Gingr installation problem from pre-compiled version

Hi.

I'm a microbiologist starting on bioinformatics. So... really, really naive in what concerns Linux. I'm working with Ubuntu 12.04 and I have just installed harvest (following the instructions for pre-compiled version). The installation was performed in /usr/local. Normally, no error was given during install but when i try to run gingr the problems start. Each time i get an error of this type:

gingr: XXXX : Gtk-CRITICAL: TA_gtk_widget_style_ref : assertion 'GTK_IS_WIDGET (widget)' failed QNativeImage: Unable to attach to shared memory segment X error : BadDrawable (invalid Pixmap or Window parameter) 9 Major opcode: 62 Resource_id 0x0

Where you read gingr: XXXX it is a 4 digit number that varies each time i call ./gingr. And it blocks by computer (graphics) so I have to kill the process.

Has anyone had this problem before? Can you help me? I would really like to test gingr and parsnps as i'm working with a few hundreds of bacterial genomes.

Thank you in advance for your feedback.

best regards, Patrícia

Hi Patrícia, I don't have an Ubuntu 12.04 install to test this on, but I suspect that whatever the problem is can be worked around by building from source. I know you don't have much Linux experience but it should be pretty straightforward if you use default options, and I can try to answer any questions you have.

First, go to the project pages (https://github.com/marbl/harvest-tools and https://github.com/marbl/gingr) and use the download ZIP button on the right. They each have INSTALL.txt files that will walk you through the process. Harvest-tools should be installed before Gingr. As far as dependencies, you will need Google Protocol Buffers, Qt 4.8, and Autoconf. These should all be available through the package manager:

sudo apt-get install libprotobuf-dev protobuf-compiler
sudo apt-get install libqt4-core libqt4-dev libqt4-gui qt4-dev-tools
sudo apt-get install autoconf

...then to build Harvest-tools:

./bootstrap.h
./configure
make
sudo make install

...and Gingr:

autoconf
./configure
qmake
make

...and if everything goes smoothly, that should be it (gingr will be in the top-level Gingr directory).

Hi again,

thanks so much for your help and quick reply. I did exactly what you said but i had a problem with harvest-tools (so i didn't even install gingr yet): here is the code pat@Pmarsim:/usr/local/harvest-tools-master$ sudo ./configure [sudo] password for pat: checking for protoc... no configure: error: Protocol Buffer compiler (protoc) not found.

I did install Google Protocole Buffers, Qt 4.8 and Autoconf using the lines (you so kindly) wrote. All worked well with no error message. I them restarted the computer.

Can you, once more, help me ? By the way, on the INSTALL.txt of harvest there is another dependency mentioned: Zlib

Thanks in advance.

Regards, Patricia

Hopefully this is just a path issue. Can you check if you have /usr/local/bin/protoc? If so, you just need to add export PATH=$PATH:/usr/local/bin to your ~/.bashrc and open a new terminal.

Hi,

I checked and I have protoc in /usr/bin/protoc and not in /usr/local/bin/protoc. so, I added the export line to ~/.bashrc using /usr/bin instead of /usr/local/bin. I opened a new terminal and tried to do ./ configure on /usr/local/harvest-tools-master ... and i get the same error.

so here is what i did next (always on /usr/local): $ rm -r harvest-tools-master $ sudo apt-get install libprotobuf-dev protobuf-compiler Reading package lists... Done Building dependency tree
Reading state information... Done libprotobuf-dev is already the newest version. protobuf-compiler is already the newest version. The following package was automatically installed and is no longer required: libkms1 Use 'apt-get autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt-get install libqt4-core libqt4-dev libqt4-gui qt4-dev-tools Reading package lists... Done Building dependency tree
Reading state information... Done libprotobuf-dev is already the newest version. protobuf-compiler is already the newest version. The following package was automatically installed and is no longer required: libkms1 Use 'apt-get autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt-get install libqt4-core libqt4-dev libqt4-gui qt4-dev-tools Reading package lists... Done Building dependency tree
Reading state information... Done libqt4-dev is already the newest version. libqt4-gui is already the newest version. qt4-dev-tools is already the newest version. libqt4-core is already the newest version. The following package was automatically installed and is no longer required: libkms1 Use 'apt-get autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ sudo apt-get install autoconf Reading package lists... Done Building dependency tree
Reading state information... Done autoconf is already the newest version. The following package was automatically installed and is no longer required: libkms1 Use 'apt-get autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ dpkg -L protobuf-compiler /. /usr /usr/share /usr/share/doc /usr/share/doc/protobuf-compiler /usr/share/doc/protobuf-compiler/README.txt.gz /usr/share/doc/protobuf-compiler/examples /usr/share/doc/protobuf-compiler/examples/list_people.py /usr/share/doc/protobuf-compiler/examples/AddPerson.java /usr/share/doc/protobuf-compiler/examples/list_people.cc /usr/share/doc/protobuf-compiler/examples/ListPeople.java /usr/share/doc/protobuf-compiler/examples/README.txt /usr/share/doc/protobuf-compiler/examples/add_person.cc /usr/share/doc/protobuf-compiler/examples/Makefile /usr/share/doc/protobuf-compiler/examples/addressbook.proto /usr/share/doc/protobuf-compiler/examples/add_person.py /usr/share/doc/protobuf-compiler/copyright /usr/share/doc/protobuf-compiler/CONTRIBUTORS.txt /usr/share/doc/protobuf-compiler/editors /usr/share/doc/protobuf-compiler/editors/README.txt /usr/share/doc/protobuf-compiler/editors/protobuf-mode.el.gz /usr/share/doc/protobuf-compiler/editors/proto.vim /usr/share/man /usr/share/man/man1 /usr/share/man/man1/protoc.1.gz /usr/bin /usr/bin/protoc /usr/share/doc/protobuf-compiler/changelog.Debian.gz

