Make fails on Fedora 28

[claggner]

Hi,

Make works for a while, then fails on my 64bit Fedora 28 machine with the following output:

... gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/mdparams.c -o obj/mdparams.o gcc obj/mdpmain.o obj/mdpocket.o obj/mdpbase.o obj/mdpout.o obj/psorting.o obj/pscoring.o obj/mdparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/mdpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ obj/mdpocket.o: In function mdpocket_detect': /home/christian/Downloads/fpocket/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/christian/Downloads/fpocket/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status make: *** [makefile:145: bin/mdpocket] Error 1

gcc: 8.1.1-1 netcdf-devel: 4.4.1.1-9

Any ideas what's wrong? Thanks, Christian

[pschmidtke]

Hey,

yes I also experienced that lately when deploying the current code on RHEL based systems. Actually this is because of mdpocket using the molfile_plugin from VMD now to read MD trajectories...and right now it is shipped in a compiled way (debian flavors).

So first option: You don't care about mdpocket and just want to use fpocket, then just comment out the mdpocket compilation in the makefile and it should be OK.

If you want to use mdpocket, you can compile the molfile plugin yourself on your environment and then place the libmolfile_plugin.a + all the .so's where they are now in the src folder.

Else you'll have to wait a bit as I still have to rewrite the makefile etc so that compilation of this is easy. Sorry about that.

I can ship you with precompiled so files for rhel based systems too as a quick fix...:)

[claggner]

Thanks for the quick reply. Yeah, I actually want to try out mdpocket, but don't know how to compile the molfile plugin. So if you could send me the precompiled files that would be great. Thanks!

[pschmidtke]

replace the LINUXAMD64 folder in the plugins directory and rebuild everything (make clean; make) LINUXAMD64.tar.gz

[claggner]

That doesn't change anything (removed everything and restarted with git clone). In fact, the contents of the archive seem to be identical to what already was in LINUXAMD64. Which new files am I looking for?

[shozebhaider]

Hi, Any idea when you would get a chance to write the makefile that you mention above that works for mdpocket? I have compiled vmd plugins (*.so), and placed them in the plugins folder. There is no libmolfile_plugin.a and also not sure where you want the files to go in the src folder ? Upon running make, it gives the following error:

/usr/local/fpocket/src/mdpocket.c:96: undefined reference to molfile_netcdfplugin_init' /usr/local/fpocket/src/mdpocket.c:97: undefined reference tomolfile_netcdfplugin_register'

Thanks.

[wbarber1]

Hello, getting the same makefile error, but if I comment out the mdpocket lines, I still have issues with the make install:

mkdir -p /usr/local/bin/ mkdir -p /usr/local/man/man8/ cp bin/fpocket /usr/local/bin/ cp bin/tpocket /usr/local/bin/ cp bin/dpocket /usr/local/bin/ cp bin/ /usr/local/bin/ cp: omitting directory 'bin/' makefile:148: recipe for target 'install' failed make: *** [install] Error 1

This is on Ubuntu 16.04 LTS.

[pschmidtke]

Just type make (not make install for now) and post the output. Here the copy of the binaries seems to fail somehow

From: wbarber1 notifications@github.com Sent: mercredi 18 juillet 2018 16:13 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

Hello, getting the same makefile error, but if I comment out the mdpocket lines, I still have issues with the make install:

mkdir -p /usr/local/bin/ mkdir -p /usr/local/man/man8/ cp bin/fpocket /usr/local/bin/ cp bin/tpocket /usr/local/bin/ cp bin/dpocket /usr/local/bin/ cp bin/ /usr/local/bin/ cp: omitting directory 'bin/' makefile:148: recipe for target 'install' failed make: *** [install] Error 1

This is on Ubuntu 16.04 LTS.

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[wbarber1]

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char * restrict’ but argument is of type ‘char (*)[3]’ __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char * restrict’ but argument is of type ‘char (*)[3]’ __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets *pockets,s_pdb *pdb,s_fparams *params, s_pdb *pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets *pockets, s_fparams *params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/*" within comment [-Wcomment] if (!tweight) return 0; /* usually due to empty clusters */ ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int** mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void *v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to __builtin___strncat_chk might overflow destination buffer return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

[pschmidtke]

Can you check if fpocket is available in the bin folder? If yes it compiled fine

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:24, wbarber1 notifications@github.com<mailto:notifications@github.com> wrote:

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict __src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets pockets,s_pdb pdb,s_fparams params, s_pdb pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets pockets, s_fparams params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/" within comment [-Wcomment] if (!tweight) return 0; / usually due to empty clusters */ ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int* mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin_strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

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[wbarber1]

Thanks, that worked. Ideally I'd like to be able to use mdpocket, but I'm unsure how to go about recompiling the plugin you mentioned. I don't suppose you could explain in a bit more detail? Thanks for all the help so far.

On Wed, Jul 18, 2018 at 10:37 AM, Peter Schmidtke notifications@github.com wrote:

Can you check if fpocket is available in the bin folder? If yes it compiled fine

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:24, wbarber1 <notifications@github.com<mailto: notifications@github.com>> wrote:

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char

• restrict’ but argument is of type ‘char ()[3]’ __NTH (strncpy (char restrict dest, const char *restrict src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char
• restrict’ but argument is of type ‘char ()[3]’ __NTH (strncpy (char restrict dest, const char restrict src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets pockets,s_pdb pdb,s_fparams params, s_pdb pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets pockets, s_fparams params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/" within comment [-Wcomment] if (!tweight) return 0; / usually due to empty clusters / ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int* mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

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[shozebhaider]

Any ideas on how we can make mdpocket to work on Ubuntu ?

