[package - main-armv7-default][biology/molden] Failed for molden-5.8.2_4,1 in stage
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Date: Sat, 11 Sep 2021 16:16:50 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jmd@FreeBSD.org
Log URL: http://beefy12.nyi.freebsd.org/data/main-armv7-default/pfda1da2d7917_s9939af1a16/logs/molden-5.8.2_4,1.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=pfda1da2d7917_s9939af1a16
Log:
=>> Building biology/molden
build started at Sat Sep 11 15:44:59 UTC 2021
port directory: /usr/ports/biology/molden
package name: molden-5.8.2_4,1
building for: FreeBSD main-armv7-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 arm
maintained by: jmd@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400003
Jail OSVERSION: 1400032
Job Id: 13
!!! Jail is newer than host. (Jail: 1400032, Host: 1400003) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for molden-5.8.2_4,1:
DATA=on: Install data files
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
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jmd@FreeBSD.org
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--PLIST_SUB--
PORTDOCS="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/molden" EXAMPLESDIR="share/examples/molden" DATADIR="share/molden" WWWDIR="www/molden" ETCDIR="etc/molden"
--End PLIST_SUB--
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=======================<phase: check-sanity >============================
===> License Molden accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> molden-5.8.2_4,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.1.pkg
[main-armv7-default-job-13] Installing pkg-1.17.1...
[main-armv7-default-job-13] Extracting pkg-1.17.1: .......... done
===> molden-5.8.2_4,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of molden-5.8.2_4,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License Molden accepted by the user
=> molden5.8.2.tar.gz doesn't seem to exist in /portdistfiles/.
<snip>
gen_arc_recurse(&comp_sph_pts[j], &comp_sph_pts[i], sp_points,&k,atom_id, 1);
^
tessel_patches.c:262:3: warning: implicit declaration of function 'find_sphere_points' is invalid in C99 [-Wimplicit-function-declaration]
find_sphere_points(&(center.vt), 0, ave_center, &atoms[atom_id]);
^
tessel_patches.c:286:7: warning: implicit declaration of function 'new_gen_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
new_gen_sphere_tris(&sp_points[i+1], &sp_points[i], ¢er, atom_id);
^
tessel_patches.c:300:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_arc_recurse(bp0, bp1, sp_points, j, atom_id, convex)
^
tessel_patches.c:312:5: warning: implicit declaration of function 'find_mid_pt' is invalid in C99 [-Wimplicit-function-declaration]
find_mid_pt(&new_bp, bp0, bp1, atom_id);
^
tessel_patches.c:327:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
find_sphere_points(sph_pts, j, comp_vert, atom_ptr)
^
tessel_patches.c:342:3: warning: implicit declaration of function 'find_ray_sphere_int' is invalid in C99 [-Wimplicit-function-declaration]
find_ray_sphere_int(sph_pts[j].Coord,tempv,ray_dir,atom_ptr->center,ext_rad);
^
tessel_patches.c:360:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
find_torus_points(tor_pts, mid_cusp_pts, num_pts, atom_ptr, probe_centers,
^
23 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -c tessel_convex.c
tessel_convex.c:67:3: warning: implicit declaration of function 'initialize_r' is invalid in C99 [-Wimplicit-function-declaration]
initialize_r(big_p, sph_side, q, num_p, &num_sph_side, num_q, same_order, atom_id, full_torus);
^
tessel_convex.c:82:5: warning: implicit declaration of function 'get_full_torus_mesh' is invalid in C99 [-Wimplicit-function-declaration]
get_full_torus_mesh(sph_side, num_sph_side, torus_side, num_q,
^
tessel_convex.c:85:5: warning: implicit declaration of function 'get_partial_torus_mesh' is invalid in C99 [-Wimplicit-function-declaration]
get_partial_torus_mesh(sph_side, num_sph_side, torus_side, num_q,
^
tessel_convex.c:97:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
initialize_r(big_p, r, q, num_p, num_r, num_q, same_order, atom_id, full_torus)
^
tessel_convex.c:112:7: warning: implicit declaration of function 'gen_arc_recurse' is invalid in C99 [-Wimplicit-function-declaration]
gen_arc_recurse(&big_p[i], &big_p[i+1], r, &j, atom_id, 1);
^
tessel_convex.c:117:7: warning: implicit declaration of function 'gen_arc_recurse' is invalid in C99 [-Wimplicit-function-declaration]
gen_arc_recurse(&big_p[i], &big_p[i-1], r, &j, atom_id, 1);
