Source: pbseqlib
Version: 0~20161219-2
Severity: normal
Tags: patch
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hi,
pbseqlib FTBFS with HDF5 1.10.2 currently in experimental:
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1
-I/usr/include -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o
HDFWriterBase.o
In file included from BufferedHDFArray.hpp:213:0,
from HDFWriterBase.hpp:14,
from HDFWriterBase.cpp:3:
BufferedHDFArrayImpl.hpp: In member function 'void
BufferedHDFArray<T>::Flush(bool, DSLength)':
BufferedHDFArrayImpl.hpp:143:11: error: 'class H5::DataSetIException' has no
member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int
BufferedHDFArray<T>::UpdateH5Dataspace()':
BufferedHDFArrayImpl.hpp:295:11: error: 'class H5::DataSetIException' has no
member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp:332:11: error: 'class H5::Exception' has no member
named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
BufferedHDFArrayImpl.hpp: In member function 'int
BufferedHDFArray<T>::Resize(DSLength)':
BufferedHDFArrayImpl.hpp:354:11: error: 'class H5::DataSetIException' has no
member named 'printError'; did you mean 'printErrorStack'?
e.printError();
^~~~~~~~~~
printErrorStack
make[3]: *** [/<<PKGBUILDDIR>>/hdf//../rules.mk:20: HDFWriterBase.o] Error 1
Please consider the attached patch to fix the issue.
Thanks,
_g.
- -- System Information:
Distributor ID: PureOS
Description: PureOS GNU/Linux 8
Release: 8
Codename: green
Architecture: x86_64
Kernel: Linux 4.14.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8),
LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
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diff -Nru pbseqlib-0~20161219/debian/changelog
pbseqlib-0~20161219/debian/changelog
--- pbseqlib-0~20161219/debian/changelog 2017-11-10 04:48:55.000000000
+0100
+++ pbseqlib-0~20161219/debian/changelog 2018-04-08 18:32:30.000000000
+0200
@@ -1,3 +1,10 @@
+pbseqlib (0~20161219-2.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload
+ * Add support for HDF5 1.10.2
+
+ -- Gilles Filippini <p...@debian.org> Sun, 08 Apr 2018 18:32:30 +0200
+
pbseqlib (0~20161219-2) unstable; urgency=medium
* Add support for HDF5 1.10.1
diff -Nru pbseqlib-0~20161219/debian/patches/hdf5-1.10.2-support.patch
pbseqlib-0~20161219/debian/patches/hdf5-1.10.2-support.patch
--- pbseqlib-0~20161219/debian/patches/hdf5-1.10.2-support.patch
1970-01-01 01:00:00.000000000 +0100
+++ pbseqlib-0~20161219/debian/patches/hdf5-1.10.2-support.patch
2018-04-08 18:32:30.000000000 +0200
@@ -0,0 +1,52 @@
+Index: pbseqlib-0~20161219/hdf/BufferedHDFArrayImpl.hpp
+===================================================================
+--- pbseqlib-0~20161219.orig/hdf/BufferedHDFArrayImpl.hpp
++++ pbseqlib-0~20161219/hdf/BufferedHDFArrayImpl.hpp
+@@ -140,7 +140,11 @@ void BufferedHDFArray<T>::Flush(bool app
+ }
+ catch(H5::DataSetIException e) {
+ std::cout <<"ERROR! Could not write HDF5 data." << std::endl;
++#ifdef HAVE_HDF5_1_10_1
++ e.printErrorStack();
++#else
+ e.printError();
++#endif
+ exit(1);
+ }
+ memorySpace.close();
+@@ -292,7 +292,11 @@ int BufferedHDFArray<T>::UpdateH5Dataspa
+ dataspace = dataset.getSpace();
+ }
+ catch(H5::DataSetIException &e) {
++#ifdef HAVE_HDF5_1_10_1
++ e.printErrorStack();
++#else
+ e.printError();
++#endif
+ return 0;
+ }
+ maxDims = MAX_DIMS;
+@@ -329,7 +329,11 @@ int BufferedHDFArray<T>::UpdateH5Dataspa
+ dataspace.close();
+ }
+ catch(H5::Exception& e) {
++#ifdef HAVE_HDF5_1_10_1
++ e.printErrorStack();
++#else
+ e.printError();
++#endif
+ return 0;
+ }
+ return 1;
+@@ -351,7 +351,11 @@ int BufferedHDFArray<T>::Resize(const DS
+ dataset.extend(fileArraySize);
+ fileSpace.close();
+ } catch(H5::DataSetIException &e) {
++#ifdef HAVE_HDF5_1_10_1
++ e.printErrorStack();
++#else
+ e.printError();
++#endif
+ return 0;
+ }
+ return 1;
diff -Nru pbseqlib-0~20161219/debian/patches/series
pbseqlib-0~20161219/debian/patches/series
--- pbseqlib-0~20161219/debian/patches/series 2017-11-10 04:48:55.000000000
+0100
+++ pbseqlib-0~20161219/debian/patches/series 2018-04-08 18:32:30.000000000
+0200
@@ -1 +1,2 @@
hdf5-1.10.1-support.patch
+hdf5-1.10.2-support.patch
