WARNING: [license.mk] Every package should define a LICENSE. => Checksum BLAKE2s OK for RasMol_2.7.3.tar.gz => Checksum SHA512 OK for RasMol_2.7.3.tar.gz ===> Installing dependencies for rasmol-2.7.3nb2 => Tool dependency imake-[0-9]*: found imake-1.0.10 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency libXext>=1.1: found libXext-1.3.6 => Full dependency libXi>=1.0.0: found libXi-1.8.2 => Build dependency xcb-proto>=1.4: found xcb-proto-1.17.0nb5 => Build dependency xorgproto>=2016.1: found xorgproto-2024.1 => Full dependency libX11>=1.5: found libX11-1.8.12 => Full dependency libXau>=1.0: found libXau-1.0.12 => Full dependency libXdmcp>=0.99: found libXdmcp-1.1.5 => Full dependency libXfixes>=4.0.1: found libXfixes-6.0.2 => Full dependency libxcb>=1.6: found libxcb-1.17.0 ===> Overriding tools for rasmol-2.7.3nb2 ===> Extracting for rasmol-2.7.3nb2 cd /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/src && /bin/rm -rf RCS doc/RCS src/RCS src/msc/RCS ===> Patching for rasmol-2.7.3nb2 => Applying pkgsrc patches for rasmol-2.7.3nb2 => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-aa => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-aa Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-aa,v 1.2 2005/10/07 15:13:21 perry Exp $ | |--- Imakefile.orig 2005-10-06 17:57:49.000000000 -0400 |+++ Imakefile 2005-10-06 18:01:41.000000000 -0400 -------------------------- Patching file Imakefile using Plan A... Hunk #1 succeeded at 92. Hunk #2 succeeded at 108. Hunk #3 succeeded at 177. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-ab => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-ab Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ab,v 1.2 2005/10/07 15:13:21 perry Exp $ | |--- cif_ctonum.c.orig 2005-10-06 18:05:48.000000000 -0400 |+++ cif_ctonum.c 2005-10-06 18:07:54.000000000 -0400 -------------------------- Patching file cif_ctonum.c using Plan A... Hunk #1 succeeded at 173. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-ac => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/rasmol/patches/patch-ac Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-ac,v 1.4 2025/04/21 16:24:05 wiz Exp $ | |--- rasmol.h.orig 2005-04-28 18:57:25.000000000 -0400 |+++ rasmol.h -------------------------- Patching file rasmol.h using Plan A... Hunk #1 succeeded at 113. done ===> Creating toolchain wrappers for rasmol-2.7.3nb2 ===> Configuring for rasmol-2.7.3nb2 /bin/ln -sf /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/doc /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/src /bin/ln -sf /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/data /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/src cd /Users/pbulk/build/biology/rasmol/work/RasMol_2.7.3/src && /opt/pkg/bin/nbsed "s#@@PREFIX@@#/opt/pkg#" rasmol.h > rasmol.h.new && /bin/mv rasmol.h.new rasmol.h imake -DUseInstalled -I/opt/pkg/lib/X11/config /opt/pkg/bin/imake: Warning: cleaning Imakefile imake: executing: /opt/pkg/bin/tradcpp -I. -D__aarch64__ -traditional -D__APPLE__ -D__DARWIN__ -debuglog .imake.cpplog -DUseInstalled -I/opt/pkg/lib/X11/config -DBuildHtmlManPages=NO .imake.start.c In file included from .imake.start.c:14:2: In file included from /opt/pkg/lib/X11/config/Imake.tmpl:109:2: /opt/pkg/lib/X11/config/darwin.cf:255:11: Warning: non-identical redefinition of OptimizedCDebugFlags In file included from .imake.start.c:14:2: In file included from /opt/pkg/lib/X11/config/Imake.tmpl:109:2: /opt/pkg/lib/X11/config/darwin.cf:236:11: Previous definition was here make Makefiles make includes make depend makedepend -- -I/opt/pkg/include -D__aarch64__ -D__DARWIN__ -DNO_ALLOCA -DCSRG_BASED -DRASMOLDIR=\"/opt/pkg/share/doc/rasmol/\" -D_USE_RASMOL_H_ -DUSE_MAKEDEPEND -- rasmol.c rasmol.h molecule.c molecule.h abstree.c abstree.h cmndline.c cmndline.h command.c command.h tokens.h transfor.c transfor.h render.c render.h x11win.c graphics.h pixutils.c pixutils.h font.h outfile.c outfile.h script.c script.h infile.c infile.h repres.c repres.h tokens.c cif_fract.c cif_fract.h cif.c cif.h cif_ctonum.c cif_ctonum.h cif_stx.c multiple.h multiple.c vector.h vector.c wbrotate.c wbrotate.c langsel.h langsel.c makedepend: warning: rasmol.c, line 97: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: rasmol.c, line 99: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: rasmol.c, line 100: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: rasmol.c, line 101: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: rasmol.c, line 102: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: rasmol.c, line 104: cannot find include file "signal.h" not in /opt/pkg/include/signal.h not in /usr/include/signal.h makedepend: warning: rasmol.c (reading rasmol.h, line 129): cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: rasmol.c (reading rasmol.h, line 224): cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: rasmol.c, line 130: cannot find include file "unistd.h" not in /opt/pkg/include/unistd.h not in /usr/include/unistd.h makedepend: warning: rasmol.c, line 134: cannot find include file "sys/types.h" not in /opt/pkg/include/sys/types.h not in /usr/include/sys/types.h makedepend: warning: rasmol.c, line 136: cannot find include file "sys/time.h" not in /opt/pkg/include/sys/time.h not in /usr/include/sys/time.h makedepend: warning: rasmol.c, line 143: cannot find include file "sys/types.h" not in /opt/pkg/include/sys/types.h not in /usr/include/sys/types.h makedepend: warning: rasmol.c, line 144: cannot find include file "sys/time.h" not in /opt/pkg/include/sys/time.h not in /usr/include/sys/time.h makedepend: warning: rasmol.c, line 145: cannot find include file "termios.h" not in /opt/pkg/include/termios.h not in /usr/include/termios.h makedepend: warning: rasmol.c, line 167: cannot find include file "sys/socket.h" not in /opt/pkg/include/sys/socket.h not in /usr/include/sys/socket.h makedepend: warning: rasmol.c, line 168: cannot find include file "netinet/in.h" not in /opt/pkg/include/netinet/in.h not in /usr/include/netinet/in.h makedepend: warning: rasmol.c, line 169: cannot find include file "netdb.h" not in /opt/pkg/include/netdb.h not in /usr/include/netdb.h makedepend: warning: rasmol.h, line 129: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: rasmol.h, line 224: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: molecule.c, line 100: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: molecule.c, line 103: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: molecule.c, line 107: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: molecule.c, line 109: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: molecule.c, line 110: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: molecule.c, line 111: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: abstree.c, line 65: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: abstree.c, line 67: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: abstree.c, line 71: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: abstree.c, line 73: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: abstree.c, line 74: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: abstree.c, line 75: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: cmndline.c, line 75: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: cmndline.c, line 78: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: cmndline.c, line 79: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: cmndline.c, line 80: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: command.c, line 86: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: command.c, line 89: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: command.c, line 93: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: command.c, line 95: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: command.c, line 96: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: command.c, line 99: cannot find include file "pwd.h" not in /opt/pkg/include/pwd.h not in /usr/include/pwd.h makedepend: warning: command.c, line 122: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: transfor.c, line 115: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: transfor.c, line 116: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: transfor.c, line 117: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: transfor.c, line 118: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: render.c, line 113: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: render.c, line 116: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: render.c, line 117: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: render.c, line 118: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: render.c, line 119: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: x11win.c, line 100: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: x11win.c, line 102: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: x11win.c, line 103: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: x11win.c, line 104: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: x11win.c, line 105: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: x11win.c (reading /opt/pkg/include/X11/Xlib.h, line 38): cannot find include file "sys/types.h" not in /opt/pkg/include/sys/types.h not in /usr/include/sys/types.h makedepend: warning: x11win.c (reading /opt/pkg/include/X11/Xlib.h, line 51): cannot find include file "stddef.h" not in /opt/pkg/include/stddef.h not in /usr/include/stddef.h makedepend: warning: x11win.c, line 344: cannot find include file "sys/types.h" not in /opt/pkg/include/sys/types.h not in /usr/include/sys/types.h makedepend: warning: x11win.c, line 345: cannot find include file "sys/ipc.h" not in /opt/pkg/include/sys/ipc.h not in /usr/include/sys/ipc.h makedepend: warning: x11win.c, line 346: cannot find include file "sys/shm.h" not in /opt/pkg/include/sys/shm.h not in /usr/include/sys/shm.h makedepend: warning: pixutils.c, line 109: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: pixutils.c, line 110: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: outfile.c, line 102: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: outfile.c, line 