Best Wishes

Shozeb

On 18 Jul 2018, at 15:37, Peter Schmidtke notifications@github.com wrote:

Can you check if fpocket is available in the bin folder? If yes it compiled fine

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:24, wbarber1 notifications@github.com<mailto:notifications@github.com> wrote:

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict __src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets pockets,s_pdb pdb,s_fparams params, s_pdb pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets pockets, s_fparams params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/" within comment [-Wcomment] if (!tweight) return 0; / usually due to empty clusters */ ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int* mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin_strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

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[pschmidtke]

Sorry about these issues linked to vmd molfile plugin. Good news is that it works on Ubuntu. I'm on the road right now but will try to look into it next week to see how to make this on different Linux flavors .

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:47, shozebhaider notifications@github.com<mailto:notifications@github.com> wrote: Any ideas on how we can make mdpocket to work on Ubuntu ?

Best Wishes

Shozeb

On 18 Jul 2018, at 15:37, Peter Schmidtke notifications@github.com wrote:

Can you check if fpocket is available in the bin folder? If yes it compiled fine

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:24, wbarber1 notifications@github.com<mailto:notifications@github.com> wrote:

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char restrict’ but argument is of type ‘char ()[3]’ NTH (strncpy (char *restrict dest, const char *restrict __src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets pockets,s_pdb pdb,s_fparams params, s_pdb pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets pockets, s_fparams params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/" within comment [-Wcomment] if (!tweight) return 0; / usually due to empty clusters */ ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int* mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin_strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

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[wbarber1]

Well be safe on the road, I'll take another look next week and see where we are at then I guess. Thanks!

Will

On Wed, Jul 18, 2018 at 10:51 AM, Peter Schmidtke notifications@github.com wrote:

Sorry about these issues linked to vmd molfile plugin. Good news is that it works on Ubuntu. I'm on the road right now but will try to look into it next week to see how to make this on different Linux flavors .

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:47, shozebhaider <notifications@github.com<mailto: notifications@github.com>> wrote: Any ideas on how we can make mdpocket to work on Ubuntu ?

Best Wishes

Shozeb

On 18 Jul 2018, at 15:37, Peter Schmidtke notifications@github.com wrote:

Can you check if fpocket is available in the bin folder? If yes it compiled fine

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 18, 2018, at 16:24, wbarber1 <notifications@github.com<mailto: notifications@github.com>> wrote:

As per request from the author, here's the results of a make with the commenting out of mdpocket:

gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpmain.c -o obj/fpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/psorting.c -o obj/psorting.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pscoring.c -o obj/pscoring.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/utils.c -o obj/utils.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pertable.c -o obj/pertable.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/memhandler.c -o obj/memhandler.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi.c -o obj/voronoi.o src/voronoi.c: In function ‘load_vvertices_DEPRECATED’: src/voronoi.c:85:12: warning: format not a string literal and no format arguments [-Wformat-security] printf(tmpn1); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/sort.c -o obj/sort.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/calc.c -o obj/calc.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepdb.c -o obj/writepdb.o src/writepdb.c: In function ‘write_pdb_atom_line’: src/writepdb.c:85:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status = 0 ; ^ src/writepdb.c:73:72: warning: unused parameter ‘occ’ [-Wunused-parameter] int res_id, const char insert, float x, float y, float z, float occ, ^ src/writepdb.c: In function ‘write_pqr_atom_line’: src/writepdb.c:164:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/rpdb.c -o obj/rpdb.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tparams.c -o obj/tparams.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fparams.c -o obj/fparams.o src/fparams.c: In function ‘get_fpocket_args’: src/fparams.c:153:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==2) strncpy(&(par->xlig_resname), pt, 3); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char

