libzstd 1.1.2 contains embedded zlib fork

[Sascha Steinbiss]

Hi Kevin,

here on the Debian Med sprint I was looking to update libzstd to the current 
upstream version 1.1.2. Besides some minor changes to the patches I had to 
make, I also noticed that it now includes an embedded copy of some zlib code, 
which -- according to the inline comments -- was adapted to be ready to compile 
with the zlibwrapper. It wasn’t clear to me whether this was really necessary; 
when these files are removed from the affected Makefile (and some minor 
adjustments are made) the build still finishes fine.

TBH I don’t feel I should upload this after consulting with you. I have pushed 
my changes (tagged as UNRELEASED) and would be happy if you could take a second 
look.

Many thanks
Sascha


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Will you prepare update to bart 0.4.00

[Andreas Tille]

Hi Martin,

I noticed that there is a new release of bart.  It might make sense to
upload it as quick as possible to make it into testing soon.  I'm at
your service at Debian Med sprint for sponsering.

Kind regards

  Andreas.

-- 
http://fam-tille.de

Putting tvc under Debian Med team maintenance

[Andreas Tille]

Hi Dominique,

I wonder why tvc is not under Debian Med team maintenance.  It somehow
went in under my radar and I just noticed it when checking rdepends of
libbamtools.  Since I simply assume that you are fine with Debian Med
team maintenance I'm moving it in our Git applying Debian Med policy
when sitting at the Debian Med sprint in Bukarest.

Kind regards

   Andreas.

-- 
http://fam-tille.de

`internal compiler error: Segmentation fault` & `internal compiler error` w/ Seqan2

[Michael Crusoe]

Hello Alpha team,

Can you help diagnose the errors I get at
https://buildd.debian.org/status/fetch.php?pkg=seqan2=alpha=2.3.0~1.20161019~af07bc1%2Bdfsg-4=148010
?

Thanks!

-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project 
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+1 480 627 9108
+32 2 808 25 58

Re: Putting tvc under Debian Med team maintenance

[Andreas Tille]

Hi again,

I'd like to give a status update:

On Fri, Jan 13, 2017 at 11:06:00AM +0100, Andreas Tille wrote:
> I wonder why tvc is not under Debian Med team maintenance.  It somehow
> went in under my radar and I just noticed it when checking rdepends of
> libbamtools.  Since I simply assume that you are fine with Debian Med
> team maintenance I'm moving it in our Git applying Debian Med policy
> when sitting at the Debian Med sprint in Bukarest.

  1. Injected into Git[1]
  2. Tried to write a watch file but even failed to find any upstream
 source
  3. Failed in replacing the vcflib code copy by the Debian packaged one

For the last issue I'd be happy to get some help by the Debian Med
sprinters.  The error is:

...
[ 27%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o
/usr/bin/c++   -DALIGNSTATS_IGNORE -I/usr/include/smithwaterman 
-I/usr/include/vcflib -I/build/tvc-5.0.3+dfsg1/external/freebayes/src 
-I/usr/include/jsoncpp -I/usr/include/bamtools 
-I/build/tvc-5.0.3+dfsg1/VariantCaller 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/FlowDistEval 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/EnsembleEval 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/Bookkeeping 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/Reads 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/Splice 
-I/build/tvc-5.0.3+dfsg1/VariantCaller/Filter 
-I/build/tvc-5.0.3+dfsg1/realignment -I/build/tvc-5.0.3+dfsg1/file-io 
-I/build/tvc-5.0.3+dfsg1/BaseCaller -I/build/tvc-5.0.3+dfsg1/Calibration 
-I/build/tvc-5.0.3+dfsg1/Util -I/build/tvc-5.0.3+dfsg1  -g -O2 
-fdebug-prefix-map=/build/tvc-5.0.3+dfsg1=. -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3   -o 
CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c 
/build/tvc-5.0.3+dfsg1/obj-x86_64-linux-gnu/IonVersion.cpp
In file included from 
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.cpp:27:0:
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h: In constructor 
'bgzf_stream::bgzf_stream(std::__cxx11::string&, unsigned int)':
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:42:74: error: 
'_bgzf_open' was not declared in this scope
   : bgzf(NULL), WINDOW_SIZE(ws) { bgzf = _bgzf_open(path.c_str(), 
"w");data.reserve(2 * WINDOW_SIZE); }
  ^
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h: In destructor 
'bgzf_stream::~bgzf_stream()':
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:44:54: error: 
'_bgzf_close' was not declared in this scope
   ~bgzf_stream() { if (bgzf) flush();_bgzf_close(bgzf);  }
  ^
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h: At global scope:
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:56:37: error: 'vcf' 
is not a class, namespace, or enumeration
 class ComparableVcfVariant : public vcf::Variant {
 ^~~
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:56:42: error: 
expected '{' before 'Variant'
 class ComparableVcfVariant : public vcf::Variant {
  ^~~
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:57:3: error: expected 
primary-expression before 'const'
   const VcfOrderedMerger& merger;
   ^
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:57:3: error: expected 
'}' before 'const'
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:59:1: error: expected 
unqualified-id before 'public'
 public:
 ^~
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:63:41: error: 'bool 
operator<(ComparableVcfVariant&)' must take exactly two arguments
   bool operator<(ComparableVcfVariant& b);
 ^
/build/tvc-5.0.3+dfsg1/VariantCaller/tvcutils/unify_vcf.h:64:1: error: expected 
declaration before '}' token
 };
 ^
CMakeFiles/tvcutils.dir/build.make:137: recipe for target 
'CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o' failed
make[3]: *** [CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o] 
Error 1
make[3]: *** Waiting for unfinished jobs
make[3]: Leaving directory '/build/tvc-5.0.3+dfsg1/obj-x86_64-linux-gnu'
...


If adapting to the Debian Med packaged vcslib might be to complicated
this could be droped again - I just wanted to try doing things right.

Kind regards

  Andreas.



[1] https://anonscm.debian.org/git/debian-med/tvc.git 

-- 
http://fam-tille.de

Re: Putting tvc under Debian Med team maintenance

[Dominique Belhachemi]

On Fri, Jan 13, 2017 at 5:06 AM, Andreas Tille  wrote:

> Hi Dominique,
>
> I wonder why tvc is not under Debian Med team maintenance.  It somehow
> went in under my radar and I just noticed it when checking rdepends of
> libbamtools.  Since I simply assume that you are fine with Debian Med
> team maintenance I'm moving it in our Git applying Debian Med policy
> when sitting at the Debian Med sprint in Bukarest.
>
>
Hi Andreas,

Feel free to take over tvc, I don't use it anymore.

The tool is currently only in the Debian experimental branch and you can
download the source code from here:
http://updates.iontorrent.com/tvc_standalone/

Best
-Dominique