Hello Steffen, Admittingly, I was unaware of this missing library when I was patching OCaml support for MCL (this was the prime focus, to get pplacer linking against and compiling). Although, libimpala shouldn't belong in /usr/lib/ocaml. I do not see libmcl_stubs(*) errors during linkage from your log. Does pplacer build for you then? I will certainly have a look at pplacer when I wake up. Thanks for raising this. I think focusing on libimpala could result in compilation for pplacer. Kind regards, Shayan Doust On 20/06/2020 02:03, Steffen Möller wrote: > Hello, > > I had a look at the MCL package and found that it is very much focused > on the MCL library but apparently does not feature the impala library > that ships the implementation of mclgUnionv. Proof below, I compiled MCL > myself and copied libimpala.a to the ocaml directory. > > I am mostly clueless about ocaml. Does this help anyone to fix the > problem or have a chat with the Debian maintainer of the mcl package? Uh > - that's us. :o/ > > Steffen > > moeller@steffen-laptop-debian:~/git/med-team/pplacer/_build$ ocamlfind > ocamlopt -ccopt -static -linkpkg -package batteries -package csv > -package xmlm -package gsl -package sqlite3 -package zip -packag > e mcl -thread -cclib -lpthread -cclib -lpplacercside -cclib > -Lpplacer_src -cclib -lcdd -cclib -Lcdd_src -cclib -lpplacer_pam -cclib > -Lpam_src -cclib -lgsl -I cdd_src -I common_src -I json_src -I pplac > er_src -I pam_src cdd_src/cdd.cmx common_src/ppr.cmx > common_src/mapsSets.cmx common_src/number.cmx common_src/algMap.cmx > common_src/ppatteries.cmx common_src/linear_utils.cmx > json_src/jsontype.cmx jso > n_src/jsonparse.cmx json_src/jsonlex.cmx json_src/json.cmx > pplacer_src/simple_json.cmx pplacer_src/refpkg_parse.cmx > pplacer_src/fasta.cmx pplacer_src/nuc_models.cmx > pplacer_src/prot_models.cmx pplacer > _src/stockholm.cmx common_src/alignment.cmx common_src/batchfile.cmx > common_src/delayed.cmx common_src/file_parsing.cmx > common_src/power_iteration.cmx common_src/sql.cmx > common_src/subcommand.cmx comm > on_src/uptri.cmx common_src/version.cmx pplacer_src/myxml.cmx > pplacer_src/newick_bark.cmx pplacer_src/bark_map.cmx > pplacer_src/stree.cmx pplacer_src/gtree.cmx pplacer_src/edge_rdist.cmx > pplacer_src/ne > wick_parse_state.cmx pplacer_src/newick_parser.cmx > pplacer_src/newick_lexer.cmx pplacer_src/tax_id.cmx > pplacer_src/placement.cmx pplacer_src/pquery.cmx > pplacer_src/pquery_io.cmx pplacer_src/newick_gtr > ee.cmx pplacer_src/placerun.cmx pplacer_src/mass_map.cmx > pplacer_src/matrix.cmx pam_src/pam_solver.cmx > pplacer_src/kr_distance.cmx pplacer_src/barycenter.cmx > pplacer_src/decor.cmx pplacer_src/decor_ba > rk.cmx pplacer_src/decor_gtree.cmx pplacer_src/tensor.cmx > pplacer_src/linear.cmx pplacer_src/diagd.cmx pplacer_src/gamma.cmx > pplacer_src/glvm.cmx pplacer_src/glv_arr.cmx pplacer_src/glv_edge.cmx pplac > er_src/gstar_support.cmx pplacer_src/like_stree.cmx > pplacer_src/gcat_model.cmx pplacer_src/prefs.cmx > pplacer_src/parse_stats.cmx pplacer_src/gmix_model.cmx > pplacer_src/tax_classify.cmx pplacer_src/tax > _seqinfo.cmx pplacer_src/tax_taxonomy.cmx pplacer_src/tax_map.cmx > pplacer_src/refpkg.cmx pplacer_src/convex.cmx > pplacer_src/edge_painting.cmx pplacer_src/classif_map.cmx > pplacer_src/bayes_factor.cmx p > placer_src/biom.cmx pplacer_src/bootstrap.cmx pplacer_src/check.cmx > pplacer_src/fig.cmx pplacer_src/integration.cmx > pplacer_src/minimization.cmx pplacer_src/three_tax.cmx > pplacer_src/core.cmx pplacer_ > src/edpl.cmx pplacer_src/string_matrix.cmx pplacer_src/fantasy.cmx > pplacer_src/gaussian_approx.cmx pplacer_src/tax_mass.cmx > pplacer_src/mokaphy_common.cmx pplacer_src/phyloxml.cmx > pplacer_src/placerun > _io.cmx pplacer_src/visualization.cmx pplacer_src/voronoi.cmx > pplacer_src/guppy_cmdobjs.cmx pplacer_src/guppy_adcl.cmx > pplacer_src/guppy_bary.cmx