Build:
- 0
2026-06-24 17:25.13: New job: build lbvs_consent.2.1.1 (60793286fe0b)
2026-06-24 17:25.13: Waiting for resource in pool day11-builds
2026-06-24 18:13.48: Got resource from pool day11-builds
2026-06-24 18:13.48: [profile full] build lbvs_consent.2.1.1
2026-06-24 18:13.48: build lbvs_consent.2.1.1 (60793286fe0b)
=== DEPENDENCIES (49 transitive) ===
base-bigarray.base 2e16f77d4cae
base-bytes.base c40d17bc86b5
base-threads.base c9e7bdbf5823
base-unix.base 7d1428be9ddb
batteries.3.10.0 3a8b7aeb2b17
bitv.2.1 b81131182699
camlp-streams.5.0.1 28f363162dde
camltc.0.9.8 3b7b659c7701
camlzip.1.14 b2a1cb874022
conf-bash.1 6730968932c0
conf-boost.1 00039ec33118
conf-openbabel.0.1 1ad0df739c45
conf-pkg-config.5 d5de2c6a88f9
conf-python-3.9.0.0 6d72fcfa5947
conf-rdkit.1 86320d042a70
conf-zlib.1 5297f1b9477f
cpm.12.2.0 c30ed7781529
cppo.1.8.0 5f3f70cae95b
csexp.1.5.2 610c78f17734
dokeysto.4.0.2 41b43c7a5031
dokeysto_camltc.4.0.2 2a4d927770d2
dolog.4.0.0 277d80d7a963
dune.3.23.1 848a72441e15
dune-configurator.3.23.1 bc97ce98d8a9
extunix.0.4.4 2f5005f9562f
logs.0.10.0 d5622efb8b7e
lwt.6.1.2 d46d0c4f757d
minicli.5.0.2 0aa0a091666d
minivpt.2.0.0 1b8c7daad56e
num.1.6 110cee7a7e2e
obuild.0.2.2 797d55b0b90e
ocaml.4.14.4 b047fb9251f4
ocaml-base-compiler.4.14.4 d3b7ccb2c6fb
ocaml-compiler-libs.v0.12.4 2aecf989b0b2
ocaml-config.2 2d9c209f5590
ocamlbuild.0.16.1 7e0d6aadb209
ocamlfind.1.9.8 214dd418ac02
ocplib-endian.1.2 380dd426e898
ounit2.2.2.7 c47e2d37575c
parmap.1.2.5 d90fd02d799c
ppx_derivers.1.2.1 9245877bc46e
ppxlib.0.38.0 c54fe6e3bf29
qcheck.0.91 ea356ff9dda9
qcheck-core.0.91 529e7a902678
qcheck-ounit.0.91 abf3a0f52267
seq.base 0160fc3002c2
sexplib0.v0.17.0 86d78ae8a795
stdlib-shims.0.3.0 de5202e23add
topkg.1.1.1 511e1a1958da
=== STDOUT ===
Processing: [default: loading data]
[lbvs_consent.2.1.1: dl]
[lbvs_consent.2.1.1: extract]
[lbvs_consent.2.1.1/makefile.patch: dl]
-> retrieved lbvs_consent.2.1.1 (https://opam.ocaml.org/cache)
[lbvs_consent: patch] applying makefile.patch
[lbvs_consent: make obmaccs]
+ /usr/bin/make "obmaccs" (CWD=/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1)
- cd src; make
- make[1]: Entering directory '/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1/src'
- c++ -W -Wall `pkg-config --silence-errors --cflags openbabel-2.0 || pkg-config --cflags openbabel-3` ob_maccs.cpp \
- -o lbvs_consent_ob_maccs `pkg-config --silence-errors --libs openbabel-2.0 || pkg-config --libs openbabel-3` -Wl,-R/usr/lib
- In file included from /usr/include/openbabel3/openbabel/fingerprint.h:28,
- from ob_maccs.cpp:1:
- /usr/include/openbabel3/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
- 41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
- | ^~~~~~~~~~~~~~~
- In file included from /usr/include/c++/12/bits/stl_tree.h:65,
- from /usr/include/c++/12/map:60,
- from /usr/include/openbabel3/openbabel/fingerprint.h:23:
- /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
- 131 | struct binary_function
- | ^~~~~~~~~~~~~~~
- In file included from /usr/include/openbabel3/openbabel/mol.h:48,
- from ob_maccs.cpp:2:
- /usr/include/openbabel3/openbabel/base.h: In member function 'virtual const char* OpenBabel::OBBase::GetTitle(bool) const':
- /usr/include/openbabel3/openbabel/base.h:286:49: warning: unused parameter 'replaceNewlines' [-Wunused-parameter]
- 286 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
- | ^
- /usr/include/openbabel3/openbabel/base.h:37:20: note: in definition of macro 'UNUSED'
- 37 | # define UNUSED(x) x
- | ^
- make[1]: Leaving directory '/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1/src'
[lbvs_consent: dune build]
+ /home/opam/.opam/default/bin/dune "build" "-p" "lbvs_consent" "-j" "39" (CWD=/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1)
- (cd _build/default && /home/opam/.opam/default/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.lbvs_consent.objs/byte -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/byte/lbvs_consent__MyList.cmo -c -impl src/myList.ml)
- File "src/myList.ml", line 51, characters 13-31:
- 51 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 64, characters 13-31:
- 64 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 193, characters 14-30:
- 193 | map of_str (BatString.nsplit s' ~by:";")
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/default/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.lbvs_consent.objs/byte -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/byte/lbvs_consent__MyIntSet.cmo -c -impl src/myIntSet.ml)
- File "src/myIntSet.ml", line 22, characters 20-36:
