Re: Packaging SMALT for Debian
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Hi again,
I made some step forward with the tests (see below)
On Tue, Apr 08, 2014 at 07:38:54PM +0200, Andreas Tille wrote:
> ERROR when mapping: returned with code 1
> FAIL: bam_cigar_test.py
> =================================
> 1 of 7 tests failed
> Please report to hp3@sanger.ac.uk
> =================================
According to the logfile this is related to the fact that bambamc
library is missing. While I plan to package bambamc library as well
(just contacted the author[1]) for now I builded the package with the
option --with-bambamc=no. Unfortunately this did not helped excluding
the test and I think the problem is in the test/Makefile.am which says:
if WITH_BAMBAMC
TESTS += ioform_test.py xali_test.py
endif
if WITH_SAMTOOLS_EXEC
TESTS += bam_cigar_test.py
endif
So bam_cigar_test.py is not excluded from the tests if bambamc is
missing. I tried some patch to Makefile.am (attached) but this fails
unfortunately. I have to admit I had to fight through strange automake
warnings telling me I should enable
AUTOMAKE_OPTIONS = subdir-objects
and to set
AM_PROG_AR
in the main Makefile.am. Perhaps these are some "features" of later
automake versions. Unfortunately I ended up with a Makefile which
contains a line
... am__expect_failure=no;; esac; /usr/bin/python /bin/bash ../test-driver --test-name "$f"
which is totally stupid since python tries to call /bin/bash which for
sure ends up in a failure. I have no clue why automake might create
this nonsense and I think I'll leave it to you how to drop the
bam_cigar_test.py apropriately from the tests if bambamc is missing.
Kind regards
Andreas.
[1] https://lists.debian.org/debian-med/2014/04/msg00023.html
--
http://fam-tille.de
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -1,4 +1,6 @@
## Process this file with automake to produce Makefile.in
+AUTOMAKE_OPTIONS = subdir-objects
+
DIST_SUBDIRS = data
INCLUDE_PATTERN = -I%
@@ -87,11 +89,11 @@ endif
TESTS += ${TEST_DRIVERS}
-if WITH_BAMBAMC
+if WITH_SAMTOOLS_EXEC
TESTS += ioform_test.py xali_test.py
endif
-if WITH_SAMTOOLS_EXEC
+if WITH_BAMBAMC
TESTS += bam_cigar_test.py
endif
--- a/misc/Makefile.am
+++ b/misc/Makefile.am
@@ -1,4 +1,6 @@
## Process this file with automake to produce Makefile.in
+AUTOMAKE_OPTIONS = subdir-objects
+
AM_CFLAGS = -I../src/
if ICC_COMPILER
if ICC_MMIC
--- a/configure.ac
+++ b/configure.ac
@@ -35,7 +35,7 @@ AC_PROG_CC([icc gcc cc])
# AM_PROG_CC_C_O
# we use a archiver, so add support for unusual archivers
-# AM_PROG_AR
+AM_PROG_AR
# find pkg-config tests
PKG_PROG_PKG_CONFIG
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