105: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: outfile.c, line 106: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: outfile.c, line 107: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: script.c, line 102: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: script.c, line 106: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: script.c, line 107: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: script.c, line 108: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: script.c, line 109: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: infile.c, line 94: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: infile.c, line 97: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: infile.c, line 101: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: infile.c, line 103: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: infile.c, line 104: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: infile.c, line 105: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: infile.c (reading cif.h, line 294): cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: infile.c, line 122: cannot find include file "sys/types.h" not in /opt/pkg/include/sys/types.h not in /usr/include/sys/types.h makedepend: warning: infile.c, line 124: cannot find include file "sys/time.h" not in /opt/pkg/include/sys/time.h not in /usr/include/sys/time.h makedepend: warning: infile.c, line 126: cannot find include file "time.h" not in /opt/pkg/include/time.h not in /usr/include/time.h makedepend: warning: repres.c, line 108: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: repres.c, line 111: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: repres.c, line 112: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: repres.c, line 113: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: repres.c, line 114: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: tokens.c, line 86: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: tokens.c, line 87: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: cif_fract.c, line 186: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: cif.c, line 265: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: cif.c, line 268: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: cif.c, line 269: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: cif.c, line 270: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: cif.c, line 271: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: cif.c, line 275: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: cif.h, line 294: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: cif_ctonum.c, line 187: cannot find include file "float.h" not in /opt/pkg/include/float.h not in /usr/include/float.h makedepend: warning: cif_ctonum.c, line 191: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: cif_ctonum.c, line 192: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: cif_ctonum.c, line 196: cannot find include file "strings.h" not in /opt/pkg/include/strings.h not in /usr/include/strings.h makedepend: warning: cif_stx.c, line 204: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: cif_stx.c, line 205: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: cif_stx.c, line 206: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: cif_stx.c, line 226: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: cif_stx.c, line 260: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: multiple.c, line 124: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: multiple.c, line 127: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: multiple.c, line 128: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: multiple.c, line 129: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h makedepend: warning: multiple.c, line 132: cannot find include file "pwd.h" not in /opt/pkg/include/pwd.h not in /usr/include/pwd.h makedepend: warning: multiple.c, line 135: cannot find include file "stdarg.h" not in /opt/pkg/include/stdarg.h not in /usr/include/stdarg.h makedepend: warning: vector.c, line 107: cannot find include file "stdlib.h" not in /opt/pkg/include/stdlib.h not in /usr/include/stdlib.h makedepend: warning: vector.c, line 110: cannot find include file "ctype.h" not in /opt/pkg/include/ctype.h not in /usr/include/ctype.h makedepend: warning: vector.c, line 111: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: vector.c, line 114: cannot find include file "pwd.h" not in /opt/pkg/include/pwd.h not in /usr/include/pwd.h makedepend: warning: vector.c, line 117: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: wbrotate.c, line 118: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: wbrotate.c, line 119: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: wbrotate.c, line 118: cannot find include file "stdio.h" not in /opt/pkg/include/stdio.h not in /usr/include/stdio.h makedepend: warning: wbrotate.c, line 119: cannot find include file "math.h" not in /opt/pkg/include/math.h not in /usr/include/math.h makedepend: warning: langsel.c, line 91: cannot find include file "string.h" not in /opt/pkg/include/string.h not in /usr/include/string.h