• restrict’ but argument is of type ‘char ()[3]’ __NTH (strncpy (char restrict dest, const char *restrict src, ^ src/fparams.c:154:57: warning: passing argument 1 of ‘strncpy’ from incompatible pointer type [-Wincompatible-pointer-types] else if(custom_ligand_i==3) strncpy(&(par->xlig_chain_code),pt,1); ^ In file included from /usr/include/features.h:367:0, from /usr/include/stdio.h:27, from src/../headers/fparams.h:16, from src/fparams.c:2: /usr/include/x86_64-linux-gnu/bits/string3.h:123:1: note: expected ‘char
• restrict’ but argument is of type ‘char ()[3]’ __NTH (strncpy (char restrict dest, const char restrict src, ^ src/fparams.c:107:11: warning: unused variable ‘xflag’ [-Wunused-variable] short xflag; ^ src/fparams.c:106:11: warning: unused variable ‘j’ [-Wunused-variable] short j = 0; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/pocket.c -o obj/pocket.o src/pocket.c: In function ‘set_pockets_descriptors’: src/pocket.c:575:60: warning: unused parameter ‘pdb’ [-Wunused-parameter] void set_pockets_descriptors(c_lst_pockets pockets,s_pdb pdb,s_fparams params, s_pdb pdb_w_lig) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/refine.c -o obj/refine.o src/refine.c: In function ‘apply_clustering’: src/refine.c:58:58: warning: unused parameter ‘params’ [-Wunused-parameter] void apply_clustering(c_lst_pockets pockets, s_fparams params) ^ src/refine.c: In function ‘drop_tiny’: src/refine.c:167:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(npcur->pocket->v_lst->n_vertices < params->min_pock_nb_asph){ ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/descriptors.c -o obj/descriptors.o src/descriptors.c: In function ‘set_descriptors’: src/descriptors.c:246:13: warning: implicit declaration of function ‘set_ASA’ [-Wimplicit-function-declaration] set_ASA(desc, pdb, tvert, nvert); ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/aa.c -o obj/aa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpocket.c -o obj/fpocket.o src/fpocket.c: In function ‘search_pocket’: src/fpocket.c:62:16: warning: unused variable ‘et’ [-Wunused-variable] time_t bt, et; ^ src/fpocket.c:62:12: warning: variable ‘bt’ set but not used [-Wunused-but-set-variable] time_t bt, et; ^ src/fpocket.c:61:16: warning: unused variable ‘e’ [-Wunused-variable] clock_t b, e; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/write_visu.c -o obj/write_visu.o src/write_visu.c: In function ‘write_vmd’: src/write_visu.c:83:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ src/write_visu.c: In function ‘write_pymol’: src/write_visu.c:166:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] int status ; ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/fpout.c -o obj/fpout.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/atom.c -o obj/atom.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/writepocket.c -o obj/writepocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/voronoi_lst.c -o obj/voronoi_lst.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/asa.c -o obj/asa.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/clusterlib.c -o obj/clusterlib.o src/clusterlib.c: In function ‘euclid’: src/clusterlib.c:1005:27: warning: "/" within comment [-Wcomment] if (!tweight) return 0; / usually due to empty clusters / ^ src/clusterlib.c: In function ‘spearman’: src/clusterlib.c:1488:29: warning: unused parameter ‘weight’ [-Wunused-parameter] int* mask2, const double weight[], int index1, int index2, int transpose) ^ src/clusterlib.c: In function ‘kendall’: src/clusterlib.c:1616:16: warning: unused parameter ‘weight’ [-Wunused-parameter] const double weight[], int index1, int index2, int transpose) ^ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/energy.c -o obj/energy.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/topology.c -o obj/topology.o src/topology.c: In function ‘register_cb’: src/topology.c:12:30: warning: unused parameter ‘v’ [-Wunused-parameter] static int register_cb(void v, vmdplugin_t *p) { ^ gcc -O -g -pg -ansi -c src/qhull/geom2.c -o src/qhull/geom2.o gcc -O -g -pg -ansi -c src/qhull/geom.c -o src/qhull/geom.o gcc -O -g -pg -ansi -c src/qhull/global.c -o src/qhull/global.o In file included from /usr/include/string.h:635:0, from src/qhull/qhull_a.h:39, from src/qhull/global.c:19: In function ‘strncat’, inlined from ‘qh_initflags’ at src/qhull/global.c:617:7: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/io.c -o src/qhull/io.o gcc -O -g -pg -ansi -c src/qhull/libqhull.c -o src/qhull/libqhull.o gcc -O -g -pg -ansi -c src/qhull/mem.c -o src/qhull/mem.o gcc -O -g -pg -ansi -c src/qhull/merge.c -o src/qhull/merge.o gcc -O -g -pg -ansi -c src/qhull/poly2.c -o src/qhull/poly2.o gcc -O -g -pg -ansi -c src/qhull/poly.c -o src/qhull/poly.o gcc -O -g -pg -ansi -c src/qhull/qset.c -o src/qhull/qset.o gcc -O -g -pg -ansi -c src/qhull/random.c -o src/qhull/random.o gcc -O -g -pg -ansi -c src/qhull/rboxlib.c -o src/qhull/rboxlib.o In file included from /usr/include/string.h:635:0, from src/qhull/rboxlib.c:22: In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:127:3: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ In function ‘strncat’, inlined from ‘qh_rboxpoints’ at src/qhull/rboxlib.c:350:5: /usr/include/x86_64-linux-gnu/bits/string3.h:156:10: warning: call to builtin___strncat_chk might overflow destination buffer return builtin_strncat_chk (dest, src, len, bos (dest)); ^ gcc -O -g -pg -ansi -c src/qhull/stat.c -o src/qhull/stat.o gcc -O -g -pg -ansi -c src/qhull/user.c -o src/qhull/user.o gcc -O -g -pg -ansi -c src/qhull/usermem.c -o src/qhull/usermem.o gcc -O -g -pg -ansi -c src/qhull/userprintf.c -o src/qhull/userprintf.o gcc -O -g -pg -ansi -c src/qhull/qvoronoi.c -o src/qhull/qvoronoi.o gcc -O -g -pg -ansi -c src/qhull/qconvex.c -o src/qhull/qconvex.o gcc obj/fpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/fpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpmain.c -o obj/tpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/tpocket.c -o obj/tpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/neighbor.c -o obj/neighbor.o gcc obj/tpmain.o obj/psorting.o obj/pscoring.o obj/utils.o obj/pertable.o obj/memhandler.o obj/voronoi.o obj/sort.o obj/calc.o obj/writepdb.o obj/rpdb.o obj/tparams.o obj/fparams.o obj/pocket.o obj/refine.o obj/tpocket.o obj/descriptors.o obj/aa.o obj/fpocket.o obj/write_visu.o obj/fpout.o obj/atom.o obj/writepocket.o obj/voronoi_lst.o obj/neighbor.o obj/asa.o obj/clusterlib.o obj/energy.o obj/topology.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o -o bin/tpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpmain.c -o obj/dpmain.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dpocket.c -o obj/dpocket.o gcc -Wall -Wextra -Wwrite-strings -Wstrict-prototypes -DM_OS_LINUX -DMNO_MEM_DEBUG -O2 -g -pg -std=c99 -Iplugins/include -Iplugins/LINUXAMD64/molfile -c src/dparams.c -o obj/dparams.o gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ gcc obj/dpmain.o obj/psorting.o obj/pscoring.o obj/dpocket.o obj/dparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/geom2.o src/qhull/geom.o src/qhull/global.o src/qhull/io.o src/qhull/io.h src/qhull/libqhull.o src/qhull/mem.o src/qhull/merge.o src/qhull/poly2.o src/qhull/poly.o src/qhull/qset.o src/qhull/random.o src/qhull/rboxlib.o src/qhull/stat.o src/qhull/user.o src/qhull/usermem.o src/qhull/userprintf.o src/qhull/qvoronoi.o src/qhull/qconvex.o obj/energy.o obj/topology.o -o bin/dpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

