython-1.30 ended up like this:

....
ld -shared build/temp.irix-5.3-2.2/lex.yy.o
build/temp.irix-5.3-2.2/MMCIFlexmodule.o -lfl -o
build/lib.irix-5.3-2.2/Bio/PDB/mmCIF/MMCIFlex.so
/usr/local/pkg/bin/ld: cannot find -lfl
error: command 'ld' failed with exit status 1

The reason is that there is only libfl.a (installed by flex package), no .so
files.



wip/bioruby: ftp.bioruby.org does no longer seem to exist. Besides, it looks
like bioruby is currently at 0.6.2 already.

wip/emboss: EMBOSS-2.9.0.tar.gz is no longer available (at least where pkgsrc
expects it) since there is already a later version out.

wip/fasta:
the package fails for me with a checksum error:

===> *** No /usr/people/schwarz/pkgsrc/distfiles/pkg-vulnerabilities file
found,
===> *** skipping vulnerability checks. To fix, install
===> *** the pkgsrc/security/audit-packages package and run
===> *** '/usr/local/pkg/sbin/download-vulnerability-list'.
=> Checksum SHA1 mismatch for fasta3.shar.Z.
=> No RMD160 checksum recorded for fasta3.shar.Z.
M

wip/glimmerm uses c++ but fails to say so.

In addition, my cc does not work with strings extending over several
lines as found in train/build-icm.c; I manuallyto join the lines first.

wip/gstat:

Requesting http://www.gstat.org/bin/gstat-2.4.3.tar.gz
100% |*************************************|  1155 KB   68.13 KB/s    00:00
ETA
1183179 bytes retrieved in 00:17 (67.85 KB/s)
=> Checksum SHA1 mismatch for gstat-2.4.3.tar.gz.
=> No RMD160 checksum recorded for gstat-2.4.3.tar.gz.
Make sure the Makefile and checksum file
(/usr/people/schwarz/pkgsrc/wip/gstat/distinfo)
are up to date.  If you want to override this check, type
"/usr/local/pkg/bin/bmake NO_CHECKSUM=yes [other args]".


wip/libGenome needs c++ but does not say so

wip/grasse5: I had to add to Makefile
.include "../../devel/zlib/buildlink3.mk"
Otherwise HAVE_ZLIB_H  is not defined and compiling fails in gis/flate.c.

wip/manatee:
../../wip/p5-Tree-DAG_Node: Does not exist
bmake: "../../mk/../../mk/reduce-depends.mk" line 2: warning: "cd
../../wip/p5-Tree-DAG_Node && /sbin/pwd" returned non-zero status


wip/mapserver:
bmake: "/usr/people/schwarz/pkgsrc/wip/mapserver/Makefile" line 60: Could not
find ../../wip/mk/postgis.buildlink3.mk

wip/molmol:
assumes to use /usr/bin/gcc, as a result of makedefs.lnx being used. Other
platforms should get other makefef files, which probably need to be patched
similarly to what patch-ab does.

wip/ncbi-bin:

cc -mips1  -O -c  -I../include -DWIN_MOTIF blast_dust.c
as1: Warning: blast_dust.c, line 189: Division by zero

This probably refers to line 206 of that file. I am not sure if that line is
reached for loop equal 0.

wip/postgis:
bmake: "/usr/people/schwarz/pkgsrc/wip/postgis/Makefile" line 24: Could not
find ../../databases/postgresql/Makefile.common
bmake: "/usr/people/schwarz/pkgsrc/wip/postgis/Makefile" line 63: Could not
find ../../databases/postgresql-lib/buildlink3.mk
bmake: Fatal errors encountered -- cannot continue

wip/postgresql80-postgis:

===> Applying pkgsrc patches for postgresql80-postgis-1.0.0-rc2
**************************************
Ignoring unknown patch file:
/usr/people/schwarz/pkgsrc/wip/postgresql80-postgis/../../databases/postgresql
80/patches/patch-ab

redoing makepatchsum solves this issue. Anyway, I still end up like this:

gmake[1]: Entering directory
`/usr/people/schwarz/pkgsrc/wip/postgresql80-postgis/work/postgresql-8.0.1/con
trib/postgis-1.0.0-rc2/lwgeom'
../Makefile.config:90:
/usr/people/schwarz/pkgsrc/wip/postgresql80-postgis/../../src/Makefile.global:
No such file or directory
Makefile:98: /src/Makefile.shlib: No such file or directory
gmake[1]: *** No rule to make target `/src/Makefile.shlib'.  Stop.
gmake[1]: Leaving directory
`/usr/people/schwarz/pkgsrc/wip/postgresql80-postgis/work/postgresql-8.0.1/con
trib/postgis-1.0.0-rc2/lwgeom'
gmake: *** [liblwgeom] Error 2
*** Error code 2


wip/qgis:

bmake: "/usr/people/schwarz/pkgsrc/wip/qgis/Makefile" line 26: Could not find
../../wip/grass/buildlink3.mk

wip/shapelib:

/bin/sh ./libtool --mode=link gcc  -g -O2  -o libshp.la -rpath /usr/local/lib
-version-info 1:1:0 shpopen.lo shptree.lo dbfopen.lo
rm -fr .libs/libshp.la .libs/libshp.* .libs/libshp.*
gcc -shared  shpopen.lo shptree.lo dbfopen.lo  -lc  -Wl,-soname
-Wl,libshp.so.1 -o .libs/libshp.so.1.0.1
(cd .libs && rm -f libshp.so.1 && ln -s libshp.so.1.0.1 libshp.so.1)
(cd .libs && rm -f libshp.so && ln -s libshp.so.1.0.1 libshp.so)
ar cru .libs/libshp.a  shpopen.o shptree.o dbfopen.o 
ranlib .libs/libshp.a
creating libshp.la
(cd .libs && rm -f libshp.la && ln -s ../libshp.la libshp.la)
rm -fr .libs/libshp.la .libs/libshp.* .libs/libshp.*
rm -fr .libs/libshp.lax
mkdir .libs/libshp.lax
/usr/bin/ld -G -h libshp.so.1 -o .libs/libshp.so.1.0.1  shpopen.lo shptree.lo
dbfopen.lo  -lc
/usr/bin/../lib/ld:
Can't open: libshp.so.1 (No such file or directory)


wip/socket++ needs c++ but does not declare so.

/socket++/sockinet.cpp and socket++/sockstream.cpp need to typedef socklen_t
for IRIX5 just as they do for __APPLE right now.
In socket++/sockstream.cpp  EPROCLIM is unknown on IRIX5 just as on __linux__.
I can provide patches if you like.

sockstream.cpp uses FIONCLEX. Where is this supposed to be defined?

wip/treeview:

ends up with
=> Couldn't fetch tv-0.3.tar.gz - please try to retrieve this
=> file manually into /usr/people/schwarz/pkgsrc/distfiles/ and try again.
*** Error code 1


wip/xgobi: to compile I had to add the following patch:

--- src/inference.c.orig        2005-04-02 20:00:20.000000000 +0200
+++ src/inference.c     2005-04-02 20:15:56.000000000 +0200
@@ -232,7 +232,8 @@
     for (i=0; i<xg->nrows; i++)
       sort_data[i] = xg->tform1[i][j];
 
-    qsort((char *) sort_data, xg->nrows, sizeof(float), sort_compare);
+    qsort((char *) sort_data, xg->nrows, sizeof(float), 
+       (int (* )(const void *  , const void * )) sort_compare);
    
     for (i=0; i<xg->nrows; i++)
       xg->tform2[i][j] = sort_data[i]; 


in order to install wip/xmim, I had to patch configure similarly as patch-ab
does it for NetBSD already (maybe configure.in should also be patched, as
patch-aa does?):

--- configure.orig1     2005-04-02 21:55:36.000000000 +0200
+++ configure   2005-04-02 22:04:19.000000000 +0200
@@ -1122,6 +1122,7 @@
                *freebsd*) SYSTEM="freebsd" ;;
                *netbsd*) SYSTEM="netbsd" ;;
                *solaris*) SYSTEM="solaris" ;;
+               *irix*) SYSTEM="irix" ;;
                *) SYSTEM="generic" ;;
        esac
 
@@ -1145,6 +1146,11 @@
        MIMCFLAGS=""
        MIMLIBS="-lpthread -lsocket -lnsl"
 fi
+if test "$SYSTEM" = "irix"; then
+       MIMCC="cc -DBIG_ENDIAN -DRTP_BIG_ENDIAN -DREENTRANT -DNEED_INET_NTOP"
+       MIMCFLAGS=""
+       MIMLIBS="-lpthread"
+fi
 if test "$SYSTEM" = "generic"; then
   MIMCC="gcc -DLIL_ENDIAN -DRTP_LITTLE_ENDIAN -DREENTRANT -Wall"
   MIMCFLAGS="-pthread"

I would appreciate if this could be incorporated and maybe even reported back
to the original source.


If there is anything unclear, please do not hestitate to ask.


Georg

 

-- 
Georg Schwarz    http://home.pages.de/~schwarz/
 georg.schwarz%freenet.de@localhost     +49 178 8545053


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