compilation on slackware64 14.1

[Rob van Nues]

Hi,

I got this error when compiling on  Slackware linux (64 bit, version 14.1 )

===(       2;0  1/?  1/?  0/? )=========================================

#   Failed test 'test6 worked (../fastq-mcf -l 15 in/mcf/test.fa in/mcf/test1.fq -o tmp/mcf.t.RAIQv/test6.out.gz > tmp/mcf.t.RAIQv/test6.err 2>&1)'

#   at t/mcf.t line 30.

gzip: tmp/mcf.t.RAIQv/test6.out.gz: unexpected end of file

#   Failed test 'Files equal: tmp/mcf.t.RAIQv/test6.out.gz == out/mcf/test6.out.gz'

#   at t/test-prep.pl line 48.

#   Failed test 'Files equal: tmp/mcf.t.RAIQv/test6.err == out/mcf/test6.err'

#   at t/test-prep.pl line 48.

# removing tmp/join.t.6jdJA

t/join.t ... ok                                                         

===(      38;0  20/?  0/? )=============================================# Looks like you failed 3 tests of 28.

t/mcf.t .... Dubious, test returned 3 (wstat 768, 0x300)                

Failed 3/28 subtests 

t/multx.t .. 4/? 

#   Failed test 'test2 worked (../fastq-multx -l in/multx/master-barcodes.txt in/multx/mxtest_2.fastq in/multx/mxtest_1.fastq in/multx/mxtest_3.fastq -o n/a -o tmp/multx.t.Zi8vW/mxout_%_1.fq.gz -o tmp/multx.t.Zi8vW/mxout_%_2.fq.gz > tmp/multx.t.Zi8vW/test2.out 2> tmp/multx.t.Zi8vW/test2.err)'

#   at t/multx.t line 25.

#   Failed test 'Files equal: tmp/multx.t.Zi8vW/test2.out == out/multx/test2.out'

#   at t/test-prep.pl line 48.

#   Failed test 'Files equal: tmp/multx.t.Zi8vW/test2.err == out/multx/test2.err'

#   at t/test-prep.pl line 48.

# Looks like you failed 3 tests of 12.

t/multx.t .. Dubious, test returned 3 (wstat 768, 0x300)

Failed 3/12 subtests 

Test Summary Report

-------------------

t/mcf.t  (Wstat: 768 Tests: 28 Failed: 3)

  Failed tests:  17-19

  Non-zero exit status: 3

t/multx.t (Wstat: 768 Tests: 12 Failed: 3)

  Failed tests:  4-6

  Non-zero exit status: 3

Files=3, Tests=58,  2 wallclock secs ( 0.04 usr  0.00 sys +  0.64 cusr  1.44 csys =  2.12 CPU)

Result: FAIL

make: *** [check] Error 1

bash-4.3# 

.

I noticed there was a complaint early on about automake & aclocal, which are version 1.14 on my installation and not the expected 1.11; My autoconf version is 2.69 (not 2.68)

config.status: executing depfiles commands

make[1]: Entering directory `/home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2'

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run aclocal-1.11 -I m4

/home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2/missing: line 52: aclocal-1.11: command not found

WARNING: `aclocal-1.11' is missing on your system.  You should only need it if

         you modified `acinclude.m4' or `configure.ac'.  You might want

         to install the `Automake' and `Perl' packages.  Grab them from

         any GNU archive site.

 cd . && /bin/sh /home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run automake-1.11 --gnu

/home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2/missing: line 52: automake-1.11: command not found

WARNING: `automake-1.11' is missing on your system.  You should only need it if

         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.

         You might want to install the `Automake' and `Perl' packages.

         Grab them from any GNU archive site.

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /home/rob/WORK/BIOINFO/EA-UTILS/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run autoconf

aclocal.m4:16: warning: this file was generated for autoconf 2.68.

You have another version of autoconf.  It may work, but is not guaranteed to.

If you have problems, you may need to regenerate the build system entirely.

To do so, use the procedure documented by the package, typically `autoreconf'.

/bin/sh ./config.status --recheck

running CONFIG_SHELL=/bin/sh /bin/sh ./configure --no-create --no-recursion

checking for a BSD-compatible install... /bin/ginstall -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

Trying to follow the hint does not give anything

bash-4.3# cd sparsehash-2.0.2/

bash-4.3# autoreconf

/usr/share/aclocal/imlib.m4:9: warning: underquoted definition of AM_PATH_IMLIB

/usr/share/aclocal/imlib.m4:9:   run info Automake 'Extending aclocal'

/usr/share/aclocal/imlib.m4:9:   or see http://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal

configure.ac:16: error: required file './compile' not found

configure.ac:16:   'automake --add-missing' can install 'compile'

Makefile.am:156: warning: source file 'src/hashtable_test.cc' is in a subdirectory,

Makefile.am:156: but option 'subdir-objects' is disabled

automake: warning: possible forward-incompatibility.

automake: At least a source file is in a subdirectory, but the 'subdir-objects'

automake: automake option hasn't been enabled.  For now, the corresponding output

automake: object file(s) will be placed in the top-level directory.  However,

automake: this behaviour will change in future Automake versions: they will

automake: unconditionally cause object files to be placed in the same subdirectory

automake: of the corresponding sources.

automake: You are advised to start using 'subdir-objects' option throughout your

automake: project, to avoid future incompatibilities.

Makefile.am:140: warning: source file 'src/libc_allocator_with_realloc_test.cc' is in a subdirectory,

Makefile.am:140: but option 'subdir-objects' is disabled

Makefile.am:172: warning: source file 'src/simple_compat_test.cc' is in a subdirectory,

Makefile.am:172: but option 'subdir-objects' is disabled

Makefile.am:166: warning: source file 'src/simple_test.cc' is in a subdirectory,

Makefile.am:166: but option 'subdir-objects' is disabled

Makefile.am:148: warning: source file 'src/sparsetable_unittest.cc' is in a subdirectory,

Makefile.am:148: but option 'subdir-objects' is disabled

Makefile.am:125: warning: source file 'src/template_util_unittest.cc' is in a subdirectory,

Makefile.am:125: but option 'subdir-objects' is disabled

Makefile.am:179: warning: source file 'src/time_hash_map.cc' is in a subdirectory,

Makefile.am:179: but option 'subdir-objects' is disabled

Makefile.am:132: warning: source file 'src/type_traits_unittest.cc' is in a subdirectory,

Makefile.am:132: but option 'subdir-objects' is disabled

parallel-tests: error: required file './test-driver' not found

parallel-tests:   'automake --add-missing' can install 'test-driver'

autoreconf: automake failed with exit status: 1

Sorry, I am not familiar with C to troubleshoot this any further.....

Do you have any idea how to get this working?

Thanks in advance

Rob

[Rob van Nues]

Further noticed that

Enter code here...utils.cppis lacking(dangling symlink  tidx/utils.cpp ->../utils.cpp)

 but dunno whether that is relevant

Thanks in advance

Rob

[Erik Aronesty]

- tidx isn't necessary for most ofd what people do with ea-utils that's a utility for highspeed annotation.   

for the other errors, you need "libtool" installed:

sudo apt-get install automake autoconf libtool