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[ektapathak08]

Hi the make doesn't work on ubuntu 16.04 LTS (on my 64 bit machine)also. I wish to use mdpocket. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

[pschmidtke]

You are sure that you have the netcdf plugin built? Check if there is a netcdf.sohttp://netcdf.so in the plugin folder along with the other data formats. I noticed that vmd silently let's some of these fail. For netcdf you need to specify so.e specific environment variables to make it build as well.

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 21, 2018, at 14:39, ektapathak08 notifications@github.com<mailto:notifications@github.com> wrote:

Hi the make doesn't work on ubuntu 16.04 LTS also. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

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[ektapathak08]

Hi Peter, thanks for a reply

I have checked pluggin folder and there is a netcdfplugin.so file present at fpocket-master/plugins/LINUXAMD64/molfile. In fact, it is there for all environment like IRIX6, SOLARIS, LINUX*. But there is no netcdf.so file in pluggin folder.

And how to specify so.e specific environment variables for netcdf?

On Mon, Jul 23, 2018 at 11:04 AM, Peter Schmidtke notifications@github.com wrote:

You are sure that you have the netcdf plugin built? Check if there is a netcdf.sohttp://netcdf.so in the plugin folder along with the other data formats. I noticed that vmd silently let's some of these fail. For netcdf you need to specify so.e specific environment variables to make it build as well.

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 21, 2018, at 14:39, ektapathak08 <notifications@github.com<mailto: notifications@github.com>> wrote:

Hi the make doesn't work on ubuntu 16.04 LTS also. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/ fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ Discngine/fpocket/issues/9#issuecomment-406794113, or mute the thread< https://github.com/notifications/unsubscribe-auth/AOhZZ550_ neJ0PYmwzjnGY0E313CWEuXks5uIyDmgaJpZM4Ut-jn>.

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--

Thanks n RegardsDr. Ekta PathakResearch fellowBioinformaticsBanaras Hindu University

[pschmidtke]

More info on compiling this here :

From: ektapathak08 notifications@github.com Sent: lundi 23 juillet 2018 09:56 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

Hi Peter, thanks for a reply

I have checked pluggin folder and there is a netcdfplugin.so file present at fpocket-master/plugins/LINUXAMD64/molfile. In fact, it is there for all environment like IRIX6, SOLARIS, LINUX*. But there is no netcdf.so file in pluggin folder.

And how to specify so.e specific environment variables for netcdf?

On Mon, Jul 23, 2018 at 11:04 AM, Peter Schmidtke notifications@github.com<mailto:notifications@github.com> wrote:

You are sure that you have the netcdf plugin built? Check if there is a netcdf.sohttp://netcdf.so in the plugin folder along with the other data formats. I noticed that vmd silently let's some of these fail. For netcdf you need to specify so.e specific environment variables to make it build as well.

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 21, 2018, at 14:39, ektapathak08 <notifications@github.com<mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.commailto:notifications@github.com>> wrote:

Hi the make doesn't work on ubuntu 16.04 LTS also. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/ fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> Discngine/fpocket/issues/9#issuecomment-406794113>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AOhZZ550_ neJ0PYmwzjnGY0E313CWEuXks5uIyDmgaJpZM4Ut-jn>.

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--

Thanks n RegardsDr. Ekta PathakResearch fellowBioinformaticsBanaras Hindu University

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Discngine/fpocket/issues/9#issuecomment-406972186, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AOhZZ9J4lYNsB5nai7YIZrnAMwofpQQIks5uJYGcgaJpZM4Ut-jn.

[pschmidtke]

More info on compiling vmd plugins here : http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html#compiling

Look especially at the Libraries required by plugins section for the netcdf specific parts.

Sorry I couldn’t automate this yet, it’s a bit a tricky dependency.

Peter

From: ektapathak08 notifications@github.com Sent: lundi 23 juillet 2018 09:56 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

Hi Peter, thanks for a reply

I have checked pluggin folder and there is a netcdfplugin.so file present at fpocket-master/plugins/LINUXAMD64/molfile. In fact, it is there for all environment like IRIX6, SOLARIS, LINUX*. But there is no netcdf.so file in pluggin folder.

