[lsst-dm-stack-users] astrometry_net build fail
Hu Zhan
zhanhu at nao.cas.cn
Sat Aug 9 19:27:28 PDT 2014
Hi All,
I succeeded with "eups distrib install sims_maf -t sims" on ubuntu 12.04 but
also encountered a problem with astrometry_net while installing lsst_sims. I
was able to go a bit further than Chuck after installing a few dependencies.
But now it complains about "conflicting types for qsort_r" in the build log
(see the attachment) and "undefined reference to roundf" in the output
below. Could someone point me to a fix?
Thanks,
Hu
Here is the output of "eups distrib install lsst_sims -t sims"
eups distrib install lsst_sims -t sims
[ 1/61 ] cfitsio 3310+2 (already installed)
done.
[ 2/61 ] doxygen 1.8.2+2 (already installed)
done.
[ 3/61 ] eigen 3.1.1+2 (already installed)
done.
[ 4/61 ] fftw 3.3.2+2 (already installed)
done.
[ 5/61 ] freetds 2014.04.07 (already installed)
done.
[ 6/61 ] gsl 1.15+2 (already installed)
done.
[ 7/61 ] minuit2 5.22.00+2 (already installed)
done.
[ 8/61 ] mysqlclient 5.1.65+3 (already installed)
done.
[ 9/61 ] pyephem 3.7.5.1 (already installed)
done.
[ 10/61 ] python 0.0.1 (already installed)
done.
[ 11/61 ] sims_dustmaps 2014.04.17 (already installed)
done.
[ 12/61 ] sims_sed_library 2014.04.23 (already installed)
done.
[ 13/61 ] swig 2.0.12 (already installed)
done.
[ 14/61 ] throughputs master-ga6e2efc0c9 (already installed)
done.
[ 15/61 ] xpa 2.1.14+2 (already installed)
done.
[ 16/61 ] astrometry_net 0.30+3 ...
***** error: from
/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/build.log:
cc -std=gnu89 -std=gnu89 -g -Wall -ffinite-math-only -fno-signaling-nans
-pthread -mtune=generic -O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/freetype2 -I/usr/include/libpng12 -I../gsl-an
-I../qfits-an/include -I../libkd -I. -c -o hd.o hd.c
In file included from starutil.h:219:0,
from hd.c:22:
starutil.inc: In function ‘star_coords’:
starutil.inc:203:22: warning: variable ‘etaz’ set but not used
[-Wunused-but-set-variable]
rm -f libanfiles.a
ar rc libanfiles.a index.o codekd.o starkd.o rdlist.o xylist.o starxy.o
an-catalog.o qidxfile.o quadfile.o scamp-catalog.o hd.o
ranlib libanfiles.a
cc -shared -fPIC -o _sip.so sip-utils.o sip.o starutil.o mathutil.o
sip_qfits.o fitsioutils.o ioutils.o bl.o os-features.o an-endian.o errors.o
log.o ../qfits-an/lib/libqfits.a
cc -shared -fPIC -o _healpix.so healpix-utils.o healpix.o permutedsort.o
starutil.o mathutil.o errors.o bl.o log.o os-features.o
cc -std=gnu89 -std=gnu89 -g -Wall -ffinite-math-only -fno-signaling-nans
-pthread -mtune=generic -O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/freetype2 -I/usr/include/libpng12 -I../gsl-an
-I../qfits-an/include -I../libkd -I. -c -o an-fitstopnm.o an-fitstopnm.c
cc -g -Wall -ffinite-math-only -fno-signaling-nans -pthread -mtune=generic
-O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline -lm an-fitstopnm.o
libanutils.a ../qfits-an/lib/libqfits.a -o an-fitstopnm
an-fitstopnm.o: In function `main':
/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/astrometry_net-0.30+3/
util/an-fitstopnm.c:348: undefined reference to `roundf'
/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/astrometry_net-0.30+3/
util/an-fitstopnm.c:339: undefined reference to `roundf'
collect2: ld returned 1 exit status
make[1]: *** [an-fitstopnm] Error 1
make[1]: Leaving directory
`/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/astrometry_net-0.30+3
/util'
make: *** [all] Error 2
+ exit -4
eups distrib: Failed to build astrometry_net-0.30+3.eupspkg: Command:
source /home/lsst/eups/bin/setups.sh; export EUPS_PATH=/home/lsst;
(/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/build.sh) >>
/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/build.log 2>&1
4>/home/lsst/EupsBuildDir/Linux64/astrometry_net-0.30+3/build.msg
exited with code 252
> -----Original Message-----
> From: Lynne Jones [mailto:ljones.uw at gmail.com]
> Sent: 2014年8月8日 3:11
> To: Chuck Claver; LSST DM Stack Users
> Cc: lsstcadence_maf at noao.edu
> Subject: Re: Another MAF build fail
>
> I’m going to kick this one straight along to the experts at
lsst-dm-stack-users, as
> astrometry.net is a tricky part of the installation.
>
> However, Chuck, I’ll let you in on a little secret I’m not supposed to
publicize
> though ― if you do
> ‘eups distrib install sims_maf -t sims’
> instead of
> 'eups distrib install lsst_sims -t sims'
> you will skip a good chunk of the installation not directly relevant to
MAF and in
> particular you will skip astrometry.net.
>
> We’re trying to get people to install the entire sims package, which has
wider
> dependencies than MAF alone, because we anticipate that you will want the
rest
> of the sims packages sooner rather than later (and we’d rather not say,
“well,
> go back and add to you install”) … but in this case, with the limited
time before
> the workshop, I’d say go ahead and try the shorter installation if you
don’t hear
> back from lsst-dm-stack-users shortly.
