Update include.mk #10
Conversation
Change the if-order to grab KYOTO dependencies from userspace (e.g. when installed using brew).
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Are you having troubles with the cactus submodule kyoto? I'm worried about using other versions as our version does contain some small changes, and it's the one we test with. Obviously if it doesn't work, being able to use your own is better than nothing, though, so this seems okay to me. @diekhans do you mind taking a look? |
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I had no troubles using Kyoto actually while running Cactus. Just to let you know, I ended up installing both Anyway, many thanks @glennhickey and @diekhans for checking this issue. |
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Hi Thiago,
The submodule copy of kyoto should just compile when you run
make in cactus. Have you tried that? If it fails, please
attached the output to a comment in this ticket
Mark
Thiago Genez <[email protected]> writes:
… I had no troubles using Kyoto actually while running Cactus. Just to let you know, I end up installing both kyoto-tycoon and kyoto-cabinet using the source indicated by (Linux)brew. Following the [build from scratch](https://github.com/ComparativeGenomicsToolkit/cactus#build-from-source) documentation, I was not clear to me to install your version of [kyoto](https://github.com/ComparativeGenomicsToolkit/kyoto). As I don't have root access, I cannot install Kyoto at `/usr/local`, by at `$HOME` where this patch aims to look for kyoto as its first option.
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#10 (comment)
I had no troubles using Kyoto actually while running Cactus. Just to let you
know, I end up installing both kyoto-tycoon and kyoto-cabinet using the source
indicated by (Linux)brew. Following the build from scratch documentation, I was
not clear to me to install your version of kyoto. As I don't have root access,
I cannot install Kyoto at /usr/local, by at $HOME where this patch aims to look
for kyoto as its first option.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or unsubscribe.*
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Hi Mark, Sorry for the late reply. I was trying compiling Cactus many times, but no success so far when using the The error occurs at the moment make command Any ideas what is the problem? Cheers, Thiago Output when make suball1 #================================================================ Ready to install.#================================================================ #================================================================ Ready to install.#================================================================ #================================================================ Ready to install.#================================================================ #================================================================ Ready to install.#================================================================ #================================================================ Thanks for using Kyoto Cabinet.#================================================================ #================================================================ Thanks for using Kyoto Tycoon.#================================================================ |
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Problem solved with my proposed patch. Basically, the original code Find below the Cactus installation using linuxbrew:
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It looks like to are picking up
/usr/local/include/kthttp.h
instead of the one built from the submodule,
cactus/submodules/kyoto/kyototycoon/kthttp.h
which is also have been copied into:
cactus/include/kthttp.h
The command:
cc -Iinc -Iimpl -I/usr/local/include -DHAVE_KYOTO_TYCOON=1 -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -std=c99 -fPIC -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I tests -o ../../sonLib/bin/sonLib_kvDatabaseTest tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++ -lz -lm ../../sonLib/lib/sonLib.a -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++ -lz -lm -lm
doesn't seem to have a -I to the right directory. I can't look at this for a couple of days,
However I make sure I can get into my EBI account so I look over your shoulder.
Mark
Thiago Genez <[email protected]> writes:
… Hi Mark,
Sorry for the late reply. I was trying compiling Cactus many times, but no success so far when using the `kyoto-tycoon` and `kyoto-cabinet` in the Cactus submodule folder. Please find the errors below. I have downgraded the `hdf5` from version `1.12` to `1.10.1` (from [here](https://github.com/ComparativeGenomicsToolkit/hal)) to avoid dependency version conflicts.
The error occurs at the moment make `Entering directory /home/user/cactus/latest/cactus/submodules/sonLib/C'`
Any ideas what is the problem?
Output when `export CXX_ABI_DEF=-D_GLIBCXX_USE_CXX11_ABI=1`:
Cheers, Thiago
make suball1
make[1]: Entering directory `/home/user/cactus/latest/cactus'
cd submodules/kyoto && make PREFIX=/home/user/cactus/latest/cactus
make[2]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto'
make -j4 -C kyotocabinet
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyotocabinet strip
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make -j4 -C kyototycoon
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyototycoon strip
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip ktutiltest ktutilmgr ktutilserv kttimedtest kttimedmgr ktserver ktremotetest ktremotemgr
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[2]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto'
cd submodules/kyoto && make PREFIX=/home/user/cactus/latest/cactus install
make[2]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto'
make -j4 -C kyotocabinet
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyotocabinet strip
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make -j4 -C kyototycoon
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyototycoon strip
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip ktutiltest ktutilmgr ktutilserv kttimedtest kttimedmgr ktserver ktremotetest ktremotemgr