$ dpkg -L libprotobuf-dev /. /usr /usr/share /usr/share/doc /usr/include /usr/include/google /usr/include/google/protobuf /usr/include/google/protobuf/stubs /usr/include/google/protobuf/stubs/once.h /usr/include/google/protobuf/stubs/common.h /usr/include/google/protobuf/generated_message_util.h /usr/include/google/protobuf/dynamic_message.h /usr/include/google/protobuf/generated_message_reflection.h /usr/include/google/protobuf/wire_format_lite_inl.h /usr/include/google/protobuf/reflection_ops.h /usr/include/google/protobuf/message_lite.h /usr/include/google/protobuf/text_format.h /usr/include/google/protobuf/descriptor.h /usr/include/google/protobuf/repeated_field.h /usr/include/google/protobuf/wire_format_lite.h /usr/include/google/protobuf/descriptor.pb.h /usr/include/google/protobuf/unknown_field_set.h /usr/include/google/protobuf/wire_format.h /usr/include/google/protobuf/service.h /usr/include/google/protobuf/extension_set.h /usr/include/google/protobuf/io /usr/include/google/protobuf/io/zero_copy_stream.h /usr/include/google/protobuf/io/zero_copy_stream_impl_lite.h /usr/include/google/protobuf/io/gzip_stream.h /usr/include/google/protobuf/io/coded_stream.h /usr/include/google/protobuf/io/zero_copy_stream_impl.h /usr/include/google/protobuf/io/tokenizer.h /usr/include/google/protobuf/io/printer.h /usr/include/google/protobuf/descriptor.proto /usr/include/google/protobuf/descriptor_database.h /usr/include/google/protobuf/message.h /usr/lib /usr/lib/libprotobuf.a /usr/lib/pkgconfig /usr/lib/pkgconfig/protobuf.pc /usr/lib/pkgconfig/protobuf-lite.pc /usr/lib/libprotobuf-lite.a /usr/share/doc/libprotobuf-dev /usr/lib/libprotobuf.so /usr/lib/libprotobuf-lite.so

$ sudo unzip harvest-tools-master.zip Archive: harvest-tools-master.zip ae6178593bdbaff3d430df1b3e719a79232ac0ba creating: harvest-tools-master/ inflating: harvest-tools-master/CITATION
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extracting: harvest-tools-master/bootstrap.sh
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creating: harvest-tools-master/src/harvest/ inflating: harvest-tools-master/src/harvest/AnnotationList.cpp
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creating: harvest-tools-master/src/harvest/pb/ inflating: harvest-tools-master/src/harvest/pb/harvest.proto
creating: harvest-tools-master/test/ inflating: harvest-tools-master/test/test2.fna
inflating: harvest-tools-master/test/test2.hvt
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$ cd harvest-tools-master $ ls bootstrap.sh configure.ac harvest-variants.py INSTALL.txt Makefile.in setup.py test CITATION harvest-snps.py INSTALL.py LICENSE.txt README src

NOTE: i don't have a bootstrap.h but a bootstrap.sh

$ sudo ./bootstrap.sh $ ./configure sudo ./configure checking for protoc... no configure: error: Protocol Buffer compiler (protoc) not found.

$sudo gedit ~/.bashrc

NOTE: the line export PATH=$PATH:/usr/bin , that i added before at the end of the file is there.