^
tessel_convex.c:130:5: warning: implicit declaration of function 'find_plane_eq' is invalid in C99 [-Wimplicit-function-declaration]
find_plane_eq(q[0].Coord, q[1].Coord, q[2].Coord, plane_eq);
^
tessel_convex.c:166:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_linear_recurse(p0, p1, r, j, center, radius, convex)
^
tessel_convex.c:202:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_flipped_sphere_tris(p0, p1, p2, atom_id, flip)
^
tessel_convex.c:208:5: warning: implicit declaration of function 'new_gen_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
new_gen_sphere_tris(p0, p1, p2, atom_id);
^
tessel_convex.c:217:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
new_gen_sphere_tris(bp0, bp1, bp2, atom_id)
^
tessel_convex.c:238:7: warning: implicit declaration of function 'multi_gen_spherical_recurse' is invalid in C99 [-Wimplicit-function-declaration]
multi_gen_spherical_recurse(bp0, bp1, &mid_pt, atom_id);
^
tessel_convex.c:243:7: warning: implicit declaration of function 'multi_gen_spherical_recurse' is invalid in C99 [-Wimplicit-function-declaration]
multi_gen_spherical_recurse(bp0, bp1, bp2, atom_id);
^
tessel_convex.c:252:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
multi_gen_spherical_recurse(pt0, pt1, pt2, atom_id)
^
tessel_convex.c:275:5: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_tris(&(tri_pt[0]->vt), &(tri_pt[1]->vt), &(tri_pt[2]->vt));
^
tessel_convex.c:278:30: warning: implicit declaration of function 'find_mid_pt' is invalid in C99 [-Wimplicit-function-declaration]
{ if(valid_point&flags[0]) find_mid_pt(&mid_pt[0],tri_pt[0],tri_pt[1],atom_id);
^
tessel_convex.c:314:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
find_mid_pt(mid_pt, tri_pt0, tri_pt1, atom_id)
^
tessel_convex.c:359:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_tris(pt0, pt1, pt2)
^
tessel_convex.c:362:4: warning: implicit declaration of function 'add_tri' is invalid in C99 [-Wimplicit-function-declaration]
add_tri(pt0, pt1, pt2, Current_atom);
^
tessel_convex.c:369:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
add_tri(pt0, pt1, pt2, atype)
^
tessel_convex.c:376:5: warning: implicit declaration of function 'write_archive_tri' is invalid in C99 [-Wimplicit-function-declaration]
write_archive_tri(pt0, pt1, pt2, atype);
^
21 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -c tessel_concave.c
tessel_concave.c:22:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_concave(tor_pts, center, flip_verts, cusp_pts, probe, n, cur_torus, torus_cusp)
^
tessel_concave.c:55:5: warning: implicit declaration of function 'gen_concave_tri' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_concave_tri(tor_pts[0][0],tor_pts[1][0],center[0], flip_verts, probe[0],
^
tessel_concave.c:75:5: warning: implicit declaration of function 'gen_concave_tri' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_concave_tri(tor_pts[1][n-1],tor_pts[0][n-1],center[1],flip_verts,probe[1],
^
tessel_concave.c:89:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_concave_tri(point0, point1, point2, flip, center, radius)
^
tessel_concave.c:101:5: warning: implicit declaration of function 'gen_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_sphere_tris(&point2, &point1, &point0, fcenter, radius, 0);
^
tessel_concave.c:104:5: warning: implicit declaration of function 'gen_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_sphere_tris(&point0, &point1, &point2, fcenter, radius, 0);
^
tessel_concave.c:131:5: warning: implicit declaration of function 'gen_cuspy_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_cuspy_sphere_tris(point2, point1, point0, fcenter, radius, plane_eq);
^
tessel_concave.c:134:5: warning: implicit declaration of function 'gen_cuspy_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_cuspy_sphere_tris(point0, point1, point2, fcenter, radius, plane_eq);
^
tessel_concave.c:143:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_cuspy_sphere_tris(pt0, pt1, pt2, center, radius, plane_eq)
^
tessel_concave.c:208:7: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_tris(points[0], points[1], points[2]);
^
tessel_concave.c:217:5: warning: implicit declaration of function 'find_line_seg_plane_int' is invalid in C99 [-Wimplicit-function-declaration]
find_line_seg_plane_int(new_point1.Coord,points[i]->Coord,points[j]->Coord,plane_eq->coeff);
^
tessel_concave.c:231:7: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_tris(points[i], &new_point1, &new_point2);
^
tessel_concave.c:269:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
