Make error for hal : /bin/sh: 1: h5c++: not found

[krostifangers]

Hello I tried to install hal and had this problem. cd hal sudo make cd api && make all make[1] : on entre dans le répertoire « /home/clemaire/hal/api » cp inc/.h ../lib// rm -f .o h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp /bin/sh: 1: h5c++: not found Makefile:21 : la recette pour la cible « ../lib//halLib.a » a échouée make[1]: [../lib//halLib.a] Erreur 127 make[1] : on quitte le répertoire « /home/clemaire/hal/api » Makefile:10 : la recette pour la cible « all.api » a échouée make: [all.api] Erreur 2

As recommended, I previously installed hdf5 following the procedure "with password" as sudo. when I manually enter the following command line, it seems to work. h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp h5c++ is working fine. Could you help me, please? Thank you in advance Christophe

[glennhickey]

Bizarre. Have you tried running make without "sudo" ?

On Thu, Apr 11, 2019 at 9:22 AM krostifangers notifications@github.com wrote:

Hello I tried to install hal and had this problem. cd hal sudo make cd api && make all make[1] : on entre dans le répertoire « /home/clemaire/hal/api » cp inc/

.h ../lib// rm -f .o h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp /bin/sh: 1: h5c++: not found Makefile:21 : la recette pour la cible « ../lib//halLib.a » a échouée make[1]: [../lib//halLib.a] Erreur 127 make[1] : on quitte le répertoire « /home/clemaire/hal/api » Makefile:10 : la recette pour la cible « all.api » a échouée make: [all.api] Erreur 2

As recommended, I previously installed hdf5 following the procedure "with password" as sudo. when I manually enter the following command line, it seems to work. h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp h5c++ is working fine. Could you help me, please? Thank you in advance Christophe

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[diekhans]

I believe this is due to sudo rest ricing your path. There is no reason to compile HAL as root

krostifangers notifications@github.com writes:

Hello I tried to install hal and had this problem. cd hal sudo make cd api && make all make[1] : on entre dans le répertoire « /home/clemaire/hal/api » cp inc/.h ../lib// rm -f .o h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp /bin/sh: 1: h5c++: not found Makefile:21 : la recette pour la cible « ../lib//halLib.a » a échouée make[1]: [../lib//halLib.a] Erreur 127 make[1] : on quitte le répertoire « /home/clemaire/hal/api » Makefile:10 : la recette pour la cible « all.api » a échouée make: [all.api] Erreur 2

As recommended, I previously installed hdf5 following the procedure "with password" as sudo. when I manually enter the following command line, it seems to work. h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I inc -I hdf5_impl -I impl -I ../lib// -c impl/.cpp hdf5_impl/.cpp h5c++ is working fine. Could you help me, please? Thank you in advance Christophe

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[diekhans]

this should be addressed, please reopen if still a problem

[sagitaninta]

Hi, I have the exact same problem when trying to make hal. So what I did is installing all dependencies, which all work perfectly, also add the locally installed hdf5 path, and do

git clone https://github.com/ComparativeGenomicsToolkit/hal.git
cd hal
make

And this is what I got:

cd api && make libs
make[1]: Entering directory '/dss/dsshome1/lxc06/ra57gih/bin/hal/api'
h5c++ -prefix=~/bin/hdf5-1.10.1 -MM -MT ../objs/api/impl/halValidate.o -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halValidate.cpp >impl/halValidate.depend
/bin/sh: h5c++: command not found
make[1]: *** [../rules.mk:18: ../objs/api/impl/halValidate.o] Error 127
make[1]: Leaving directory '/dss/dsshome1/lxc06/ra57gih/bin/hal/api'
make: *** [Makefile:13: api.libs] Error 2

I am installing this in a HPC so I cannot do anything that needs root access.