Hi Robert,
The log file contains the output below for the "perl Makefile.PL
PREFIX=..." command being run before 'make', which seems to indicate the
real problem.
Although this is clearly an error, the command exited with exit code 0
(zero), so EasyBuild couldn't know it was actually a problem, and
happily continued to run 'make'.
== 2016-04-20 15:32:05,690 run.py:99 DEBUG run_cmd: running cmd perl
Makefile.PL
PREFIX=/nethome/klimarw/.local/easybuild/software/PRINSEQ/0.20.4-goolf-1.4.10-Perl-5.16.3
(in
/nethome/klimarw/.local/easybuild/build/PRINSEQ/0.20.4/goolf-1.4.10-Perl-5.16.3/Cairo/Cairo-1.106)
== 2016-04-20 15:32:05,801 run.py:392 DEBUG cmd " perl Makefile.PL
PREFIX=/nethome/klimarw/.local/easybuild/software/PRINSEQ/0.20.4-goolf-1.4.10-Perl-5.16.3
" exited with exitcode 0 and output:
Package cairo was not found in the pkg-config search path.
Perhaps you should add the directory containing `cairo.pc'
to the PKG_CONFIG_PATH environment variable
No package 'cairo' found
at Makefile.PL line 99.
*** can not find package cairo >= 1.0.0
*** check that it is properly installed and available in PKG_CONFIG_PATH
at Makefile.PL line 99.
regards,
Kenneth
On 20/04/16 22:11, Klima, Robert (NIH/NIAID) [C] wrote:
Hi,
The run eb PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb --debug
--parallel=1 failed with error:
== FAILED: Installation ended unsuccessfully (build directory:
/nethome/klimarw/.local/easybuild/build/PRINSEQ/0.20.4/goolf-1.4.10-Perl-5.16.3):
build failed (first 300 chars): cmd " make -j 1 " exited with exitcode
2 and output:
make: *** No targets specified and no makefile found. Stop.
== Results of the build can be found in the log file
/tmp/eb-71G2kZ/easybuild-PRINSEQ-0.20.4-20160420.153152.dzvFm.log
ERROR: Build of
/sysapps/cluster/software/EasyBuild/2.7.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.7.0-py2.7.egg/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb
failed (err: 'build failed (first 300 chars): cmd " make -j 1 " exited
with exitcode 2 and output:\nmake: *** No targets specified and no
makefile found. Stop.\n')
The logfile is attached.
Thank you,
Robert
From: <[email protected]
<mailto:[email protected]>> on behalf of Kenneth Hoste
<[email protected] <mailto:[email protected]>>
Reply-To: "[email protected] <mailto:[email protected]>"
<[email protected] <mailto:[email protected]>>
Date: Wednesday, April 20, 2016 at 3:21 PM
To: "[email protected] <mailto:[email protected]>"
<[email protected] <mailto:[email protected]>>
Subject: Re: [easybuild] Cufflinks/2.2.1/goolf-1.7.20
Hi Robert,
On 20/04/16 21:09, Klima, Robert (NIH/NIAID) [C] wrote:
Hi,
I am sorry for not being clear enough at the first email.
We have installed EasyBuild/2.7.0 a couple weeks ago.
Recently I have run a couple installations and received cmd " make -j
32 " errors on some of them.
One of unsuccessful installations was Trinity. Next I tried PRINSEQ
and both installation failed;
PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb and
PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb.
I would like to follow just one installation: eb
PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb —robot
The error message:
== FAILED: Installation ended unsuccessfully (build directory:
/sysapps/cluster/build/PRINSEQ/0.20.4/goolf-1.4.10-Perl-5.16.3):
build failed (first 300 chars): cmd " make -j 32 " exited with
exitcode 2 and output:
make: *** No targets specified and no makefile found. Stop.
== Results of the build can be found in the log file
/tmp/eb-omFhgm/easybuild-PRINSEQ-0.20.4-20160420.133303.hNjww.log
ERROR: Build of
/sysapps/cluster/software/EasyBuild/2.7.0/lib/python2.7/site-packages/easybuild_easyconfigs-2.7.0-py2.7.egg/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb
failed (err: 'build failed (first 300 chars): cmd " make -j 32 "
exited with exitcode 2 and output:\nmake: *** No targets specified
and no makefile found. Stop.\n')
I am attaching log file:
/tmp/eb-omFhgm/easybuild-PRINSEQ-0.20.4-20160420.133303.hNjww.log
Please rerun with the --debug option enabled, it will provide a more
detailed log.
Also, please check if using --parallel=1 makes a difference, -j 32 is
rather high and the Makefile may not be 'ready' for it...
regards,
Kenneth
I am debugging Cufflinks missing library issue as may be related to
the different module environment.