- 22 | let int_strings = BatString.nsplit ~by:";" chopped in
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/default/bin/ocamlopt.opt -w -40 -g -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -intf-suffix .ml -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/native/lbvs_consent__MyList.cmx -c -impl src/myList.ml)
- File "src/myList.ml", line 51, characters 13-31:
- 51 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 64, characters 13-31:
- 64 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 193, characters 14-30:
- 193 | map of_str (BatString.nsplit s' ~by:";")
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/default/bin/ocamlopt.opt -w -40 -g -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -intf-suffix .ml -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/native/lbvs_consent__MyIntSet.cmx -c -impl src/myIntSet.ml)
- File "src/myIntSet.ml", line 22, characters 20-36:
- 22 | let int_strings = BatString.nsplit ~by:";" chopped in
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/default/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.mol_get.eobjs/byte -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/bytes -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/camltc -I /home/opam/.opam/default/lib/camltc/tc -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dokeysto -I /home/opam/.opam/default/lib/dokeysto_camltc -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/extunix -I /home/opam/.opam/default/lib/logs -I /home/opam/.opam/default/lib/logs/lwt -I /home/opam/.opam/default/lib/lwt -I /home/opam/.opam/default/lib/lwt/unix -I /home/opam/.opam/default/lib/minicli -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/ocplib-endian -I /home/opam/.opam/default/lib/ocplib-endian/bigstring -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -I src/.lbvs_consent.objs/byte -no-alias-deps -o src/.mol_get.eobjs/byte/mol_get.cmo -c -impl src/mol_get.ml)
- File "src/mol_get.ml", line 77, characters 22-38:
- 77 | | On_cli names -> BatString.nsplit names ~by:","
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/default/bin/ocamlopt.opt -w -40 -g -I src/.mol_get.eobjs/byte -I src/.mol_get.eobjs/native -I /home/opam/.opam/default/lib/batteries -I /home/opam/.opam/default/lib/batteries/unthreaded -I /home/opam/.opam/default/lib/bitv -I /home/opam/.opam/default/lib/bytes -I /home/opam/.opam/default/lib/camlp-streams -I /home/opam/.opam/default/lib/camltc -I /home/opam/.opam/default/lib/camltc/tc -I /home/opam/.opam/default/lib/cpm -I /home/opam/.opam/default/lib/dokeysto -I /home/opam/.opam/default/lib/dokeysto_camltc -I /home/opam/.opam/default/lib/dolog -I /home/opam/.opam/default/lib/extunix -I /home/opam/.opam/default/lib/logs -I /home/opam/.opam/default/lib/logs/lwt -I /home/opam/.opam/default/lib/lwt -I /home/opam/.opam/default/lib/lwt/unix -I /home/opam/.opam/default/lib/minicli -I /home/opam/.opam/default/lib/minivpt -I /home/opam/.opam/default/lib/num -I /home/opam/.opam/default/lib/ocaml/threads -I /home/opam/.opam/default/lib/ocplib-endian -I /home/opam/.opam/default/lib/ocplib-endian/bigstring -I /home/opam/.opam/default/lib/parmap -I /home/opam/.opam/default/lib/zip -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -intf-suffix .ml -no-alias-deps -o src/.mol_get.eobjs/native/mol_get.cmx -c -impl src/mol_get.ml)
- File "src/mol_get.ml", line 77, characters 22-38:
- 77 | | On_cli names -> BatString.nsplit names ~by:","
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
-> compiled lbvs_consent.2.1.1
[lbvs_consent: cp]
+ /usr/bin/cp "bin/lbvs_consent_ecfp4.py" "/home/opam/.opam/default/bin/lbvs_consent_ecfp4.py" (CWD=/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1)
[lbvs_consent: cp]
+ /usr/bin/cp "src/lbvs_consent_ob_maccs" "/home/opam/.opam/default/bin/lbvs_consent_ob_maccs" (CWD=/home/opam/.opam/default/.opam-switch/build/lbvs_consent.2.1.1)
-> installed lbvs_consent.2.1.1
[WARNING] Opam packages conf-boost.1, conf-openbabel.0.1, conf-python-3.9.0.0, conf-rdkit.1 and conf-zlib.1 depend on the following system packages that are no longer installed: libboost-dev libopenbabel-dev librdkit-dev python3 python3-rdkit zlib1g-dev
- conf-boost.1: depends on libboost-dev
- conf-openbabel.0.1: depends on libopenbabel-dev
- conf-python-3.9.0.0: depends on python3
- conf-rdkit.1: depends on librdkit-dev, python3-rdkit
- conf-zlib.1: depends on zlib1g-dev
=== STDERR ===
2026-06-24 18:14.03: OK: build lbvs_consent.2.1.1 (runc: 7.1s, disk: 23KB)
2026-06-24 18:14.03: Job succeeded