And how to specify so.e specific environment variables for netcdf?

On Mon, Jul 23, 2018 at 11:04 AM, Peter Schmidtke notifications@github.com<mailto:notifications@github.com> wrote:

You are sure that you have the netcdf plugin built? Check if there is a netcdf.sohttp://netcdf.so in the plugin folder along with the other data formats. I noticed that vmd silently let's some of these fail. For netcdf you need to specify so.e specific environment variables to make it build as well.

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 21, 2018, at 14:39, ektapathak08 <notifications@github.com<mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.commailto:notifications@github.com>> wrote:

Hi the make doesn't work on ubuntu 16.04 LTS also. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/ fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> Discngine/fpocket/issues/9#issuecomment-406794113>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AOhZZ550_ neJ0PYmwzjnGY0E313CWEuXks5uIyDmgaJpZM4Ut-jn>.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Discngine/fpocket/issues/9#issuecomment-406944203, or mute the thread https://github.com/notifications/unsubscribe-auth/AnPozLyl1jiHaWWMF8JdSNPuSl2yFaL5ks5uJWB4gaJpZM4Ut-jn .

--

Thanks n RegardsDr. Ekta PathakResearch fellowBioinformaticsBanaras Hindu University

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Discngine/fpocket/issues/9#issuecomment-406972186, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AOhZZ9J4lYNsB5nai7YIZrnAMwofpQQIks5uJYGcgaJpZM4Ut-jn.

[shozebhaider]

Hi Ekta

Will you ever be using trajectories in netcdf format? If not then I suggest to take those line out of the makefile in fpocket directory. mdpocket now compiles and works fine minus recognising netcdf format, although in the -help it will continue to say it does.

Best Wishes

Shozeb

On 23 Jul 2018, at 09:00, Peter Schmidtke notifications@github.com wrote:

More info on compiling vmd plugins here : http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html#compiling

Look especially at the Libraries required by plugins section for the netcdf specific parts.

Sorry I couldn’t automate this yet, it’s a bit a tricky dependency.

Peter

From: ektapathak08 notifications@github.com Sent: lundi 23 juillet 2018 09:56 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

Hi Peter, thanks for a reply

I have checked pluggin folder and there is a netcdfplugin.so file present at fpocket-master/plugins/LINUXAMD64/molfile. In fact, it is there for all environment like IRIX6, SOLARIS, LINUX*. But there is no netcdf.so file in pluggin folder.

And how to specify so.e specific environment variables for netcdf?

On Mon, Jul 23, 2018 at 11:04 AM, Peter Schmidtke notifications@github.com<mailto:notifications@github.com> wrote:

You are sure that you have the netcdf plugin built? Check if there is a netcdf.sohttp://netcdf.so in the plugin folder along with the other data formats. I noticed that vmd silently let's some of these fail. For netcdf you need to specify so.e specific environment variables to make it build as well.

Sent from BlueMailhttp://www.bluemail.me/r?b=13130 On Jul 21, 2018, at 14:39, ektapathak08 <notifications@github.com<mailto: mailto:notifications@github.com%3cmailto:%0b> notifications@github.commailto:notifications@github.com>> wrote:

Hi the make doesn't work on ubuntu 16.04 LTS also. I replaced the LINUXAMD64 folder in the plugins directory and rebuild as suggested above but it did'nt worked but got following error during installation of fpocket3 :

obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/ fpocket-master/src/mdpocket.c:96: undefined reference tomolfile_netcdfplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:97: undefined reference to `molfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1

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--

Thanks n RegardsDr. Ekta PathakResearch fellowBioinformaticsBanaras Hindu University

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[ektapathak08]

Hi Shozeb, Actually I am working on the MD trajectories obtained from Gromacs-2018. As you might be knowing that these file have extension like .trr, .tpr or .xtc. Will it work in that case?

[shozebhaider]

I use these too. Works for me.

Best Wishes

Shozeb

On 23 Jul 2018, at 09:43, ektapathak08 notifications@github.com wrote:

Hi Shozeb, Actually I am working on the MD trajectories obtained from Gromacs-2018. As you might be knowing that these file have extension like .trr, .tpr or .xtc. Will it work in that case?

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[shozebhaider]

My apologies Ekta. The change is not in makefile. I meant in mdpocket.c

Best Wishes

Shozeb

On 23 Jul 2018, at 09:43, ektapathak08 notifications@github.com wrote:

Hi Shozeb, Actually I am working on the MD trajectories obtained from Gromacs-2018. As you might be knowing that these file have extension like .trr, .tpr or .xtc. Will it work in that case?

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[pschmidtke]

Like said by @shozeb you can drop the link to netcdf dependency. Simply drop the lnetcdf flags in make file flags in the makefile and rebuild again. You also need to comment the register_necdf_plugin bit of code in mdpocket.c to deactivate that for now.

++ Peter

From: shozebhaider notifications@github.com Sent: lundi 23 juillet 2018 11:08 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

I use these too. Works for me.

Best Wishes

Shozeb

On 23 Jul 2018, at 09:43, ektapathak08 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Shozeb, Actually I am working on the MD trajectories obtained from Gromacs-2018. As you might be knowing that these file have extension like .trr, .tpr or .xtc. Will it work in that case?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

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[ektapathak08]

Thanks Peter and Shozeb

I'll try these things and will let you know

[pschmidtke]

If any of you has ideas on how to render the whole thing parametrizeable from within the makefile that would be great as these dependencies are kind of a headache right now.