Sorry for all these questions, but I don't understand why it is not working! Can you (still) halp me? Can i just forget harvest-tools and try to install Gingr and ParSnps ? and check if they are working? Or, do you think i'll have the same/similar installation problems?

Thanks a LOT for this debugging !!

regards, Patricia

Hi Patricia, Thanks for the info. It looks like I was wrong about were protobuf would end up. So you should actually add this parameter:

./configure --with-protobuf=/usr

...for both Harvest-tools and Gingr. Also, the $PATH modification shouldn't be necessary in light of this.

Hi again.

It worked ! :-) at least the ./configure step ... $ sudo ./configure --with-protbuf=/usr configure: WARNING: unrecognized options: --with-protbuf checking for protoc... no configure: error: Protocol Buffer compiler (protoc) not found. pat@Pmarsim:/usr/local/harvest-tools-master$ sudo ./configure --with-protobuf=/usr checking for protoc... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking google/protobuf/stubs/common.h usability... yes checking google/protobuf/stubs/common.h presence... yes checking for google/protobuf/stubs/common.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes configure: creating ./config.status config.status: creating Makefile

But the make and make install give errors

$ sudo make cd src; /usr/bin/protoc --cppout . harvest/pb/harvest.proto gcc -Isrc -I/usr/include -c src/harvest/AnnotationList.cpp -o src/harvest/AnnotationList.o gcc -Isrc -I/usr/include -c src/harvest/harvest.cpp -o src/harvest/harvest.o gcc -Isrc -I/usr/include -c src/harvest/HarvestIO.cpp -o src/harvest/HarvestIO.o gcc -Isrc -I/usr/include -c src/harvest/LcbList.cpp -o src/harvest/LcbList.o src/harvest/LcbList.cpp: In member function ‘void LcbList::initFromMaf(const char, ReferenceList, TrackList, PhylogenyTree, VariantList, const char_)’: src/harvest/LcbList.cpp:231:16: error: ‘numeric_limits’ was not declared in this scope src/harvest/LcbList.cpp:231:41: error: expected primary-expression before ‘>’ token src/harvest/LcbList.cpp:231:48: error: no matching function for call to ‘max()’ src/harvest/LcbList.cpp:231:48: note: candidates are: /usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template const _Tp& std::max(const _Tp&, const _Tp&) /usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare) src/harvest/LcbList.cpp:409:17: error: ‘numeric_limits’ was not declared in this scope src/harvest/LcbList.cpp:409:42: error: expected primary-expression before ‘>’ token src/harvest/LcbList.cpp:409:49: error: no matching function for call to ‘max()’ src/harvest/LcbList.cpp:409:49: note: candidates are: /usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template const _Tp& std::max(const _Tp&, const _Tp&) /usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, Compare) src/harvest/LcbList.cpp:499:44: error: ‘sort’ was not declared in this scope src/harvest/LcbList.cpp: In member function ‘void LcbList::initFromXmfa(const char, ReferenceList, TrackList, PhylogenyTree, VariantList)’: src/harvest/LcbList.cpp:922:44: error: ‘sort’ was not declared in this scope make: _\ [src/harvest/LcbList.o] Error 1

$ sudo make install gcc -Isrc -I/usr/include -c src/harvest/LcbList.cpp -o src/harvest/LcbList.o src/harvest/LcbList.cpp: In member function ‘void LcbList::initFromMaf(const char, ReferenceList, TrackList, PhylogenyTree, VariantList, const char)’: src/harvest/LcbList.cpp:231:16: error: ‘numeric_limits’ was not declared in this scope src/harvest/LcbList.cpp:231:41: error: expected primary-expression before ‘>’ token src/harvest/LcbList.cpp:231:48: error: no matching function for call to ‘max()’ src/harvest/LcbList.cpp:231:48: note: candidates are: /usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template const _Tp& std::max(const _Tp&, const _Tp&) /usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare) src/harvest/LcbList.cpp:409:17: error: ‘numeric_limits’ was not declared in this scope src/harvest/LcbList.cpp:409:42: error: expected primary-expression before ‘>’ token src/harvest/LcbList.cpp:409:49: error: no matching function for call to ‘max()’ src/harvest/LcbList.cpp:409:49: note: candidates are: /usr/include/c++/4.6/bits/stl_algobase.h:210:5: note: template const _Tp& std::max(const _Tp&, const _Tp&) /usr/include/c++/4.6/bits/stl_algobase.h:254:5: note: template<class _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, Compare) src/harvest/LcbList.cpp:499:44: error: ‘sort’ was not declared in this scope src/harvest/LcbList.cpp: In member function ‘void LcbList::initFromXmfa(const char, ReferenceList, TrackList, PhylogenyTree, VariantList)’: src/harvest/LcbList.cpp:922:44: error: ‘sort’ was not declared in this scope make: _\ [src/harvest/LcbList.o] Error 1

Were getting there... one step at the time, but were getting there. Help, again.

