Hello,
For some reason, I cannot seem to compile mcl anymore?
...
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make[4]: [Makefile:716: mcl.html] Error 1 (ignored)
groff -man mcl.1 > mcl.ps
groff -t -e -mandoc -Tascii mcl.1 | col -bx > mcl.txt
/bin/bash: col: command not found
make[4]: *** [Makefile:705: mcl.txt] Error 127
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[3]: *** [Makefile:383: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:324: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
E: Failure("Command 'make' terminated with error code 2")
I have even tried adding bsdmainutils as build depends but I do not know
why "col" command cannot be found.
I think libimpala missing issue (which featured all the object files
referenced by the stub) could be the solution.
Kind regards,
Shayan Doust
On 20/06/2020 02:11, Shayan Doust wrote:
> 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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