In case of boost installation, Boost/1.55.0-goolf-1.7.20-Python-3.5.1
and Boost/1.57.0-goolf-1.7.20-Python-2.7.9 were installed correctly.
Thank you for your help,
Robert
--
*Robert Klima, Contractor*
Sr. HPC Engineer - Linux and High Performance Computing Team
National Institute of Allergy and Infectious Diseases
SRA International Inc., A CSRA Company
office 240 669 5514 mobile 202 657 7154
[email protected] <mailto:[email protected]>
5601 Fishers Lane
Room 6A61B, MSC 9816
Bethesda, MD 20892-9816
Disclaimer: The information in this e-mail and any of its attachments
is confidential and may contain sensitive information. It should not
be used by anyone who is not the original intended recipient. If you
have received this e-mail in error please inform the sender and
delete it from your mailbox or any other storage devices. National
Institute of Allergy and Infectious Diseases shall not accept
liability for any statements made that are sender's own and not
expressly made on behalf of the NIAID by one of its representatives.
From: <[email protected]> on behalf of Robert Schmidt
<[email protected] <mailto:[email protected]>>
Reply-To: "[email protected]" <[email protected]
<mailto:[email protected]>>
Date: Wednesday, April 20, 2016 at 8:43 AM
To: "[email protected]" <[email protected]
<mailto:[email protected]>>
Subject: Re: [easybuild] Cufflinks/2.2.1/goolf-1.7.20
Can you post a full debug on gist or something? It is hard to say
from that output what the problem might be since with make -j 32 the
error could be quite a way back in the log.
I don't see why you would have had problem with boost 1.55 though.
You are saying that the easybuild config for boost didnt' work?
On Wed, Apr 20, 2016 at 8:40 AM Klima, Robert (NIH/NIAID) [C]
<[email protected] <mailto:[email protected]>> wrote:
Hi,
I was able to successfully build Cufflinks 2.2.1
using Cufflinks-2.2.1-goolf-1.7.20.eb with:
dependencies = [
('Boost', '1.55.0'),
After running submit script, I'm receiving the following error:
"cuffnorm: error while loading shared libraries:
libboost_thread.so.1.55.0: cannot open shared object file: No
such file or directory"
This is true, libboost_thread.so.1.55.0 file is missing.
Well, I changed Cufflinks-2.2.1-goolf-1.7.20.eb only to run:
dependencies = [
('Boost', '1.57.0'),
The installation failed with errors:
== FAILED: Installation ended unsuccessfully (build directory:
/sysapps/cluster/build/Cufflinks/2.2.1/goolf-1.7.20): build
failed (first 300 chars): cmd " make -j 32 " exited with
exitcode 2 and output:
make all-recursive
make[1]: Entering directory
`/sysapps/cluster/build/Cufflinks/2.2.1/goolf-1.7.20/cufflinks-2.2.1'
Making all in src
make[2]: Entering directory
`/sysapps/cluster/build/Cufflinks/2.2.1/goolf-1.7.20/cufflinks-2.2.1/src'
if g++ -
== Results of the build can be found in the log file
/tmp/eb-Og2D2j/easybuild-Cufflinks-2.2.1-20160419.162427.QEeOi.log
ERROR: Build of /nethome/klimarw/Cufflinks-2.2.1-goolf-1.7.20.eb
failed (err: 'build failed (first 300 chars): cmd " make -j 32 "
exited with exitcode 2 and output:\nmake
all-recursive\nmake[1]: Entering directory
`/sysapps/cluster/build/Cufflinks/2.2.1/goolf-1.7.20/cufflinks-2.2.1\'\nMaking
all in src\nmake[2]: Entering directory
`/sysapps/cluster/build/Cufflinks/2.2.1/goolf-1.7.20/cufflinks-2.2.1/src\'\nif
g++ -')
Do you have an idea how to correct the script/installation?
Regards,
Robert
--
*Robert Klima, Contractor*
Sr. HPC Engineer - Linux and High Performance Computing Team
National Institute of Allergy and Infectious Diseases
SRA International Inc., A CSRA Company
office 240 669 5514 mobile 202 657 7154
<mailto:[email protected]>[email protected]
5601 Fishers Lane
Room 6A61B, MSC 9816
Bethesda, MD 20892-9816
Disclaimer: The information in this e-mail and any of its
attachments is confidential and may contain sensitive
information. It should not be used by anyone who is not the
original intended recipient. If you have received this e-mail in
error please inform the sender and delete it from your mailbox
or any other storage devices. National Institute of Allergy and
Infectious Diseases shall not accept liability for any
statements made that are sender's own and not expressly made on
behalf of the NIAID by one of its representatives.