Looks like this is actually a problem with the code that was hidden on other OSs. I just pushed a fix, so if you download the harvest-tools zip again, that should fix it. Thanks for helping us work out some of these kinks.

Hi again.

Thanks for you help and for the fix. The installation of harvest went well. Now, its the Gingr installation that is posing some problems. What i did and the problem (again, installation in /usr/local): pat@Pmarsim:/usr/local$ sudo unzip gingr-master.zip pat@Pmarsim:/usr/local$ cd gingr-master/ pat@Pmarsim:/usr/local/gingr-master$ ls CITATION configure.ac gingr.pro.in html img INSTALL.txt LICENSE.txt README resource.qrc src pat@Pmarsim:/usr/local/gingr-master$ sudo autoconf pat@Pmarsim:/usr/local/gingr-master$ ls autom4te.cache configure gingr.pro.in img LICENSE.txt resource.qrc CITATION configure.ac html INSTALL.txt README src pat@Pmarsim:/usr/local/gingr-master$ sudo ./configure --with-harvest=/usr/local --with-protobuf=/usr configure: error: cannot find sources (gingr) in . or ..

What is it that I am missing this time? Can you help me (again)?

Thanks in advance.

Sincerly, Patricia

I also tried to install ParSnps without success (following the instructions on INSTALL.txt).

here are the lines: pat@Pmarsim:/usr/local$ sudo unzip parsnp-master.zip Archive: parsnp-master.zip 6b8690120c13d910a0aeb058771f6c638c497967 creating: parsnp-master/ inflating: parsnp-master/CITATION
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pat@Pmarsim:/usr/local$ cd parsnp-master/ pat@Pmarsim:/usr/local/parsnp-master$ ls autogen.sh bootstrap.sh configure.ac INSTALL LICENSE muscle README.md setup.py template.ini bin CITATION examples install.py Makefile.am Parsnp.py script src

pat@Pmarsim:/usr/local/parsnp-master$ sudo gedit INSTALL pat@Pmarsim:/usr/local/parsnp-master$ sudo ./bootstrap.sh configure.ac:2: installing ./install-sh' configure.ac:2: installing./missing' src/Makefile.am: installing `./depcomp' pat@Pmarsim:/usr/local/parsnp-master$ sudo ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking libMUSCLE/muscle.h usability... yes checking libMUSCLE/muscle.h presence... yes checking for libMUSCLE/muscle.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: executing depfiles commands

pat@Pmarsim:/usr/local/parsnp-master$ make install Making install in src make[1]: Entering directory /usr/local/parsnp-master/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-MuscleInterface.o -MD -MP -MF .deps/parsnp-MuscleInterface.Tpo -c -o parsnp-MuscleInterface.otest -f 'MuscleInterface.cpp' || echo './'MuscleInterface.cpp MuscleInterface.cpp:80:1: fatal error: opening dependency file .deps/parsnp-MuscleInterface.Tpo: Permission denied compilation terminated. make[1]: *** [parsnp-MuscleInterface.o] Error 1 make[1]: Leaving directory/usr/local/parsnp-master/src' make: * [install-recursive] Error 1 pat@Pmarsim:/usr/local/parsnp-master$ sudo make install Making install in src make[1]: Entering directory /usr/local/parsnp-master/src' g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-MuscleInterface.o -MD -MP -MF .deps/parsnp-MuscleInterface.Tpo -c -o parsnp-MuscleInterface.otest -f 'MuscleInterface.cpp' || echo './'MuscleInterface.cpp mv -f .deps/parsnp-MuscleInterface.Tpo .deps/parsnp-MuscleInterface.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-parsnp.o -MD -MP -MF .deps/parsnp-parsnp.Tpo -c -o parsnp-parsnp.otest -f 'parsnp.cpp' || echo './'parsnp.cpp mv -f .deps/parsnp-parsnp.Tpo .deps/parsnp-parsnp.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-LCB.o -MD -MP -MF .deps/parsnp-LCB.Tpo -c -o parsnp-LCB.otest -f 'LCB.cpp' || echo './'LCB.cpp mv -f .deps/parsnp-LCB.Tpo .deps/parsnp-LCB.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-LCR.o -MD -MP -MF .deps/parsnp-LCR.Tpo -c -o parsnp-LCR.otest -f 'LCR.cpp' || echo './'LCR.cpp mv -f .deps/parsnp-LCR.Tpo .deps/parsnp-LCR.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-TMum.o -MD -MP -MF .deps/parsnp-TMum.Tpo -c -o parsnp-TMum.otest -f 'TMum.cpp' || echo './'TMum.cpp mv -f .deps/parsnp-TMum.Tpo .deps/parsnp-TMum.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-Converter.o -MD -MP -MF .deps/parsnp-Converter.Tpo -c -o parsnp-Converter.otest -f 'Converter.cpp' || echo './'Converter.cpp mv -f .deps/parsnp-Converter.Tpo .deps/parsnp-Converter.Po g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.0\" -DPACKAGE_STRING=\"parsnp\ 1.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I. -I/usr/local/parsnp-master/muscle -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -MT parsnp-iniFile.o -MD -MP -MF .deps/parsnp-iniFile.Tpo -c -o parsnp-iniFile.otest -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp mv -f .deps/parsnp-iniFile.Tpo .deps/parsnp-iniFile.Po g++ -O3 -m64 -fopenmp -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -lgomp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath,/usr/local/parsnp-master/muscle/lib -L/usr/local/parsnp-master/muscle/lib -lMUSCLE-3.7 -o parsnp parsnp-MuscleInterface.o parsnp-parsnp.o parsnp-LCB.o parsnp-LCR.o parsnp-TMum.o parsnp-Converter.o parsnp-iniFile.o
/usr/bin/ld: cannot find -lMUSCLE-3.7 collect2: ld returned 1 exit status make[1]: * [parsnp] Error 1 make[1]: Leaving directory`/usr/local/parsnp-master/src' make: *\ [install-recursive] Error 1