From: ektapathak08 notifications@github.com Sent: lundi 23 juillet 2018 11:17 To: Discngine/fpocket fpocket@noreply.github.com Cc: Peter Schmidtke peter.schmidtke@discngine.com; Comment comment@noreply.github.com Subject: Re: [Discngine/fpocket] Make fails on Fedora 28 (#9)

Thanks Peter and Shozeb

I'll try these things and will let you know

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[ektapathak08]

hi I have commented

LFLAGS = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lnetcdf -lstdc++

in the makefile

and / if (!strncmp(par->traj_format, "net", 3)) { molfile_netcdfplugin_init(); molfile_netcdfplugin_register(NULL, register_cb); }/ in the mdpocket.c And performed root@ekta-Precision-T1700:/home/ekta/1_MD/Gromacs/fpocket-master# make Now getting following errors obj/mdpocket.o: In function mdpocket_detect': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:112: undefined reference tomolfile_gromacsplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:113: undefined reference to molfile_gromacsplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:108: undefined reference tomolfile_dtrplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:109: undefined reference to molfile_dtrplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:104: undefined reference tomolfile_crdplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:105: undefined reference to molfile_crdplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:100: undefined reference tomolfile_dcdplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:101: undefined reference to molfile_dcdplugin_register' obj/mdpocket.o: In functionmdpocket_characterize': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:403: undefined reference to molfile_gromacsplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:404: undefined reference tomolfile_gromacsplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:391: undefined reference to molfile_dcdplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:392: undefined reference tomolfile_dcdplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:399: undefined reference to molfile_dtrplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:400: undefined reference tomolfile_dtrplugin_register' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:395: undefined reference to molfile_crdplugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpocket.c:396: undefined reference tomolfile_crdplugin_register'

obj/mdpbase.o: In function calculate_md_dens_grid': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:132: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:133: undefined reference to roundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:134: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:144: undefined reference to floorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:147: undefined reference tofloorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:150: undefined reference to floorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:143: undefined reference toceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:146: undefined reference to ceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:149: undefined reference toceilf' obj/mdpbase.o: In function update_md_grid': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:214: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:215: undefined reference to roundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:216: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:227: undefined reference to floorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:230: undefined reference tofloorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:233: undefined reference to floorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:226: undefined reference toceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:229: undefined reference to ceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:232: undefined reference toceilf' obj/mdpbase.o: In function project_grid_on_atoms': /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:317: undefined reference tofloor' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:319: undefined reference to ceil' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:320: undefined reference toceil' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:321: undefined reference to ceil' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:324: undefined reference tofloor' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:324: undefined reference to floor' /home/ekta/1_MD/Gromacs/fpocket-master/src/mdpbase.c:335: undefined reference tolog' obj/pscoring.o: In function drug_score_pocket': /home/ekta/1_MD/Gromacs/fpocket-master/src/pscoring.c:329: undefined reference toexp' obj/voronoi.o: In function compare_vvertice_shifted_lists': /home/ekta/1_MD/Gromacs/fpocket-master/src/voronoi.c:926: undefined reference tosqrt' obj/rpdb.o: In function fill_coord_grid': /home/ekta/1_MD/Gromacs/fpocket-master/src/rpdb.c:204: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/rpdb.c:205: undefined reference to roundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/rpdb.c:206: undefined reference toroundf' obj/calc.o: In function dist': /home/ekta/1_MD/Gromacs/fpocket-master/src/calc.c:57: undefined reference tosqrtf' obj/asa.o: In function get_points_on_sphere': /home/ekta/1_MD/Gromacs/fpocket-master/src/asa.c:445: undefined reference tosincos' /home/ekta/1_MD/Gromacs/fpocket-master/src/asa.c:447: undefined reference to sqrt' obj/clusterlib.o: In functionkendall': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1719: undefined reference to sqrt' obj/clusterlib.o: In functionuacorrelation': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1479: undefined reference to sqrt' obj/clusterlib.o: In functionucorrelation': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1384: undefined reference to sqrt' obj/clusterlib.o: In functionacorrelation': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1289: undefined reference to sqrt' obj/clusterlib.o:/home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1190: more undefined references tosqrt' follow obj/clusterlib.o: In function binomial': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1842: undefined reference tolog' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1842: undefined reference to exp' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1856: undefined reference tofloor' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1881: undefined reference to log' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1887: undefined reference tolog' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1907: undefined reference to log' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1920: undefined reference tolog' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1920: undefined reference to log' obj/clusterlib.o:/home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1921: more undefined references tolog' follow obj/clusterlib.o: In function binomial': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1856: undefined reference tosqrt' obj/clusterlib.o: In function spearman': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:1607: undefined reference tosqrt' obj/clusterlib.o: In function svd': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:440: undefined reference tosqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:415: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:578: undefined reference tosqrt' obj/clusterlib.o:/home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:564: more undefined references to sqrt' follow obj/clusterlib.o: In functioncalculate_weights': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:3109: undefined reference to log' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:3109: undefined reference toexp' obj/clusterlib.o: In function somworker': /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4100: undefined reference tosqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4141: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4189: undefined reference tosqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4100: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4202: undefined reference tosqrt' obj/clusterlib.o:/home/ekta/1_MD/Gromacs/fpocket-master/src/clusterlib.c:4154: more undefined references to sqrt' follow obj/energy.o: In functionset_energies_to_grid_point': /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:254: undefined reference to pow' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:254: undefined reference topow' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:255: undefined reference to exp' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:256: undefined reference toexp' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:258: undefined reference to exp' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:251: undefined reference tosqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:250: undefined reference to sqrt' obj/energy.o: In functionget_atoms_in_near_grid_points': /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:291: undefined reference to roundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:292: undefined reference toroundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:293: undefined reference to roundf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:309: undefined reference tofloorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:312: undefined reference to floorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:315: undefined reference tofloorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:311: undefined reference to ceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:314: undefined reference toceilf' /home/ekta/1_MD/Gromacs/fpocket-master/src/energy.c:308: undefined reference to ceilf' obj/topology.o: In functionread_topology': /home/ekta/1_MD/Gromacs/fpocket-master/src/topology.c:94: undefined reference to molfile_parm7plugin_init' /home/ekta/1_MD/Gromacs/fpocket-master/src/topology.c:95: undefined reference tomolfile_parm7plugin_register' src/qhull/geom2.o: In function qh_distround': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:378: undefined reference tosqrt' src/qhull/geom2.o: In function qh_detroundoff': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:200: undefined reference tosqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:228: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:229: undefined reference tosqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:241: undefined reference to sqrt' src/qhull/geom2.o: In functionqh_gram_schmidt': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:770: undefined reference to sqrtf' src/qhull/geom2.o: In functionqh_outerinner': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:1291: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:1305: undefined reference tosqrt' src/qhull/geom2.o: In function qh_pointdist': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom2.c:1328: undefined reference tosqrtf' src/qhull/geom.o: In function qh_normalize2': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom.c:814: undefined reference tosqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom.c:816: undefined reference to sqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom.c:818: undefined reference tosqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom.c:825: undefined reference to sqrtf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/geom.c:853: undefined reference tosqrt' src/qhull/io.o: In function qh_geomplanes': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/io.c:854: undefined reference tosqrt' src/qhull/io.o: In function qh_printbegin': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/io.c:1426: undefined reference tosqrt' src/qhull/libqhull.o: In function qh_nextfurthest': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/libqhull.c:713: undefined reference tofloorf' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/libqhull.c:713: undefined reference to floorf' src/qhull/poly2.o: In functionqh_nearcoplanar': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/poly2.c:2151: undefined reference to sqrt' src/qhull/poly2.o: In functionqh_nearvertex': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/poly2.c:2222: undefined reference to sqrtf' src/qhull/poly2.o: In functionqh_initialvertices': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/poly2.c:1846: undefined reference to floorf' src/qhull/rboxlib.o: In functionqh_rboxpoints': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:231: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:272: undefined reference totrunc' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:293: undefined reference to asin' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:294: undefined reference tocos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:466: undefined reference to pow' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:509: undefined reference tosincos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:517: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:524: undefined reference tosqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:538: undefined reference to cos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:548: undefined reference tosincos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:564: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:578: undefined reference tosincos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:603: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:643: undefined reference tosincos' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:662: undefined reference to sqrt' /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/rboxlib.c:678: undefined reference tosqrt'

