[Debian-med-packaging] Bug#975858: pplacer: FTBFS: Error: Unbound module Gsl_error

Wed Nov 25 20:58:05 GMT 2020

Source: pplacer
Version: 1.1~alpha19-3
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201125 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.

Relevant part (hopefully):
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> ocamlbuild pplacer.native
> /usr/bin/ocamlopt.opt unix.cmxa -I /usr/lib/ocaml/ocamlbuild /usr/lib/ocaml/ocamlbuild/ocamlbuildlib.cmxa myocamlbuild.ml /usr/lib/ocaml/ocamlbuild/ocamlbuild.cmx -o myocamlbuild
> /bin/sh: 1: git: not found
> File "_tags", line 8, characters 154-161:
> Warning: the tag "pkg_str" is not used in any flag or dependency declaration, so it will have no effect; it may be a typo. Otherwise you can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> File "_tags", line 8, characters 112-124:
> Warning: the tag "pkg_bigarray" is not used in any flag or dependency declaration, so it will have no effect; it may be a typo. Otherwise you can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> File "_tags", line 8, characters 102-110:
> Warning: the tag "pkg_unix" is not used in any flag or dependency declaration, so it will have no effect; it may be a typo. Otherwise you can use `mark_tag_used` in your myocamlbuild.ml to disable this warning.
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddcore.c
> mv cddcore.o cdd_src/cddcore.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddio.c
> mv cddio.o cdd_src/cddio.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddlib.c
> + ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddlib.c
> cdd_src/cddlib.c: In function ‘dd_DDMain’:
> cdd_src/cddlib.c:116:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
>   116 |       for (itemp=1; cone->OrderVector[itemp]!=hh; itemp++);
>       |       ^~~
> cdd_src/cddlib.c:117:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
>   117 |         otemp=cone->OrderVector[cone->Iteration];
>       |         ^~~~~
> mv cddlib.o cdd_src/cddlib.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddlp.c
> mv cddlp.o cdd_src/cddlp.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddmp.c
> mv cddmp.o cdd_src/cddmp.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/cddproj.c
> mv cddproj.o cdd_src/cddproj.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/setoper.c
> mv setoper.o cdd_src/setoper.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/pplacer_cdd.c
> mv pplacer_cdd.o cdd_src/pplacer_cdd.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c cdd_src/caml_cdd.c
> mv caml_cdd.o cdd_src/caml_cdd.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c pam_src/pam.c
> mv pam.o pam_src/pam.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c pam_src/caml_pam.c
> + ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c pam_src/caml_pam.c
> In file included from /usr/lib/ocaml/caml/bigarray.h:23,
>                  from pam_src/caml_pam.c:2:
> pam_src/caml_pam.c: In function ‘caml_pam’:
> /usr/lib/ocaml/caml/mlvalues.h:265:23: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
>   265 | #define String_val(x) ((const char *) Bp_val(x))
>       |                       ^
> pam_src/caml_pam.c:18:16: note: in expansion of macro ‘String_val’
>    18 |   char *keep = String_val(keep_value);
>       |                ^~~~~~~~~~
> mv caml_pam.o pam_src/caml_pam.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c pplacer_src/linear_c.c
> mv linear_c.o pplacer_src/linear_c.o
> ocamlfind ocamlc -ccopt -Wall -ccopt -funroll-loops -ccopt -O3 -ccopt -fPIC -c pplacer_src/unix_support.c
> mv unix_support.o pplacer_src/unix_support.o
> /usr/bin/ocamlmklib.opt -o cdd_src/cdd cdd_src/cddcore.o cdd_src/cddio.o cdd_src/cddlib.o cdd_src/cddlp.o cdd_src/cddmp.o cdd_src/cddproj.o cdd_src/setoper.o cdd_src/pplacer_cdd.o cdd_src/caml_cdd.o
> /usr/bin/ocamlmklib.opt -o pam_src/pplacer_pam pam_src/pam.o pam_src/caml_pam.o
> /usr/bin/ocamlmklib.opt -o pplacer_src/pplacercside pplacer_src/linear_c.o pplacer_src/unix_support.o
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules pplacer_src/pplacer.ml > pplacer_src/pplacer.ml.depends
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules pplacer_src/check.ml > pplacer_src/check.ml.depends
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules common_src/ppatteries.ml > common_src/ppatteries.ml.depends
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules common_src/algMap.ml > common_src/algMap.ml.depends
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules common_src/mapsSets.ml > common_src/mapsSets.ml.depends
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules common_src/ppr.ml > common_src/ppr.ml.depends
> ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/ppr.cmo common_src/ppr.ml
> ocamlfind ocamldep -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -modules common_src/number.ml > common_src/number.ml.depends
> ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/mapsSets.cmo common_src/mapsSets.ml
> ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/number.cmo common_src/number.ml
> ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/algMap.cmo common_src/algMap.ml
> ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/ppatteries.cmo common_src/ppatteries.ml
> + ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package xmlm -package gsl -package sqlite3 -package zip -package mcl -thread -I common_src -I pplacer_src -I pam_src -I cdd_src -I tests -I json_src -I pdprune_src -I tests/rppr -I tests/guppy -I tests/json -I tests/pplacer -o common_src/ppatteries.cmo common_src/ppatteries.ml
> File "common_src/ppatteries.ml", line 784, characters 2-16:
> 784 |   Gsl_error.init ();
>         ^^^^^^^^^^^^^^
> Error: Unbound module Gsl_error
> Command exited with code 2.
> make[3]: *** [Makefile:21: pplacer.native] Error 10

The full build log is available from:
   http://qa-logs.debian.net/2020/11/25/pplacer_1.1~alpha19-3_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.