Again, thanks for the time and effort you are putting in helping me solving these problems.

Sincerely, Patricia

Looks like the Gingr problem is our fault again. You can get around this by renaming "gingr-master" to just "gingr".

As for Parsnp, did you try the pre-compiled binary distribution? It's independent from Gingr so the errors you saw with the pre-compiled Gingr shouldn't affect it.

Thanks for your quick reply.

IT worked ... no error after the directory renaming but I still get an error whan i do the last command: make

pat@Pmarsim:/usr/local/gingr$ sudo autoconf pat@Pmarsim:/usr/local/gingr$ sudo ./configure checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking google/protobuf/stubs/common.h usability... yes checking google/protobuf/stubs/common.h presence... yes checking for google/protobuf/stubs/common.h... yes checking harvest/HarvestIO.h usability... yes checking harvest/HarvestIO.h presence... yes checking for harvest/HarvestIO.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes configure: creating ./config.status config.status: creating gingr.pro

pat@Pmarsim:/usr/local/gingr$ ls autom4te.cache config.log configure gingr.pro html INSTALL.txt README src CITATION config.status configure.ac gingr.pro.in img LICENSE.txt resource.qrc

pat@Pmarsim:/usr/local/gingr$ sudo qmake

pat@Pmarsim:/usr/local/gingr$ ls autom4te.cache config.log configure gingr.pro html INSTALL.txt Makefile resource.qrc CITATION config.status configure.ac gingr.pro.in img LICENSE.txt README src pat@Pmarsim:/usr/local/gingr$