src/qhull/stat.o: In function qh_stddev': /home/ekta/1_MD/Gromacs/fpocket-master/src/qhull/stat.c:703: undefined reference tosqrtf' collect2: error: ld returned 1 exit status makefile:145: recipe for target 'bin/mdpocket' failed make: *** [bin/mdpocket] Error 1 it seems there is some issue related to linking the program with "math.h ". where am I making mistake?

[ektapathak08]

thanks for your support everyone I figured out my mistake. fpocket is working now. Yet to check mdpocket

[diallobakary4]

Hello everyone. I am having the same problem when installing fpocket. I am using bash on windows. When I run make I have the following error: make qhull make[1]: Entering directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket' cd src/qhull/ && make make[2]: Entering directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket/src/qhull' mkdir -p bin lib make[2]: Leaving directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket/src/qhull' make[1]: Leaving directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket' make fpocket make[1]: Entering directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket' gcc obj/mdpmain.o obj/mdpocket.o obj/mdpbase.o obj/mdpout.o obj/psorting.o obj/pscoring.o obj/mdparams.o obj/voronoi.o obj/sort.o obj/rpdb.o obj/descriptors.o obj/neighbor.o obj/atom.o obj/aa.o obj/pertable.o obj/calc.o obj/utils.o obj/writepdb.o obj/memhandler.o obj/pocket.o obj/refine.o obj/fparams.o obj/fpocket.o obj/fpout.o obj/writepocket.o obj/write_visu.o obj/asa.o obj/voronoi_lst.o obj/clusterlib.o src/qhull/src/libqhull/geom2.o src/qhull/src/libqhull/geom.o src/qhull/src/libqhull/global.o src/qhull/src/libqhull/io.o src/qhull/src/libqhull/io.h src/qhull/src/libqhull/libqhull.o src/qhull/src/libqhull/mem.o src/qhull/src/libqhull/merge.o src/qhull/src/libqhull/poly2.o src/qhull/src/libqhull/poly.o src/qhull/src/libqhull/qset.o src/qhull/src/libqhull/random.o src/qhull/src/libqhull/rboxlib.o src/qhull/src/libqhull/stat.o src/qhull/src/libqhull/user.o src/qhull/src/libqhull/usermem.o src/qhull/src/libqhull/userprintf.o src/qhull/src/libqhull/userprintf_rbox.o src/qhull/src/qvoronoi/qvoronoi.o src/qhull/src/qconvex/qconvex.o obj/energy.o obj/topology.o -o bin/mdpocket -lm -Lplugins/LINUXAMD64/molfile plugins/LINUXAMD64/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ obj/mdpocket.o: In functionmdpocket_detect': /mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket/src/mdpocket.c:96: undefined reference to molfile_netcdfplugin_init' /mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket/src/mdpocket.c:97: undefined reference tomolfile_netcdfplugin_register' collect2: error: ld returned 1 exit status makefile:152: recipe for target 'bin/mdpocket' failed make[1]: [bin/mdpocket] Error 1 make[1]: Leaving directory '/mnt/c/Users/Bakary/Documents/SCRACTC/fpocket/fpocket' makefile:132: recipe for target 'all' failed make: [all] Error 2`

I tried commenting line related to installing mdpocket in the makefile: I have still have the same error. But now I can see: fpocket/fpocket/bin$ ls dpocket fpocket tpocket

Still the fpocket command doesn't work. Thank you in advance.

[mkoohim]

Same issue! Could you please provide a clean tutorial to overcome this problem. This tread is too messy. Thanks.

[diallobakary4]

@mkoohim I could solve my problem following this post above: https://github.com/Discngine/fpocket/issues/9#issuecomment-398537638

[shozebhaider]

Do you want just fpocket or mdpocket? If you don’t need mdpocket then it’s straight forward.

If you want mdpocket, then

1. compile the plugins folder from vmd,
2. comment out lnetcdf flag from a makefile or comment out netcdf compilation in mdpocket.c

This should work like a piece of cake.

On 20 Aug 2018, at 20:35, diallobakary4 notifications@github.com wrote:

@mkoohim I could solve my problem following this post above: #9 (comment)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[mkoohim]

Thanks! I just need fpocket and installed it by commenting the mdpocket.

[dkoes]

I think part of the problem is the VMD molfile plugin doesn't pull in netcdf by default. You have to set NETCDFINC and NETCDFLIB and NETCDFLDFLAGS.

export NETCDFLDFLAGS=""
export NETCDFINC=" "
export NETCDFLIB=/usr/lib/x86_64-linux-gnu/libnetcdf.so

If you don't need this file format support I suspect commenting it out of mdpocket.c is easier. Also, while mdpocket builds, I haven't check that it actually works with netcdf files yet.

[dvdesolve]

Hello! I've managed to build the whole package with full NetCDF support. Newer vmd-molfile-plugins are needed (I've used 1.9.3 version). You could check my AUR package here. In few words: you should modify makefile like that (patch-friendly):

--- makefile    2019-03-29 00:31:30.876920063 +0300
+++ makefile.new    2019-03-29 00:29:17.804365698 +0300
@@ -34,11 +34,11 @@
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -Wall -Wextra -Wwrite-strings -Wstrict-prototypes

-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile #$(CGSL)
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I/usr/include/vmd-molfile-plugins/ #$(CGSL)
 QCFLAGS     = -O -g -pg -ansi

 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 
-LFLAGS     = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lnetcdf -lstdc++
+LFLAGS     = -lm -L/usr/lib/vmd-molfile-plugins /usr/lib/vmd-molfile-plugins/libmolfile_plugin.a -lnetcdf -lstdc++
 #
 #------------------------------------------------------------
 # BINARIES OBJECTS 

[pschmidtke]

wow, that’s nice.

I’ll check this asap!

On 28 Mar 2019, at 22:45, drobot viktor notifications@github.com<mailto:notifications@github.com> wrote:

Hello! I've managed to build the whole package with full NetCDF support. Newer vmd-molfile-plugins are needed (I've used 1.9.3 version). You could check my AUR package herehttps://aur.archlinux.org/packages/fpocket-git/. In few words: you should modify makefile like that (patch-friendly):

--- makefile 2019-03-29 00:31:30.876920063 +0300 +++ makefile.new 2019-03-29 00:29:17.804365698 +0300 @@ -34,11 +34,11 @@ CDEBUG = -DMNO_MEM_DEBUG CWARN = -Wall -Wextra -Wwrite-strings -Wstrict-prototypes

-CFLAGS = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile #$(CGSL) +CFLAGS = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I/usr/include/vmd-molfile-plugins/ #$(CGSL) QCFLAGS = -O -g -pg -ansi

LGSL = -L$(PATH_GSL)lib -lgsl -lgslcblas -LFLAGS = -lm -L$(PLUGINDIR)/$(ARCH)/molfile $(PLUGINDIR)/$(ARCH)/molfile/libmolfile_plugin.a -lnetcdf -lstdc++ +LFLAGS = -lm -L/usr/lib/vmd-molfile-plugins /usr/lib/vmd-molfile-plugins/libmolfile_plugin.a -lnetcdf -lstdc++ #

------------------------------------------------------------

BINARIES OBJECTS

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[pschmidtke]

Thanks @dvdesolve and sorry for the delay. Indeed the main issue was an incompatible molfile plugin compilation. I updated all the LINUXAMD64 libraries from a fresh compilation and now everything is fine again. Thanks for pointing that out.