>
> Lynne
>
>
> On Aug 7, 2014, at 12:04 PM, Chuck Claver <cclaver at noao.edu> wrote:
>
> > All,
> >
> > In my attempt to install MAF asrtometry.net failed to build due to a
missing
> "pam.h"
> >
> > Chuck
> >
> > Here is my command line:
> >
> > -> eups distrib install lsst_sims -t sims
> >
> > Here is my screen dump:
> > [ 1/61 ] cfitsio 3310+2
> done.
> > [ 2/61 ] doxygen 1.8.2+2 (already installed)
> done.
> > [ 3/61 ] eigen 3.1.1+2
> done.
> > [ 4/61 ] fftw 3.3.2+2
> done.
> > [ 5/61 ] freetds 2014.04.07
> done.
> > [ 6/61 ] gsl 1.15+2
> done.
> > [ 7/61 ] minuit2 5.22.00+2
> done.
> > [ 8/61 ] mysqlclient 5.1.65+3
> done.
> > [ 9/61 ] pyephem 3.7.5.1
> done.
> > [ 10/61 ] python 0.0.1 (already installed)
> done.
> > [ 11/61 ] sims_dustmaps 2014.04.17
> done.
> > [ 12/61 ] sims_sed_library 2014.04.23
> done.
> > [ 13/61 ] swig 2.0.12
> done.
> > [ 14/61 ] throughputs master-ga6e2efc0c9
> done.
> > [ 15/61 ] xpa 2.1.14+2
> done.
> > [ 16/61 ] astrometry_net 0.30+3 ...
> >
> > ***** error: from
> /Users/chuckclaver/src/LSST/EupsBuildDir/DarwinX86/astrometry_net-0.30+3/
> build.log:
> > ./keywords.h:84:44: note: expanded from macro 'Flatten'
> > # define Flatten __attribute__ (( flatten))
> > ^
> > 36 warnings generated.
> > rm -f libanfiles.a
> > ar rc libanfiles.a index.o codekd.o starkd.o rdlist.o xylist.o starxy.o
> an-catalog.o qidxfile.o quadfile.o scamp-catalog.o hd.o
> > ranlib libanfiles.a
> > cc -shared -dynamic -dynamiclib -fPIC -o _sip.so sip-utils.o sip.o
starutil.o
> mathutil.o sip_qfits.o fitsioutils.o ioutils.o bl.o os-features.o
an-endian.o errors.o
> log.o ../qfits-an/lib/libqfits.a
> > cc -shared -dynamic -dynamiclib -fPIC -o _healpix.so healpix-utils.o
healpix.o
> permutedsort.o starutil.o mathutil.o errors.o bl.o log.o os-features.o
> > cc -std=gnu89 -std=gnu89 -g -Wall -ffinite-math-only
-fno-signaling-nans
> -pthread -mtune=generic -O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline
> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
> -I/opt/local/include/cairo -I/opt/local/include/glib-2.0
> -I/opt/local/lib/glib-2.0/include -I/opt/local/include
> -I/opt/local/include/pixman-1 -I/opt/local/include
-I/opt/local/include/freetype2
> -I/opt/local/include -I/opt/local/include/freetype2
-I/opt/local/include/libpng16
> -I/opt/local/include -I../gsl-an -I../qfits-an/include -I../libkd -I.
-c -o
> an-fitstopnm.o an-fitstopnm.c
> > cc -g -Wall -ffinite-math-only -fno-signaling-nans -pthread
-mtune=generic
> -O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline -lm an-fitstopnm.o
> libanutils.a ../qfits-an/lib/libqfits.a -o an-fitstopnm
> > clang: warning: argument unused during compilation: '-pthread'
> > cc -std=gnu89 -std=gnu89 -g -Wall -ffinite-math-only
-fno-signaling-nans
> -pthread -mtune=generic -O3 -fomit-frame-pointer -DNDEBUG -fPIC -Winline
> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
> -I/opt/local/include/cairo -I/opt/local/include/glib-2.0
> -I/opt/local/lib/glib-2.0/include -I/opt/local/include
> -I/opt/local/include/pixman-1 -I/opt/local/include
-I/opt/local/include/freetype2
> -I/opt/local/include -I/opt/local/include/freetype2
-I/opt/local/include/libpng16
> -I/opt/local/include -I../gsl-an -I../qfits-an/include -I../libkd -I.
-c -o
> an-pnmtofits.o an-pnmtofits.c
> > an-pnmtofits.c:25:10: fatal error: 'pam.h' file not found
> > #include "pam.h"
> > ^
> > 1 error generated.
> > make[1]: *** [an-pnmtofits.o] Error 1
> > make: *** [all] Error 2
> > + exit -4
> > eups distrib: Failed to build astrometry_net-0.30+3.eupspkg: Command:
> > source /Users/chuckclaver/src/LSST/eups/bin/setups.sh; export
> EUPS_PATH=/Users/chuckclaver/src/LSST;
> (/Users/chuckclaver/src/LSST/EupsBuildDir/DarwinX86/astrometry_net-0.30+3/
> build.sh) >>
> /Users/chuckclaver/src/LSST/EupsBuildDir/DarwinX86/astrometry_net-0.30+3/
> build.log 2>&1
> 4>/Users/chuckclaver/src/LSST/EupsBuildDir/DarwinX86/astrometry_net-0.30+
> 3/build.msg
> > exited with code 252
> >
> >
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