gclib: update to new version and unblacklist

build-fail-blacklist

@@ -709,7 +709,6 @@ recipes/edlib
 recipes/esimsa
 recipes/fastuniq
 recipes/fgap
-recipes/gclib
 recipes/funcannot
 recipes/genepender
 recipes/genometester4

recipes/gclib/Makefile.osx.patch

@@ -1,17 +1,15 @@
-diff --git a/Makefile b/Makefile
-index 43a9c91..9a7beca 100644
---- a/Makefile
-+++ b/Makefile
-@@ -65,6 +65,8 @@ else
-   endif
- endif
+--- /tmp/Makefile	2018-06-26 00:26:41.000000000 +0200
++++ Makefile	2018-11-29 12:35:29.172992192 +0100
+@@ -41,7 +41,7 @@
+ CC      := g++
 
-+CFLAGS += -fPIC
-+
- %.o : %.cpp
- 	${CC} ${CFLAGS} -c $< -o $@
+ BASEFLAGS  := -Wall -Wextra ${SEARCHDIRS} $(MARCH) \
+- -D_REENTRANT -fno-exceptions -fno-rtti
++ -D_REENTRANT -fno-exceptions -fno-rtti -fPIC
 
-@@ -73,14 +75,17 @@ endif
+ #add the link-time optimization flag if gcc version > 4.5
+ GCC_VERSION:=$(subst ., ,$(shell gcc -dumpversion))
+@@ -73,14 +73,17 @@
  LINKER  := g++
  LIBS := 
  OBJS := GBase.o GStr.o GArgs.o

recipes/gclib/Makefile.patch

@@ -1,26 +1,34 @@
-diff --git a/Makefile b/Makefile
-index 43a9c91..d937ddd 100644
---- a/Makefile
-+++ b/Makefile
-@@ -65,6 +65,8 @@ else
-   endif
- endif
-
-+CFLAGS += -fPIC
-+
- %.o : %.cpp
- 	${CC} ${CFLAGS} -c $< -o $@
-
-@@ -73,14 +75,17 @@ endif
+# this patch does two things: 
+# 1. replace gcc by g++ for getting the version (otherwise 
+#    both compilers would be necessary for compiling)
+# 2. gclib does not provide the objects/libraries necessary
+#    for building gffcompare, so they are added as shared 
+#    object
+--- /tmp/Makefile	2018-06-26 00:26:41.000000000 +0200
++++ Makefile	2018-11-29 13:00:38.899628706 +0100
+@@ -41,10 +41,10 @@
+ CC      := g++
+
+ BASEFLAGS  := -Wall -Wextra ${SEARCHDIRS} $(MARCH) \
+- -D_REENTRANT -fno-exceptions -fno-rtti
++ -D_REENTRANT -fno-exceptions -fno-rtti -fPIC
+
+ #add the link-time optimization flag if gcc version > 4.5
+-GCC_VERSION:=$(subst ., ,$(shell gcc -dumpversion))
++GCC_VERSION:=$(subst ., ,$(shell g++ -dumpversion))
+ GCC_MAJOR:=$(word 1,$(GCC_VERSION))
+ GCC_MINOR:=$(word 2,$(GCC_VERSION))
+ #GCC_SUB:=$(word 3,$(GCC_VERSION))
+@@ -73,14 +73,17 @@
  LINKER  := g++
- LIBS :=
+ LIBS := 
  OBJS := GBase.o GStr.o GArgs.o
 +GCLIBS := GFastaIndex.o GFaSeqGet.o gff.o gdna.o codons.o GBase.o GStr.o GArgs.o
-
+ 
  .PHONY : all
 -all:    gtest threads
 +all:    gtest threads gffcomparelibs
-
+ 
  version: ; @echo "GCC Version is: "$(GCC_MAJOR)":"$(GCC_MINOR)":"$(GCC_SUB)
  	@echo "> GCC Opt. string is: "$(GCC45OPTS)
  debug:  gtest threads

