Closed pmsim closed 9 years ago
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
inflating: harvest-tools-master/INSTALL.py
inflating: harvest-tools-master/INSTALL.txt
inflating: harvest-tools-master/LICENSE.txt
inflating: harvest-tools-master/Makefile.in
inflating: harvest-tools-master/README
extracting: harvest-tools-master/bootstrap.sh
inflating: harvest-tools-master/configure.ac
inflating: harvest-tools-master/harvest-snps.py
inflating: harvest-tools-master/harvest-variants.py
inflating: harvest-tools-master/setup.py
creating: harvest-tools-master/src/
inflating: harvest-tools-master/src/harvest-alignments.py
inflating: harvest-tools-master/src/harvest-backbone.py
inflating: harvest-tools-master/src/harvest-phylogeny.c
inflating: harvest-tools-master/src/harvest-phylogeny.py
inflating: harvest-tools-master/src/harvest-snps.py
inflating: harvest-tools-master/src/harvest-variants.py
creating: harvest-tools-master/src/harvest/
inflating: harvest-tools-master/src/harvest/AnnotationList.cpp
inflating: harvest-tools-master/src/harvest/AnnotationList.h
inflating: harvest-tools-master/src/harvest/HarvestIO.cpp
inflating: harvest-tools-master/src/harvest/HarvestIO.h
inflating: harvest-tools-master/src/harvest/LcbList.cpp
inflating: harvest-tools-master/src/harvest/LcbList.h
inflating: harvest-tools-master/src/harvest/PhylogenyTree.cpp
inflating: harvest-tools-master/src/harvest/PhylogenyTree.h
inflating: harvest-tools-master/src/harvest/PhylogenyTreeNode.cpp
inflating: harvest-tools-master/src/harvest/PhylogenyTreeNode.h
inflating: harvest-tools-master/src/harvest/ReferenceList.cpp
inflating: harvest-tools-master/src/harvest/ReferenceList.h
inflating: harvest-tools-master/src/harvest/TrackList.cpp
inflating: harvest-tools-master/src/harvest/TrackList.h
inflating: harvest-tools-master/src/harvest/VariantList.cpp
inflating: harvest-tools-master/src/harvest/VariantList.h
inflating: harvest-tools-master/src/harvest/exceptions.h
inflating: harvest-tools-master/src/harvest/harvest.cpp
inflating: harvest-tools-master/src/harvest/parse.cpp
inflating: harvest-tools-master/src/harvest/parse.h
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
inflating: harvest-tools-master/test/test2.tree
inflating: harvest-tools-master/test/test2.vcf
inflating: harvest-tools-master/test/test2.xmfa
$ 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
$ 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
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
extracting: parsnp-master/INSTALL
inflating: parsnp-master/LICENSE
inflating: parsnp-master/Makefile.am
inflating: parsnp-master/Parsnp.py
inflating: parsnp-master/README.md
inflating: parsnp-master/autogen.sh
creating: parsnp-master/bin/
inflating: parsnp-master/bin/Profile_linux
inflating: parsnp-master/bin/Profile_osx
inflating: parsnp-master/bin/fasttree_linux
inflating: parsnp-master/bin/fasttree_osx
inflating: parsnp-master/bin/harvest_linux
inflating: parsnp-master/bin/harvest_osx
inflating: parsnp-master/bootstrap.sh
inflating: parsnp-master/configure.ac
creating: parsnp-master/examples/
creating: parsnp-master/examples/mers_virus/
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inflating: parsnp-master/muscle/libMUSCLE/estring.h
inflating: parsnp-master/muscle/libMUSCLE/fasta.cpp
inflating: parsnp-master/muscle/libMUSCLE/fasta2.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastclust.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdist.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdistjones.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdistkbit.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdistkmer.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdistmafft.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastdistnuc.cpp
inflating: parsnp-master/muscle/libMUSCLE/fastscorepath2.cpp
inflating: parsnp-master/muscle/libMUSCLE/finddiags.cpp
inflating: parsnp-master/muscle/libMUSCLE/finddiagsn.cpp
inflating: parsnp-master/muscle/libMUSCLE/gapscoredimer.h
inflating: parsnp-master/muscle/libMUSCLE/glbalign.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalign352.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbaligndiag.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalignle.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalignsimple.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalignsp.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalignspn.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalignss.cpp
inflating: parsnp-master/muscle/libMUSCLE/glbalndimer.cpp
inflating: parsnp-master/muscle/libMUSCLE/globals.cpp
inflating: parsnp-master/muscle/libMUSCLE/globalslinux.cpp
inflating: parsnp-master/muscle/libMUSCLE/globalsother.cpp
inflating: parsnp-master/muscle/libMUSCLE/globalswin32.cpp
inflating: parsnp-master/muscle/libMUSCLE/gonnet.cpp
inflating: parsnp-master/muscle/libMUSCLE/gonnet.h
extracting: parsnp-master/muscle/libMUSCLE/gotowt.cpp
inflating: parsnp-master/muscle/libMUSCLE/henikoffweight.cpp
inflating: parsnp-master/muscle/libMUSCLE/henikoffweightpb.cpp
inflating: parsnp-master/muscle/libMUSCLE/html.cpp
inflating: parsnp-master/muscle/libMUSCLE/hydro.cpp
inflating: parsnp-master/muscle/libMUSCLE/intmath.cpp
inflating: parsnp-master/muscle/libMUSCLE/intmath.h
inflating: parsnp-master/muscle/libMUSCLE/local.cpp
inflating: parsnp-master/muscle/libMUSCLE/main.cpp
inflating: parsnp-master/muscle/libMUSCLE/makerootmsa.cpp
inflating: parsnp-master/muscle/libMUSCLE/makerootmsab.cpp
inflating: parsnp-master/muscle/libMUSCLE/maketree.cpp
inflating: parsnp-master/muscle/libMUSCLE/mhack.cpp
inflating: parsnp-master/muscle/libMUSCLE/mk
inflating: parsnp-master/muscle/libMUSCLE/mpam200.cpp
inflating: parsnp-master/muscle/libMUSCLE/msa.cpp
inflating: parsnp-master/muscle/libMUSCLE/msa.h
inflating: parsnp-master/muscle/libMUSCLE/msa2.cpp
inflating: parsnp-master/muscle/libMUSCLE/msadist.h
inflating: parsnp-master/muscle/libMUSCLE/msadistkimura.cpp
inflating: parsnp-master/muscle/libMUSCLE/msf.cpp
inflating: parsnp-master/muscle/libMUSCLE/muscle.cpp
inflating: parsnp-master/muscle/libMUSCLE/muscle.h
inflating: parsnp-master/muscle/libMUSCLE/muscleout.cpp
inflating: parsnp-master/muscle/libMUSCLE/nucmx.cpp
inflating: parsnp-master/muscle/libMUSCLE/nwdasimple.cpp
inflating: parsnp-master/muscle/libMUSCLE/nwdasimple2.cpp
inflating: parsnp-master/muscle/libMUSCLE/nwdasmall.cpp
inflating: parsnp-master/muscle/libMUSCLE/nwrec.cpp
inflating: parsnp-master/muscle/libMUSCLE/nwsmall.cpp
inflating: parsnp-master/muscle/libMUSCLE/objscore.cpp
inflating: parsnp-master/muscle/libMUSCLE/objscore.h
inflating: parsnp-master/muscle/libMUSCLE/objscore2.cpp
inflating: parsnp-master/muscle/libMUSCLE/objscoreda.cpp
inflating: parsnp-master/muscle/libMUSCLE/onexception.cpp
inflating: parsnp-master/muscle/libMUSCLE/options.cpp
inflating: parsnp-master/muscle/libMUSCLE/outweights.cpp
inflating: parsnp-master/muscle/libMUSCLE/pam200mafft.cpp
inflating: parsnp-master/muscle/libMUSCLE/params.cpp
inflating: parsnp-master/muscle/libMUSCLE/params.h
inflating: parsnp-master/muscle/libMUSCLE/phy.cpp
inflating: parsnp-master/muscle/libMUSCLE/phy2.cpp
inflating: parsnp-master/muscle/libMUSCLE/phy3.cpp
inflating: parsnp-master/muscle/libMUSCLE/phy4.cpp
inflating: parsnp-master/muscle/libMUSCLE/phyfromclust.cpp
inflating: parsnp-master/muscle/libMUSCLE/phyfromfile.cpp
inflating: parsnp-master/muscle/libMUSCLE/physeq.cpp
inflating: parsnp-master/muscle/libMUSCLE/phytofile.cpp
inflating: parsnp-master/muscle/libMUSCLE/posgap.cpp
inflating: parsnp-master/muscle/libMUSCLE/ppscore.cpp
inflating: parsnp-master/muscle/libMUSCLE/profdb.cpp
inflating: parsnp-master/muscle/libMUSCLE/profile.cpp
inflating: parsnp-master/muscle/libMUSCLE/profile.h
inflating: parsnp-master/muscle/libMUSCLE/profilefrommsa.cpp
inflating: parsnp-master/muscle/libMUSCLE/profout.musc
inflating: parsnp-master/muscle/libMUSCLE/progalign.cpp
inflating: parsnp-master/muscle/libMUSCLE/progress.cpp
inflating: parsnp-master/muscle/libMUSCLE/progressivealign.cpp
inflating: parsnp-master/muscle/libMUSCLE/pwpath.cpp
inflating: parsnp-master/muscle/libMUSCLE/pwpath.h
inflating: parsnp-master/muscle/libMUSCLE/readmx.cpp
inflating: parsnp-master/muscle/libMUSCLE/realigndiffs.cpp
inflating: parsnp-master/muscle/libMUSCLE/realigndiffse.cpp
inflating: parsnp-master/muscle/libMUSCLE/refine.cpp
inflating: parsnp-master/muscle/libMUSCLE/refine.h
inflating: parsnp-master/muscle/libMUSCLE/refinehoriz.cpp
inflating: parsnp-master/muscle/libMUSCLE/refinesubfams.cpp
inflating: parsnp-master/muscle/libMUSCLE/refinetree.cpp
inflating: parsnp-master/muscle/libMUSCLE/refinetreee.cpp
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inflating: parsnp-master/muscle/libMUSCLE/refinew.cpp
inflating: parsnp-master/muscle/libMUSCLE/savebest.cpp
inflating: parsnp-master/muscle/libMUSCLE/scoredist.cpp
inflating: parsnp-master/muscle/libMUSCLE/scoregaps.cpp
inflating: parsnp-master/muscle/libMUSCLE/scorehistory.cpp
inflating: parsnp-master/muscle/libMUSCLE/scorehistory.h
inflating: parsnp-master/muscle/libMUSCLE/scorepp.cpp
inflating: parsnp-master/muscle/libMUSCLE/seq.cpp
inflating: parsnp-master/muscle/libMUSCLE/seq.h
inflating: parsnp-master/muscle/libMUSCLE/seqvect.cpp
inflating: parsnp-master/muscle/libMUSCLE/seqvect.h
inflating: parsnp-master/muscle/libMUSCLE/setblosumweights.cpp
inflating: parsnp-master/muscle/libMUSCLE/setgscweights.cpp
inflating: parsnp-master/muscle/libMUSCLE/setnewhandler.cpp
inflating: parsnp-master/muscle/libMUSCLE/spfast.cpp
inflating: parsnp-master/muscle/libMUSCLE/sptest.cpp
inflating: parsnp-master/muscle/libMUSCLE/stabilize.cpp
inflating: parsnp-master/muscle/libMUSCLE/subfam.cpp
inflating: parsnp-master/muscle/libMUSCLE/subfams.cpp
inflating: parsnp-master/muscle/libMUSCLE/sw.cpp
inflating: parsnp-master/muscle/libMUSCLE/termgaps.cpp
inflating: parsnp-master/muscle/libMUSCLE/test.musc
extracting: parsnp-master/muscle/libMUSCLE/test.out
inflating: parsnp-master/muscle/libMUSCLE/test.prof
inflating: parsnp-master/muscle/libMUSCLE/textfile.cpp
inflating: parsnp-master/muscle/libMUSCLE/textfile.h