pplacer_src/guppy_check.cmx > pplacer_src/guppy_to_rdp.c > mx pplacer_src/seq_post.cmx pplacer_src/map_seq.cmx > pplacer_src/multiprocessing.cmx pplacer_src/nbc.cmx > pplacer_src/seq_group.cmx pplacer_src/pplacer_run.cmx > pplacer_src/guppy_classify.cmx pplacer_src > /mass_overlap.cmx pplacer_src/guppy_mcl.cmx > pplacer_src/mass_compress.cmx pplacer_src/mass_islands.cmx > pplacer_src/guppy_compress.cmx pplacer_src/guppy_demulti.cmx > pplacer_src/guppy_distmat.cmx pplace > r_src/guppy_edpl.cmx pplacer_src/guppy_splitify.cmx > pplacer_src/guppy_pca.cmx pplacer_src/pca.cmx pplacer_src/som.cmx > pplacer_src/guppy_epca.cmx pplacer_src/guppy_error.cmx > pplacer_src/tax_gtree.cmx p > placer_src/guppy_fat.cmx pplacer_src/guppy_filter.cmx > pplacer_src/guppy_fpd.cmx pplacer_src/guppy_heat.cmx > pplacer_src/indep_contrasts.cmx pplacer_src/guppy_indep_c.cmx > pplacer_src/guppy_info.cmx ppla > cer_src/guppy_islands.cmx pplacer_src/r_plots.cmx > pplacer_src/guppy_kr.cmx pplacer_src/guppy_kr_heat.cmx > pplacer_src/lpca.cmx pplacer_src/guppy_lpca.cmx > pplacer_src/guppy_merge.cmx pplacer_src/guppy_m > ft.cmx pplacer_src/guppy_ograph.cmx pplacer_src/guppy_placemat.cmx > pplacer_src/guppy_pmlpca.cmx pplacer_src/rarefaction.cmx > pplacer_src/guppy_rarefact.cmx pplacer_src/guppy_rarefy.cmx > pplacer_src/gupp > y_redup.cmx pplacer_src/guppy_round.cmx pplacer_src/guppy_sing.cmx > pplacer_src/squashfunc.cmx pplacer_src/guppy_squash.cmx > pplacer_src/guppy_to_csv.cmx pplacer_src/guppy_to_json.cmx > pplacer_src/guppy_ > tog.cmx pplacer_src/guppy_trim.cmx pplacer_src/guppy_unifrac.cmx > pplacer_src/guppy_commands.cmx pplacer_src/guppy.cmx cdd_src/libcdd.a > pam_src/libpplacer_pam.a pplacer_src/libpplacercside.a /usr/lib/o > caml/libimpala.a -o pplacer_src/guppy.native && echo ok > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libsqlite3.a(sqlite3.o): in > function `unixDlOpen': > (.text+0x83c9): warning: Using 'dlopen' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(initgroups.o): in function > `unix_initgroups': > (.text+0x1f): warning: Using 'initgroups' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getgr.o): in function > `unix_getgrgid': > (.text+0x16e): warning: Using 'getgrgid' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getgr.o): in function > `unix_getgrnam': > (.text+0x114): warning: Using 'getgrnam' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getpw.o): in function > `unix_getpwnam': > (.text+0x164): warning: Using 'getpwnam' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getpw.o): in function > `unix_getpwuid': > (.text+0x1be): warning: Using 'getpwuid' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getaddrinfo.o): in function > `unix_getaddrinfo': > (.text+0x1f9): warning: Using 'getaddrinfo' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(gethost.o): in function > `unix_gethostbyaddr': > (.text+0x1bc): warning: Using 'gethostbyaddr_r' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(gethost.o): in function > `unix_gethostbyname': > (.text+0x242): warning: Using 'gethostbyname_r' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getproto.o): in function > `unix_getprotobynumber': > (.text+0xe8): warning: Using 'getprotobynumber' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getproto.o): in function > `unix_getprotobyname': > (.text+0xc1): warning: Using 'getprotobyname' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getserv.o): in function > `unix_getservbyname': > (.text+0x109): warning: Using 'getservbyname' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > /usr/bin/ld: /usr/lib/ocaml/libunix.a(getserv.o): in function > `unix_getservbyport': > (.text+0x159): warning: Using 'getservbyport' in statically linked > applications requires at runtime the shared libraries from the glibc > version used for linking > ok > >
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