recipes/gclib/chrono.patch

@@ -0,0 +1,67 @@
+# gclib includes a chrono namespace which is nowadays 
+# also in C++ stdlib. As a result the compiler complains about 
+# ambiguous namespace which is resolved by this patch
+# reported upstream: https://github.com/gpertea/gclib/issues/3
+diff -ruN /tmp/gclib-0.10.3/GThreads.cpp ./GThreads.cpp
+--- ./GThreads.cpp	2018-06-26 00:26:41.000000000 +0200
++++ ./GThreads.cpp	2018-11-29 13:55:31.212906749 +0100
+@@ -375,7 +375,7 @@
+
+ void GThread::wait_all() {
+   while (GThread::num_running()>0)
+-	this_thread::sleep_for(chrono::milliseconds(4));
++	this_thread::sleep_for(gclib::chrono::milliseconds(4));
+ }
+
+
+diff -ruN /tmp/gclib-0.10.3/GThreads.h ./GThreads.h
+--- ./GThreads.h	2018-06-26 00:26:41.000000000 +0200
++++ ./GThreads.h	2018-11-29 13:56:50.372545993 +0100
+@@ -822,7 +822,7 @@
+
+ /// Minimal implementation of the \c chrono namespace.
+ /// The \c chrono namespace provides types for specifying time intervals.
+-namespace chrono {
++namespace gclib{ namespace chrono {
+   /// Duration template class. This class provides enough functionality to
+   /// implement \c this_thread::sleep_for().
+   template <class _Rep, class _Period = ratio<1> > class duration {
+@@ -850,7 +850,7 @@
+   typedef duration<int64_t> seconds;                            ///< Duration with the unit seconds.
+   typedef duration<int64_t, ratio<60> > minutes;                ///< Duration with the unit minutes.
+   typedef duration<int64_t, ratio<3600> > hours;                ///< Duration with the unit hours.
+-}
++}}
+
+ /// The namespace \c this_thread provides methods for dealing with the
+ /// calling thread.
+@@ -879,7 +879,7 @@
+   /// @endcode
+   /// @note Supported duration types are: nanoseconds, microseconds,
+   /// milliseconds, seconds, minutes and hours.
+-  template <class _Rep, class _Period> void sleep_for(const chrono::duration<_Rep, _Period>& aTime)
++  template <class _Rep, class _Period> void sleep_for(const gclib::chrono::duration<_Rep, _Period>& aTime)
+   {
+ #if defined(_GTHREADS_WIN32_)
+     Sleep(int(double(aTime.count()) * (1000.0 * _Period::_as_double()) + 0.5));
+diff -ruN /tmp/gclib-0.10.3/threads.cpp ./threads.cpp
+--- ./threads.cpp	2018-06-26 00:26:41.000000000 +0200
++++ ./threads.cpp	2018-11-29 13:57:33.300350761 +0100
+@@ -28,7 +28,7 @@
+       //cout << " My thread id is " << thisThread->get_id() << "." << endl << flush;
+       cout << " My thread id is " << my.thread->get_id() << "." << endl << flush;
+     }
+-  this_thread::sleep_for(chrono::seconds(4));
++  this_thread::sleep_for(gclib::chrono::seconds(4));
+ }
+
+ #ifndef GTHREADS_NO_TLS
+@@ -209,7 +209,7 @@
+     // Start the waiting thread (it will wait for gCount to reach zero).
+     GThread t1(ThreadCondition2, 0);
+
+-    this_thread::sleep_for(chrono::milliseconds(400));
++    this_thread::sleep_for(gclib::chrono::milliseconds(400));
+       {
+
+        for (int c=5;c>=0;c--) {

recipes/gclib/meta.yaml

@@ -1,22 +1,22 @@
 package:
   name: gclib
-  version: "0.0.1"
+  version: "0.10.13"
 
 build:
-  number: 5
+  number: 0
   skip: False
 
 source:
-  url: https://github.com/gpertea/gclib/archive/907a9d6484b92ea0c357baf2da5d85bc6e6b82b1.tar.gz
-  md5: 13891db103fab3457beb621ab43f8843
+  url: https://github.com/gpertea/gclib/archive/v0.10.3.tar.gz 
+  sha256: f5f9d4764afe83d5b9cc851c4dab352906505be7a6c03958c2af51c554118c18
   patches:
     - Makefile.patch # [not osx]
     - Makefile.osx.patch # [osx]
+    - chrono.patch
 
 requirements:
   build:
     - {{ compiler('cxx') }}
-  run:
 
 test:
   commands: