[lsst-dm-stack-users] astrometry_net build fail
Simon Krughoff
simon.krughoff at gmail.com
Sat Aug 9 19:46:01 PDT 2014
I have seen problems like this when the libm.so distributed with anaconda
is found prior to the system libm.so (see:
https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/rX_c12a7Sps).
You could try renaming the libm in the anaconda/lib (and renaming math.h
in anaconda/include) to see if that helps.
Simon
On Sat, Aug 9, 2014 at 7:27 PM, Hu Zhan <zhanhu at nao.cas.cn> wrote:
> 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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> lsst-dm-stack-users at listserv.lsstcorp.org
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>
>
--
K. Simon Krughoff
University of Washington
Department of Astronomy
Physics-Astronomy Bldg.
3910 15th Ave NE
Room C319
Seattle WA 98195-0002
USA
(206)543-9487
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