Hi Robert,
On 23/03/2017 21:09, Klima, Robert (NIH/NIAID) [C] wrote:
Hi Kenneth.
Thank you for your recommendation. Unfortunately the pandaseq
installation failed.
Here is a tail of log file.
Can you check the config.log in
/sysapps/cluster/build/PANDAseq/2.11/foss-2016b/pandaseq-2.11 for error
messages to figure out what is failing exactly?
regards,
Kenneth
Regards,
Robert
== 2017-03-23 10:38:23,849 easyblock.py:1346 INFO Using
/sysapps/cluster/build/PANDAseq/2.11/foss-2016b/pandaseq-2.11/ as
start dir
== 2017-03-23 10:38:23,849 build_log.py:216 INFO configuring...
== 2017-03-23 10:38:23,850 easyblock.py:2286 INFO Starting configure step
== 2017-03-23 10:38:23,850 easyblock.py:2289 INFO Running method
configure_step part of step configure
== 2017-03-23 10:38:23,850 run.py:162 INFO running cmd: ./autogen.sh
&& ./configure --prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b
== 2017-03-23 10:38:37,351 build_log.py:147 ERROR EasyBuild crashed
with an error (at ?:124 in __init__): cmd "./autogen.sh && ./configure
--prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b " exited
with exitcode 77 and output:
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:17: installing './ar-lib'
configure.ac:18: installing './compile'
configure.ac:19: installing './config.guess'
configure.ac:19: installing './config.sub'
configure.ac:3: installing './install-sh'
configure.ac:3: installing './missing'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in
`/sysapps/cluster/build/PANDAseq/2.11/foss-2016b/pandaseq-2.11':
configure: error: C compiler cannot create executables
See `config.log' for more details
(at easybuild/tools/run.py:449 in parse_cmd_output)
== 2017-03-23 10:38:37,352 easyblock.py:2518 WARNING build failed
(first 300 chars): cmd "./autogen.sh && ./configure
--prefix=/sysapps/cluster/software/PANDAseq/2.11-foss-2016b " exited
with exitcode 77 and output:
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4
== 2017-03-23 10:38:37,353 easyblock.py:276 INFO Closing log for
application name PANDAseq version 2.11
*From: *<[email protected]> on behalf of Kenneth Hoste
<[email protected]>
*Reply-To: *"[email protected]" <[email protected]>
*Date: *Thursday, March 23, 2017 at 10:28 AM
*To: *"[email protected]" <[email protected]>
*Subject: *Re: [easybuild] PANDAseq - static
Hi Robert,
On 23/03/2017 14:12, Klima, Robert (NIH/NIAID) [C] wrote:
Hi,
I am trying to install a static version of PANDAseq. I have
modified pandaseq to use PANDAseq vers. 2.11 and toolchain
foss-2016b.
I have added:
configopts = ['--enable-static=yes']
The installation was:
COMPLETED: Installation ended successfully.
However, I received the "error while loading shared libraries:
libbz2.so.1.0".
What other options should I use to create a static version?
Maybe this this:
toolchainopts = {'static': True}
This will make EasyBuild include a -static in $CFLAGS and friends,
which may be sufficient...
regards,
Kenneth
Thank you,
Robert
-----
name = 'PANDAseq'
version = '2.11'
homepage = 'https://github.com/neufeld/pandaseq'
description = """PANDAseq assembles Illumina Solexa overlapping
pair-end reads."""
toolchain = {'name': 'foss', 'version': '2016b'}
configopts = ['--enable-static=yes']
# source_urls =
['https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz']
sources = [SOURCELOWER_TAR_GZ]
dependencies = [
('libtool', '2.4.6'),
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
]
builddependencies = [('Autoconf', '2.69')]
preconfigopts = "./autogen.sh &&"
sanity_check_paths = {
'files': ['bin/pandaseq', 'bin/pandaseq-checkid',
'bin/pandaseq-hang', 'bin/pandaxs',
'lib/libpandaseq.%s' % SHLIB_EXT, 'lib/libpandaseq.a',
'lib/pkgconfig/pandaseq-%(version_major)s.pc'],
'dirs': ['include/pandaseq-%(version_major)s'],
}
moduleclass = 'bio'