pat@Pmarsim:/usr/local/gingr$ sudo make g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o Alignment.o src/Alignment.cpp src/Alignment.cpp: In member function ‘bool Alignment::init(const LcbList&, const VariantList&, const ReferenceList&, const TrackList&)’: src/Alignment.cpp:220:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/Alignment.cpp:293:6: warning: ‘posLast’ may be used uninitialized in this function [-Wuninitialized] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o AlignmentView.o src/AlignmentView.cpp src/AlignmentView.cpp: In member function ‘void AlignmentView::drawLcbs(QPainter, int, int)’: src/AlignmentView.cpp:392:17: warning: unused variable ‘trackRef’ [-Wunused-variable] src/AlignmentView.cpp:394:17: warning: unused variable ‘track2’ [-Wunused-variable] src/AlignmentView.cpp:396:6: warning: variable ‘indexLast1’ set but not used [-Wunused-but-set-variable] src/AlignmentView.cpp:397:6: warning: variable ‘indexLast2’ set but not used [-Wunused-but-set-variable] src/AlignmentView.cpp: At global scope: src/AlignmentView.cpp:390:6: warning: unused parameter ‘painter’ [-Wunused-parameter] src/AlignmentView.cpp: In member function ‘void AlignmentView::initializePalette(int, int)’: src/AlignmentView.cpp:444:8: warning: variable ‘hue’ set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o AnnotationView.o src/AnnotationView.cpp src/AnnotationView.cpp: In member function ‘void AnnotationView::drawLcbs(QPainter)’: src/AnnotationView.cpp:858:6: warning: variable ‘xLast’ set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BaseBuffer.o src/BaseBuffer.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BaseImage.o src/BaseImage.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockStatusBar.o src/BlockStatusBar.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockView.o src/BlockView.cpp In file included from src/BlockView.h:15:0, from src/BlockView.cpp:7: src/SnpBuffer.h: In member function ‘void SnpBuffer::threadError(QString)’: src/SnpBuffer.h:49:53: error: ‘printf’ was not declared in this scope src/BlockView.cpp: In member function ‘virtual void BlockView::paintEvent(QPaintEvent)’: src/BlockView.cpp:181:6: warning: unused variable ‘lcbHoverX’ [-Wunused-variable] src/BaseImage.h: At global scope: src/BaseImage.h:25:15: warning: ‘colorRef’ defined but not used [-Wunused-variable] src/BaseImage.h:35:15: warning: ‘colorRefLegend’ defined but not used [-Wunused-variable] src/BaseImage.h:45:15: warning: ‘colorSnp’ defined but not used [-Wunused-variable] src/BaseImage.h:55:15: warning: ‘colorRefFont’ defined but not used [-Wunused-variable] src/BaseImage.h:65:15: warning: ‘colorRefLegendFont’ defined but not used [-Wunused-variable] src/BaseImage.h:75:15: warning: ‘colorSnpFont’ defined but not used [-Wunused-variable] src/BaseImage.h:85:15: warning: ‘colorLightRef’ defined but not used [-Wunused-variable] src/BaseImage.h:96:15: warning: ‘colorLightRefLegend’ defined but not used [-Wunused-variable] src/BaseImage.h:107:15: warning: ‘colorLightSnp’ defined but not used [-Wunused-variable] src/BaseImage.h:117:15: warning: ‘colorLightRefFont’ defined but not used [-Wunused-variable] src/BaseImage.h:128:15: warning: ‘colorLightRefLegendFont’ defined but not used [-Wunused-variable] src/BaseImage.h:139:15: warning: ‘colorLightSnpFont’ defined but not used [-Wunused-variable] make: _\ [BlockView.o] Error 1

I did install the pre-compiled parsnp. no problem there. i'll test it to check if it is working alright.

I updated the source again (you'll have to re-download the Gingr zip; renaming the folder shouldn't be necessary this time). Hopefully this is the last of these code problems.

I did download the latest zip file. but i still get an eror when i do the "make" command

