Status of dotur

2013-11-20 Thread Andreas Tille 
Hi Patrick,

as you might know the program dotur is distributed in Debian (maintained
by Debian Med team).  I realised that the former download place

   http://www.plantpath.wisc.edu/fac/joh/DOTUR/

vanished and a further research leaded to

   http://www.mothur.org/software/dotur.html

which says:

   Please use mothur instead, feel free to contact Pat Schloss for more
   information.

Could you please so kind and enlight us with more information?  We would
like to know whether we should remove dotur from Debian and how exactly
we could replace it by mothur (which is packaged as well).  Is there any
wrapper script that behaves explicitly like dotur (just in case some
user have scripts hanging around which are relying on dotur).

Kind regards

   Andreas.

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Re: No relro when building from inside a Git package ?

2013-11-20 Thread Andreas Tille 
Hi Charles,

without having checked out the repository and diving into it:  Can you
post a diff of the two build logs?

Kind regards

Andreas.

On Wed, Nov 20, 2013 at 02:44:39PM +0900, Charles Plessy wrote:
> Dear all,
> 
> I am experience a strange variation when building package from a Git 
> repository
> or from the same source with the .git directory deleted.
> 
> In the first case I have the Lintian warning 'libhts0: hardening-no-relro
> usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1', but not in the second case.
> 
> The only git-dependant code that I found is to create a package version, but
> I override it in debian/rules by the Debian package's version.
> 
> In Makefile:
> 
> ifneq "$(wildcard .git)" ""
> original_version := $(PACKAGE_VERSION)
> PACKAGE_VERSION := $(shell git describe --always --dirty)
> 
> In debian/rules:
> 
> override_dh_auto_build:
>   dh_auto_build -- \
> CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
> CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
> LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \
> PACKAGE_VERSION="$(DEB_VERSION)"
> 
> override_dh_auto_install:
>   dh_auto_install -- prefix=/usr PACKAGE_VERSION="$(DEB_VERSION)"
> 
> (Digression: I do this because after tagging a debian revision, for instance
> 'debian/0.2.0_rc3-1', the package will fail to build from the Git repository
> since the tag becomes used for the soversion of the library, and the slash is
> mistaken as a directory separator.  Is there a smart solution to this problem 
> ?)
> 
> You can get the source with 'gbp clone https://github.com/Debian/htslib'.  
> Does
> anybody see why the hardening-no-relro is triggered when building in presence
> of the .git directory ?
> 
> Cheers,
> 
> -- 
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> 
> 
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> 

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Re: No relro when building from inside a Git package ?

2013-11-20 Thread Charles Plessy 
Le Wed, Nov 20, 2013 at 10:24:29PM +0100, Andreas Tille a écrit :
> 
> without having checked out the repository and diving into it:  Can you
> post a diff of the two build logs?

Hi Andreas,

here it is (attached).  Could the problem be a side effect of the test suite ?

Cheers,

-- 
Charles
--- with-.git   2013-11-21 09:32:14.244499056 +0900
+++ without-.git2013-11-21 09:34:12.908497923 +0900
@@ -150,15 +150,6 @@
 dh_auto_test
make -j1 test
 make[2]: Entering directory `/tmp/htslib'
-echo '#define HTS_VERSION "debian/0.2.0_rc3-1-38-g9469458"' > version.h
-gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c
-ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o 
hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o 
cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o 
cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o 
cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o 
cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
-ranlib libhts.a
-gcc -pthread  -o test/fieldarith test/fieldarith.o libhts.a  -lz
-gcc  -o test/hfile test/hfile.o libhts.a  -lz
-gcc -pthread  -o test/test_view test/test_view.o libhts.a  -lz
-gcc -pthread  -o test/test-vcf-api test/test-vcf-api.o libhts.a  -lz
-gcc -pthread  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a  -lz
 test/fieldarith test/fieldarith.sam
 test/hfile
 cd test && ./test_view.pl
@@ -456,11 +447,11 @@
 Failures  0
 cd test && ./test.pl
 test_vcf_api:
-   /tmp/htslib/test/test-vcf-api /tmp/Vvj_N60T4W/test-vcf-api.bcf
+   /tmp/htslib/test/test-vcf-api /tmp/cUKPv4vctM/test-vcf-api.bcf
 .. ok
 
 test_vcf_sweep:
-   /tmp/htslib/test/test-vcf-sweep /tmp/Vvj_N60T4W/test-vcf-api.bcf
+   /tmp/htslib/test/test-vcf-sweep /tmp/cUKPv4vctM/test-vcf-api.bcf
 .. ok
 
 
@@ -495,10 +486,6 @@
make -j1 install DESTDIR=/tmp/htslib/debian/tmp AM_UPDATE_INFO_DIR=no 
prefix=/usr PACKAGE_VERSION=0.2.0\~rc4-1
 make[2]: Entering directory `/tmp/htslib'
 mkdir -p /tmp/htslib/debian/tmp/usr/include/htslib 
/tmp/htslib/debian/tmp/usr/lib /tmp/htslib/debian/tmp/usr/share/man/man5
-echo '#define HTS_VERSION "0.2.0~rc4-1"' > version.h
-gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -fpic -c -o hts.pico hts.c
-gcc -shared -Wl,-soname,libhts.so.0  -o libhts.so kfunc.pico knetfile.pico 
kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico sam.pico 
synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico 
cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico 
cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico 
cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico 
cram/open_trace_file.pico cram/pooled_alloc.pico cram/sam_header.pico 
cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico  -lz
-ln -sf libhts.so libhts.so.0
 install -p -m 644 libhts.so 
/tmp/htslib/debian/tmp/usr/lib/libhts.so.0.2.0~rc4-1
 ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so
 ln -sf libhts.so.0.2.0~rc4-1 /tmp/htslib/debian/tmp/usr/lib/libhts.so.0
@@ -660,7 +647,7 @@
 dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see 
diff output below
 dpkg-gensymbols: warning: debian/libhts0/DEBIAN/symbols doesn't match 
completely debian/libhts0.symbols
 --- debian/libhts0.symbols (libhts0_0.2.0~rc4-1_amd64)
-+++ dpkg-gensymbolskXM3kh  2013-11-21 09:32:00.312499189 +0900
 dpkg-gensymbols4DQT53  2013-11-21 09:34:08.056497969 +0900
 @@ -230,6 +230,7 @@
   cram_huffman_encode_int0@Base 0.2.0~rc3
   cram_huffman_encode_int@Base 0.2.0~rc3
@@ -675,12 +662,12 @@
rm -f debian/htslib-test/DEBIAN/shlibs
dh_shlibdeps
dpkg-shlibdeps -Tdebian/libhts0.substvars 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0\~rc4-1
-dpkg-shlibdeps: warning: symbol exp used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
-dpkg-shlibdeps: warning: symbol pthread_join used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
-dpkg-shlibdeps: warning: symbol pthread_kill used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
 dpkg-shlibdeps: warning: symbol pthread_create used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
+dpkg-shlibdeps: warning: symbol exp used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
 dpkg-shlibdeps: warning: symbol lgamma used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
+dpkg-shlibdeps: warning: symbol pthread_kill used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 found in none of 
the libraries
 dpkg-shlibdeps: warning: symbol log used by 
debian/libhts0/usr/lib/x86_64-linux-gnu/libhts.so.0.2.0~rc4-1 fou