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STARDEV  January 2019

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Subject:

Problem with Astro-FITS-CFITSIO-1.12

From:

Tom Marsh <[log in to unmask]>

Reply-To:

Starlink development <[log in to unmask]>

Date:

Mon, 7 Jan 2019 14:10:12 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (86 lines)

Hello, I thought I was going to manage to get through the whole starlink compilation without problem (on Centos 7) for the first time ever, but hit an issue during the perl module stage -- see below. I had a look at the CFITSIO.so library referred to, and there is indeed an undefined symbol there:

nm CFITSIO.so  | grep ffgsky
00000000000579f0 t XS_Astro__FITS__CFITSIO_ffgsky
                 U ffgsky


A quick google suggests a more recent cfitsio version is needed (3.39). Looking on the system here I see version 3.370, but I assumed starlink shipped its own version of cfitsio?

Any suggestions on what I should do at this point? Perhaps not important from the point of view of making my PAMELA mod? 

Tom

The output from the installation showing the problem:

more /home/astro/phsaap/.cpanm/work/1546868621.14559/build.log
cpanm (App::cpanminus) 1.7044 on perl 5.026001 built for x86_64-linux
Work directory is /home/astro/phsaap/.cpanm/work/1546868621.14559
You have make /usr/bin/make
You have LWP 6.36
You have /usr/bin/tar: tar (GNU tar) 1.26
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching Astro::FITS::CFITSIO () on cpanmetadb ...
--> Working on Astro::FITS::CFITSIO
Fetching http://www.cpan.org/authors/id/P/PR/PRATZLAFF/Astro-FITS-CFITSIO-1.12.tar.gz
-> OK
Unpacking Astro-FITS-CFITSIO-1.12.tar.gz
Entering Astro-FITS-CFITSIO-1.12
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.24)
Configuring Astro-FITS-CFITSIO-1.12
Running Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Astro::FITS::CFITSIO
Writing MYMETA.yml and MYMETA.json
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.24)
Building and testing Astro-FITS-CFITSIO-1.12
cp CFITSIO.pm blib/lib/Astro/FITS/CFITSIO.pm
AutoSplitting blib/lib/Astro/FITS/CFITSIO.pm (blib/lib/auto/Astro/FITS/CFITSIO)
Running Mkbootstrap for CFITSIO ()
chmod 644 "CFITSIO.bs"
"/storage/astro1/phsaap/software/star/Perl/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CFITSIO.bs blib/arch/auto/Astro/FITS/CFITSIO/CFIT
SIO.bs 644
"/storage/astro1/phsaap/software/star/Perl/bin/perl" "/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/ExtUtils/xsubpp"  -typemap '/stor
age/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/ExtUtils/typemap' -typemap '/home/astro/phsaap/.cpanm/work/1546868621.14559/Astro-FITS-CFITS
IO-1.12/typemap'  CFITSIO.xs > CFITSIO.xsc
mv CFITSIO.xsc CFITSIO.c
gcc -c  -I/storage/astro1/phsaap/software/star -I/storage/astro1/phsaap/software/star/include -fwrapv -fno-strict-aliasing -pipe -fstack-protector
-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -g -O2   -DVERSION=\"1.12\" -DXS_VERSION=\"1.12\" -fPI
C "-I/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/CORE"   CFITSIO.c
gcc -c  -I/storage/astro1/phsaap/software/star -I/storage/astro1/phsaap/software/star/include -fwrapv -fno-strict-aliasing -pipe -fstack-protector
-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -g -O2   -DVERSION=\"1.12\" -DXS_VERSION=\"1.12\" -fPI
C "-I/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/CORE"   util.c
rm -f blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so
LD_RUN_PATH="/storage/astro1/phsaap/software/star/lib" gcc  -shared -g -O2 -L/storage/astro1/phsaap/software/lib -L/usr/local/lib -fstack-protector-strong CFITSIO.o util.o  -o blib/arch
/auto/Astro/FITS/CFITSIO/CFITSIO.so  \
   -L/storage/astro1/phsaap/software/star -L/storage/astro1/phsaap/software/star/lib -lcfitsio -lm   \
  
chmod 755 blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so
Manifying 1 pod document
"/storage/astro1/phsaap/software/star/Perl/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CFITSIO.bs blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.bs 644
PERL_DL_NONLAZY=1 "/storage/astro1/phsaap/software/star/Perl/bin/perl" "-Iblib/lib" "-Iblib/arch" test.pl

Loading................................Can't load 'blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so' for module Astro::FITS::CFITSIO: blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so: undefined
 symbol: ffgsky at /storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/DynaLoader.pm line 193.

Compilation failed in require at test.pl line 26.
BEGIN failed--compilation aborted at test.pl line 26.
make: *** [test_dynamic] Error 2
-> FAIL Installing Astro::FITS::CFITSIO failed. See /home/astro/phsaap/.cpanm/work/1546868621.14559/build.log for details. Retry with --force to force install it.
shika:perlmods> 

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