pat@Pmarsim:/usr/local/gingr-master$ sudo make g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o Alignment.o src/Alignment.cpp src/Alignment.cpp: In member function ‘bool Alignment::init(const LcbList&, const VariantList&, const ReferenceList&, const TrackList&)’: src/Alignment.cpp:220:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/Alignment.cpp:293:6: warning: ‘posLast’ may be used uninitialized in this function [-Wuninitialized] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o AlignmentView.o src/AlignmentView.cpp src/AlignmentView.cpp: In member function ‘void AlignmentView::drawLcbs(QPainter, int, int)’: src/AlignmentView.cpp:392:17: warning: unused variable ‘trackRef’ [-Wunused-variable] src/AlignmentView.cpp:394:17: warning: unused variable ‘track2’ [-Wunused-variable] src/AlignmentView.cpp:396:6: warning: variable ‘indexLast1’ set but not used [-Wunused-but-set-variable] src/AlignmentView.cpp:397:6: warning: variable ‘indexLast2’ set but not used [-Wunused-but-set-variable] src/AlignmentView.cpp: At global scope: src/AlignmentView.cpp:390:6: warning: unused parameter ‘painter’ [-Wunused-parameter] src/AlignmentView.cpp: In member function ‘void AlignmentView::initializePalette(int, int)’: src/AlignmentView.cpp:444:8: warning: variable ‘hue’ set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o AnnotationView.o src/AnnotationView.cpp src/AnnotationView.cpp: In member function ‘void AnnotationView::drawLcbs(QPainter)’: src/AnnotationView.cpp:858:6: warning: variable ‘xLast’ set but not used [-Wunused-but-set-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BaseBuffer.o src/BaseBuffer.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BaseImage.o src/BaseImage.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockStatusBar.o src/BlockStatusBar.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockView.o src/BlockView.cpp src/BlockView.cpp: In member function ‘virtual void BlockView::paintEvent(QPaintEvent)’: src/BlockView.cpp:181:6: warning: unused variable ‘lcbHoverX’ [-Wunused-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockViewMain.o src/BlockViewMain.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o BlockViewMap.o src/BlockViewMap.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o DrawingArea.o src/DrawingArea.cpp src/DrawingArea.cpp: In member function ‘virtual void DrawingArea::resizeEvent(QResizeEvent)’: src/DrawingArea.cpp:73:6: warning: unused variable ‘width’ [-Wunused-variable] src/DrawingArea.cpp:74:6: warning: unused variable ‘height’ [-Wunused-variable] src/DrawingArea.cpp:79:6: warning: unused variable ‘width2’ [-Wunused-variable] src/DrawingArea.cpp:80:6: warning: unused variable ‘height2’ [-Wunused-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o FileInput.o src/FileInput.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o FilterControl.o src/FilterControl.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o ImportWindow.o src/ImportWindow.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o LcbView.o src/LcbView.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o LinkedSplitter.o src/LinkedSplitter.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o main.o src/main.cpp src/MainWindow.h:38:13: warning: ‘async’ defined but not used [-Wunused-variable] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o MainWindow.o src/MainWindow.cpp src/MainWindow.cpp: In member function ‘void MainWindow::rerootTree(const PhylogenyTreeNode)’: src/MainWindow.cpp:482:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/MainWindow.cpp: At global scope: src/MainWindow.cpp:1021:6: warning: unused parameter ‘event’ [-Wunused-parameter] src/MainWindow.cpp: In member function ‘void MainWindow::exportFileBackground(const QString&, ImportWindow::FileType)’: src/MainWindow.cpp:1151:9: warning: enumeration value ‘GINGR’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘ALN_MAF’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘ALN_MFA’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘ALN_NXS’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘TRE_NXS’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘ANN_GBK’ not handled in switch [-Wswitch] src/MainWindow.cpp:1151:9: warning: enumeration value ‘NEXUS’ not handled in switch [-Wswitch] src/MainWindow.cpp: In member function ‘void MainWindow::loadAlignmentBackground(const QString&, const QString&, ImportWindow::FileType)’: src/MainWindow.cpp:1771:11: warning: enumeration value ‘GINGR’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘ALN_NXS’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘VAR_MFA’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘TRE_NWK’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘TRE_NXS’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘ANN_GBK’ not handled in switch [-Wswitch] src/MainWindow.cpp:1771:11: warning: enumeration value ‘NEXUS’ not handled in switch [-Wswitch] src/MainWindow.cpp: In member function ‘void MainWindow::updateTrackHeights(bool)’: src/MainWindow.cpp:2035:8: warning: unused variable ‘trackHeightLast’ [-Wunused-variable] src/MainWindow.cpp: At global scope: src/MainWindow.cpp:2032:6: warning: unused parameter ‘setTargets’ [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o NameListView.o src/NameListView.cpp src/NameListView.cpp:44:6: warning: unused parameter ‘event’ [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o OptionButton.o src/OptionButton.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o OptionPanel.o src/OptionPanel.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o PhylogenyTreeStatusBar.o src/PhylogenyTreeStatusBar.