inflating: parsnp-master/muscle/libMUSCLE/threadstorage.h
inflating: parsnp-master/muscle/libMUSCLE/threewaywt.cpp
inflating: parsnp-master/muscle/libMUSCLE/timing.h
inflating: parsnp-master/muscle/libMUSCLE/tomhydro.cpp
inflating: parsnp-master/muscle/libMUSCLE/traceback.cpp
inflating: parsnp-master/muscle/libMUSCLE/tracebackopt.cpp
inflating: parsnp-master/muscle/libMUSCLE/tracebacksw.cpp
inflating: parsnp-master/muscle/libMUSCLE/tree.h
inflating: parsnp-master/muscle/libMUSCLE/treefrommsa.cpp
inflating: parsnp-master/muscle/libMUSCLE/types.h
inflating: parsnp-master/muscle/libMUSCLE/typetostr.cpp
inflating: parsnp-master/muscle/libMUSCLE/unixio.h
inflating: parsnp-master/muscle/libMUSCLE/upgma2.cpp
inflating: parsnp-master/muscle/libMUSCLE/usage.cpp
inflating: parsnp-master/muscle/libMUSCLE/validateids.cpp
inflating: parsnp-master/muscle/libMUSCLE/vtml2.cpp
inflating: parsnp-master/muscle/libMUSCLE/writescorefile.cpp
inflating: parsnp-master/muscle/libtool
creating: parsnp-master/muscle/m4/
inflating: parsnp-master/muscle/m4/ax_openmp.m4
inflating: parsnp-master/muscle/m4/ax_prog_doxygen.m4
inflating: parsnp-master/muscle/m4/libtool.m4
inflating: parsnp-master/muscle/m4/ltoptions.m4
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inflating: parsnp-master/muscle/m4/ltversion.m4
inflating: parsnp-master/muscle/m4/lt~obsolete.m4
creating: parsnp-master/script/
inflating: parsnp-master/script/shuffle.py
inflating: parsnp-master/setup.py
creating: parsnp-master/src/
inflating: parsnp-master/src/Converter.cpp
inflating: parsnp-master/src/Converter.h
inflating: parsnp-master/src/LCB.cpp
inflating: parsnp-master/src/LCB.hh
inflating: parsnp-master/src/LCR.cpp
inflating: parsnp-master/src/LCR.hh
inflating: parsnp-master/src/Makefile.am
inflating: parsnp-master/src/MuscleInterface.cpp
inflating: parsnp-master/src/MuscleInterface.h
inflating: parsnp-master/src/Stack.h
inflating: parsnp-master/src/TMum.cpp
inflating: parsnp-master/src/TMum.hh
creating: parsnp-master/src/csgmum/
extracting: parsnp-master/src/csgmum/README
inflating: parsnp-master/src/csgmum/csg.c
inflating: parsnp-master/src/csgmum/csg.h
inflating: parsnp-master/src/csgmum/fastaread.c
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inflating: parsnp-master/src/csgmum/mum.c
inflating: parsnp-master/src/csgmum/mum.h
inflating: parsnp-master/src/csgmum/types.h
creating: parsnp-master/src/ext/
inflating: parsnp-master/src/ext/README
inflating: parsnp-master/src/ext/iniFile.cpp
inflating: parsnp-master/src/ext/iniFile.h
inflating: parsnp-master/src/parsnp.cpp
inflating: parsnp-master/src/parsnp.hh
inflating: parsnp-master/template.ini
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.o
test -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.o
test -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.o
test -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.o
test -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.o
test -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.o
test -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.o
test -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.o
test -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
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
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.
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