gen_sphere_tris(pt0, pt1, pt2, center, radius, convex)
^
tessel_concave.c:345:5: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
gen_tris(points[0], points[1], points[2]);
^
14 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -c tessel_torus.c
tessel_torus.c:22:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
get_full_torus_mesh(sph, num_sph, torus, num_torus, flip, atom_id)
^
tessel_torus.c:41:3: warning: implicit declaration of function 'find_plane_eq' is invalid in C99 [-Wimplicit-function-declaration]
find_plane_eq(torus[0].vt.Coord,torus[1].vt.Coord,torus[2].vt.Coord,plane_eq);
^
tessel_torus.c:52:9: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&torus[t_index], &sph[next_s_index], &sph[s_index], atom_id, flip);
^
tessel_torus.c:56:9: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&sph[s_index], &torus[t_index], &torus[next_t_index], atom_id, flip);
^
tessel_torus.c:74:9: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&sph[s_index], &torus[t_index], &torus[next_t_index], atom_id, flip);
^
tessel_torus.c:87:9: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&torus[t_index], &sph[next_s_index], &sph[s_index], atom_id, flip);
^
tessel_torus.c:106:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
get_partial_torus_mesh(sph, num_sph, torus, num_torus, flip, atom_id)
^
tessel_torus.c:117:4: warning: implicit declaration of function 'find_plane_eq' is invalid in C99 [-Wimplicit-function-declaration]
find_plane_eq(torus[0].vt.Coord,torus[1].vt.Coord,torus[2].vt.Coord,plane_eq);
^
tessel_torus.c:127:10: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&torus[t_index], &sph[next_s_index], &sph[s_index], atom_id, flip);
^
tessel_torus.c:131:10: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&sph[s_index], &torus[t_index], &torus[next_t_index], atom_id, flip);
^
tessel_torus.c:140:8: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&sph[s_index], &torus[i], &torus[i+1], atom_id, flip);
^
tessel_torus.c:145:8: warning: implicit declaration of function 'gen_flipped_sphere_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ gen_flipped_sphere_tris(&torus[t_index], &sph[i+1], &sph[i], atom_id, flip);
^
tessel_torus.c:190:3: warning: implicit declaration of function 'gen_linear_recurse' is invalid in C99 [-Wimplicit-function-declaration]
gen_linear_recurse(tor_pts[0][0],tor_pts[1][0],r[0],&j,fcenter,fradius,0);
^
tessel_torus.c:209:17: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ if (flip) gen_tris(&r[l][m], &r[k][m+1], &r[k][m]);
^
tessel_torus.c:219:19: warning: implicit declaration of function 'gen_tris' is invalid in C99 [-Wimplicit-function-declaration]
{ if (flip) gen_tris(&r[l][m], &r[l][m+1], &r[k][j-1]);
^
15 warnings generated.
/nxb-bin/usr/bin/cc -O2 -pipe -DFREEBSD -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -I/usr/local/include -Wno-return-type -fstack-protector-strong -fno-strict-aliasing surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o tessel_patches.o tessel_convex.o tessel_concave.o tessel_torus.o -o surf -lm
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/molden/work/molden5.8/surf'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/molden/work/molden5.8'
===========================================================================
=======================<phase: run-depends >============================
===> molden-5.8.2_4,1 depends on executable: gfortran10 - found
===> molden-5.8.2_4,1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===========================================================================
=======================<phase: stage >============================
===> Staging for molden-5.8.2_4,1
===> Generating temporary packing list
(cd /wrkdirs/usr/ports/biology/molden/work/molden5.8 && install -s -m 555 molden /wrkdirs/usr/ports/biology/molden/work/stage/usr/local/bin)
(cd /wrkdirs/usr/ports/biology/molden/work/molden5.8 && install -s -m 555 gmolden /wrkdirs/usr/ports/biology/molden/work/stage/usr/local/bin)
(cd /wrkdirs/usr/ports/biology/molden/work/molden5.8/ambfor && install -s -m 555 ambfor /wrkdirs/usr/ports/biology/molden/work/stage//usr/local/bin)
(cd /wrkdirs/usr/ports/biology/molden/work/molden5.8/surf && install -s -m 555 surf /wrkdirs/usr/ports/biology/molden/work/stage//usr/local/bin)
(cd /wrkdirs/usr/ports/biology/molden/work/molden5.8/test && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/molden/work/stage/usr/local/share/molden/test)
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/molden