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o PhylogenyTreeView.o src/PhylogenyTreeView.cpp src/PhylogenyTreeView.cpp: In member function ‘void PhylogenyTreeView::drawNode(QPainter, const PhylogenyTreeNode, bool, float, int, float, float, int) const’: src/PhylogenyTreeView.cpp:716:91: warning: enumeral and non-enumeral type in conditional expression [enabled by default] src/PhylogenyTreeView.cpp: At global scope: src/PhylogenyTreeView.cpp:734:6: warning: unused parameter ‘weightTop’ [-Wunused-parameter] src/PhylogenyTreeView.cpp:734:6: warning: unused parameter ‘weightBottom’ [-Wunused-parameter] src/PhylogenyTreeView.cpp: In member function ‘void PhylogenyTreeView::drawLabel(QPainter, int, int, float, bool) const’: src/PhylogenyTreeView.cpp:849:7: warning: variable ‘brightness’ set but not used [-Wunused-but-set-variable] src/PhylogenyTreeView.cpp:748:6: warning: variable ‘shade’ set but not used [-Wunused-but-set-variable] src/PhylogenyTreeView.cpp: At global scope: src/PhylogenyTreeView.cpp:973:6: warning: unused parameter ‘colorStart’ [-Wunused-parameter] src/PhylogenyTreeView.cpp: In member function ‘void PhylogenyTreeView::updateNodeViews(const PhylogenyTreeNode_)’: src/PhylogenyTreeView.cpp:1057:43: warning: ‘childMaxY’ may be used uninitialized in this function [-Wuninitialized] src/PhylogenyTreeView.cpp:1057:43: warning: ‘childMinY’ may be used uninitialized in this function [-Wuninitialized] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o PhylogenyTreeViewMain.o src/PhylogenyTreeViewMain.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o PhylogenyTreeViewMap.o src/PhylogenyTreeViewMap.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o ReferenceView.o src/ReferenceView.cpp src/ReferenceView.cpp: In member function ‘virtual void ReferenceView::updateBuffer()’: src/ReferenceView.cpp:110:74: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o Region.o src/Region.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o RegionView.o src/RegionView.cpp src/RegionView.cpp: In member function ‘void RegionView::draw(QRgb, const QRgb, const int, int, bool, int, float, int) const’: src/RegionView.cpp:74:7: warning: variable ‘lightness’ set but not used [-Wunused-but-set-variable] src/RegionView.cpp: In member function ‘void RegionView::drawHighlight(QRgb_, int, int, float, bool, float, int) const’: src/RegionView.cpp:138:32: warning: suggest parentheses around comparison in operand of ‘==’ [-Wparentheses] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o RulerView.o src/RulerView.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SearchControl.o src/SearchControl.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnapshotWindow.o src/SnapshotWindow.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnpBuffer.o src/SnpBuffer.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnpData.o src/SnpData.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnpLegend.o src/SnpLegend.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnpPalette.o src/SnpPalette.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SnpWorker.o src/SnpWorker.cpp src/SnpWorker.cpp: In constructor ‘SnpWorker::SnpWorker(const Alignment, SnpData, const std::vector, QMutex, int, const SnpPalette, const SyntenyPalette_)’: src/SnpWorker.cpp:32:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] src/SnpWorker.cpp: In member function ‘void SnpWorker::drawSynteny()’: src/SnpWorker.cpp:589:131: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] src/SnpWorker.cpp:594:10: warning: unused variable ‘startScaledRef’ [-Wunused-variable] src/SnpData.h: In member function ‘void SnpWorker::computeSnps()’: src/SnpData.h:85:62: warning: ‘id’ may be used uninitialized in this function [-Wuninitialized] src/SnpWorker.cpp:194:9: note: ‘id’ was declared here g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o StatusBar.o src/StatusBar.cpp src/StatusBar.cpp:15:6: warning: unused parameter ‘gapped’ [-Wunused-parameter] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o StatusLabel.o src/StatusLabel.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o SyntenyPalette.o src/SyntenyPalette.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o Timer.o src/Timer.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o Track.o src/Track.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o TrackHeightController.o src/TrackHeightController.cpp g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQTSHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o TrackListView.o src/TrackListView.cpp src/TrackListView.cpp: In member function ‘void TrackListView::setIdByTrack(const std::vector)’: src/TrackListView.cpp:41:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] g++ -c -m64 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I../../share/qt4/mkspecs/linux-g++-64 -I. -I../../include/qt4/QtCore -I../../include/qt4/QtGui -I../../include/qt4/QtXml -I../../include/qt4 -I. -Isrc -I../include -I../include -I. -o TrackView.o src/TrackView.cpp src/TrackView.cpp: In member function ‘int TrackView::getLcb(int, int, float&) const’: src/TrackView.cpp:133:18: error: ‘printf’ was not declared in this scope src/TrackView.cpp: At global scope: src/TrackView.cpp:142:6: warning: unused parameter ‘newOffsetY’ [-Wunused-parameter] src/TrackView.cpp:142:6: warning: unused parameter ‘newHeight’ [-Wunused-parameter] src/TrackView.cpp: In member function ‘int TrackView::getLcb(int, int, float&) const’: src/TrackView.cpp:135:1: warning: control reaches end of non-void function [-Wreturn-type] make: *\ [TrackView.o] Error 1

Ok, I fixed this one, but it's looking like I will have to set up an Ubuntu VM here to continue debugging this, rather than making you do all this work for every problem. I will probably not get to that until next week. The new source is posted if you feel like trying it out in the meantime, but there's no guarantee there won't be more of these errors. Thanks again for your patience with this.

Hi again,

have you had the chance to pre-compile Gingr in the Ubuntu environment ?

Hi Patricia, We still need to track down an Ubuntu machine to test the build and Brian has been out this week. Will keep you posted. Thanks for your patience!

Best, -Adam

This should be fixed in v1.1.

Closing issue; the latest binary (v1.1) was tested in an Ubuntu 12.0.4 virtual machine and fixes this problem. The source for 1.1 also builds on Ubuntu 12.0.4. This version of Gingr is currently only available standalone, but will soon be bundled with the next Harvest release.

Patrícia, if you have any more problems, please let us know and/or reopen the issue.

marbl / gingr

Gingr installation problem from pre-compiled version #3