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make -j4 -C kyotocabinet install DESTDIR=""
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
mkdir -p /home/user/cactus/latest/cactus/include
cp -Rf kccommon.h kcutil.h kcthread.h kcfile.h kccompress.h kccompare.h kcmap.h kcregex.h kcdb.h kcplantdb.h kcprotodb.h kcstashdb.h kccachedb.h kchashdb.h kcdirdb.h kctextdb.h kcpolydb.h kcdbext.h kclangc.h /home/user/cactus/latest/cactus/include
mkdir -p /home/user/cactus/latest/cactus/lib
cp -Rf libkyotocabinet.a /home/user/cactus/latest/cactus/lib
mkdir -p /home/user/cactus/latest/cactus/bin
cp -Rf kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest /home/user/cactus/latest/cactus/bin
mkdir -p /home/user/cactus/latest/cactus/share/man/man1
cd man && cp -Rf kcutiltest.1 kcutilmgr.1 kcprototest.1 kcstashtest.1 kccachetest.1 kcgrasstest.1 kchashtest.1 kchashmgr.1 kctreetest.1 kctreemgr.1 kcdirtest.1 kcdirmgr.1 kcforesttest.1 kcforestmgr.1 kcpolytest.1 kcpolymgr.1 kclangctest.1 /home/user/cactus/latest/cactus/share/man/man1
mkdir -p /home/user/cactus/latest/cactus/share/doc/kyotocabinet
cp -Rf COPYING FOSSEXCEPTION ChangeLog doc kyotocabinet.idl /home/user/cactus/latest/cactus/share/doc/kyotocabinet
mkdir -p /home/user/cactus/latest/cactus/lib/pkgconfig
cp -Rf kyotocabinet.pc /home/user/cactus/latest/cactus/lib/pkgconfig
#================================================================
# Thanks for using Kyoto Cabinet.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyotocabinet'
make -j4 -C kyototycoon install DESTDIR=""
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
mkdir -p /home/user/cactus/latest/cactus/include
cp -Rf ktcommon.h ktutil.h ktsocket.h ktthserv.h kthttp.h ktrpc.h ktulog.h ktshlib.h kttimeddb.h ktdbext.h ktremotedb.h ktplugserv.h ktplugdb.h /home/user/cactus/latest/cactus/include
mkdir -p /home/user/cactus/latest/cactus/lib
cp -Rf libkyototycoon.a /home/user/cactus/latest/cactus/lib
mkdir -p /home/user/cactus/latest/cactus/libexec
if [ -n "" ] ; then cp -Rf /home/user/cactus/latest/cactus/libexec ; fi
mkdir -p /home/user/cactus/latest/cactus/bin
cp -Rf ktutiltest ktutilmgr ktutilserv kttimedtest kttimedmgr ktserver ktremotetest ktremotemgr /home/user/cactus/latest/cactus/bin
mkdir -p /home/user/cactus/latest/cactus/share/man/man1
cd man && cp -Rf ktutiltest.1 ktutilmgr.1 ktutilserv.1 kttimedtest.1 kttimedmgr.1 ktserver.1 ktremotetest.1 ktremotemgr.1 /home/user/cactus/latest/cactus/share/man/man1
mkdir -p /home/user/cactus/latest/cactus/share/doc/kyototycoon
cp -Rf COPYING ChangeLog doc kyototycoon.idl /home/user/cactus/latest/cactus/share/doc/kyototycoon
mkdir -p /home/user/cactus/latest/cactus/lib/pkgconfig
cp -Rf kyototycoon.pc /home/user/cactus/latest/cactus/lib/pkgconfig
#================================================================
# Thanks for using Kyoto Tycoon.
#================================================================
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto/kyototycoon'
make[2]: Leaving directory `/home/user/cactus/latest/cactus/submodules/kyoto'
cd submodules/sonLib && PKG_CONFIG_PATH=/home/user/cactus/latest/cactus/lib/pkgconfig: make
make[2]: Entering directory `/home/user/cactus/latest/cactus/submodules/sonLib'
cd externalTools && make all
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools'
cd cutest && make all
cd quicktree_1.1 && make all CC="cc"
make[4]: Entering directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools/quicktree_1.1'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools/quicktree_1.1'
make[4]: Entering directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools/cutest'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools/cutest'
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/sonLib/externalTools'
cd C && make all
make[3]: Entering directory `/home/user/cactus/latest/cactus/submodules/sonLib/C'
cc -Iinc -Iimpl -I/usr/local/include -DHAVE_KYOTO_TYCOON=1 -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -std=c99 -fPIC -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I tests -o ../../sonLib/bin/sonLib_kvDatabaseTest tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++ -lz -lm ../../sonLib/lib/sonLib.a -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lkyototycoon -lkyotocabinet -lz -lbz2 -lpthread -lm -lstdc++ -lz -lm -lm
/home/user/thiagogenez/.linuxbrew/bin/ld: ../../sonLib/lib/sonLib.a(sonLibKVDatabase_KyotoTycoon.o): in function `kyototycoon::HTTPClient::open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, double)':
/usr/local/include/kthttp.h:401: undefined reference to `kyototycoon::Socket::get_local_host_name[abi:cxx11]()'
/home/user/thiagogenez/.linuxbrew/bin/ld: /usr/local/include/kthttp.h:402: undefined reference to `kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/home/user/thiagogenez/.linuxbrew/bin/ld: /usr/local/include/kthttp.h:407: undefined reference to `kyototycoon::Socket::open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/home/user/thiagogenez/.linuxbrew/bin/ld: ../../sonLib/lib/sonLib.a(sonLibKVDatabase_KyotoTycoon.o): in function `kyototycoon::HTTPClient::fetch(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, kyototycoon::HTTPClient::Method, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const*, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const*)':
/usr/local/include/kthttp.h:482: undefined reference to `kyototycoon::Socket::send(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status
make[3]: *** [../../sonLib/bin/sonLib_kvDatabaseTest] Error 1
make[3]: Leaving directory `/home/user/cactus/latest/cactus/submodules/sonLib/C'
make[2]: *** [cP] Error 2
make[2]: Leaving directory `/home/user/cactus/latest/cactus/submodules/sonLib'
make[1]: *** [suball.sonLib] Error 2
make[1]: Leaving directory `/home/user/cactus/latest/cactus'
make: *** [all] Error 2
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3 participants
Change the if-else-order to grab KYOTO dependencies from
CACTUS_DIR/include/The original
include.mkfile grabs *.h files from Kyoto already installed in the system (i.e., at/usr/local/include/) instead of grabbing the *.h files (registered by pkg-config during Cactus compilation) provided atCACTUS_DIR/include/.