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 

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