Ticket #35063: main.log

File main.log, 10.3 KB (added by richard.zuerner@…, 12 years ago)

main log of tophat installation. Clearly shows errors leading to problem.

Line 
1version:1
2:debug:main epoch: in tree: 0 installed: 0
3:debug:main zlib 1.2.7_0 exists in the ports tree
4:debug:main zlib 1.2.7_0  is the latest installed
5:debug:main zlib 1.2.7_0  is active
6:debug:main Merging existing variants '' into variants
7:debug:main new fully merged portvariants:
8:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/zlib
9:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
10:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
11:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
12:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
13:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
14:debug:main adding the default universal variant
15:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
16:debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
17:debug:main epoch: in tree: 0 installed: 0
18:debug:main samtools 0.1.17_0 exists in the ports tree
19:debug:main samtools 0.1.17_0  is the latest installed
20:debug:main samtools 0.1.17_0  is active
21:debug:main Merging existing variants '' into variants
22:debug:main new fully merged portvariants:
23:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/samtools
24:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
25:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
26:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
27:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
28:debug:main universal_variant is false, so not adding the default universal variant
29:debug:main No need to upgrade! samtools 0.1.17_0 >= samtools 0.1.17_0
30:debug:main epoch: in tree: 0 installed: 0
31:debug:main bowtie 0.12.7_0 exists in the ports tree
32:debug:main bowtie 0.12.7_0  is the latest installed
33:debug:main bowtie 0.12.7_0  is active
34:debug:main Merging existing variants '' into variants
35:debug:main new fully merged portvariants:
36:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/bowtie
37:debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386
38:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
39:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
40:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
41:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
42:debug:main universal variant already exists, so not adding the default one
43:debug:main No need to upgrade! bowtie 0.12.7_0 >= bowtie 0.12.7_0
44:msg:main --->  Computing dependencies for tophat:info:main .:debug:main tophat has no conflicts
45:debug:main Searching for dependency: zlib
46:debug:main Found Dependency: receipt exists for zlib
47:debug:main Searching for dependency: samtools
48:debug:main Found Dependency: receipt exists for samtools
49:debug:main Searching for dependency: bowtie
50:debug:main Found Dependency: receipt exists for bowtie
51:msg:main
52:debug:main Executing org.macports.main (tophat)
53:debug:main changing euid/egid - current euid: 0 - current egid: 0
54:debug:main egid changed to: 501
55:debug:main euid changed to: 502
56:debug:main Skipping completed org.macports.archivefetch (tophat)
57:debug:main Privilege de-escalation not attempted as not running as root.
58:debug:main Skipping completed org.macports.fetch (tophat)
59:debug:main Privilege de-escalation not attempted as not running as root.
60:debug:main Skipping completed org.macports.checksum (tophat)
61:debug:main Privilege de-escalation not attempted as not running as root.
62:debug:main Skipping completed org.macports.extract (tophat)
63:debug:main Privilege de-escalation not attempted as not running as root.
64:debug:main Skipping completed org.macports.patch (tophat)
65:debug:main Privilege de-escalation not attempted as not running as root.
66:debug:main Skipping completed org.macports.configure (tophat)
67:debug:main Privilege de-escalation not attempted as not running as root.
68:debug:build build phase started at Tue Jul  3 10:13:03 CEST 2012
69:notice:build --->  Building tophat
70:debug:build Executing org.macports.build (tophat)
71:debug:build port disallows a parallel build
72:debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7'
73:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all'
74:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all
75:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0'
76:info:build /usr/bin/make  all-recursive
77:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0'
78:info:build Making all in src
79:info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0/src'
80:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \
81:info:build     then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi
82:info:build In file included from GFaSeqGet.cpp:1:
83:info:build In file included from ./GFaSeqGet.h:4:
84:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
85:info:build  int result=-1;
86:info:build      ^
87:info:build GFaSeqGet.cpp:62:17: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?
88:info:build  if (fofs!=0) { fseeko(fh,fofs,SEEK_SET); } //e.g. for offsets provided by cdbyank
89:info:build                 ^~~~~~
90:info:build                 fseek
91:info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
92:info:build int      fseek(FILE *, long, int);
93:info:build          ^
94:info:build GFaSeqGet.cpp:128:2: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?
95:info:build  fseeko(fh,fseqstart,SEEK_SET);
96:info:build  ^~~~~~
97:info:build  fseek
98:info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
99:info:build int      fseek(FILE *, long, int);
100:info:build          ^
101:info:build GFaSeqGet.cpp:261:3: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?
102:info:build   fseeko(fh, fstart, SEEK_SET);
103:info:build   ^~~~~~
104:info:build   fseek
105:info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
106:info:build int      fseek(FILE *, long, int);
107:info:build          ^
108:info:build GFaSeqGet.cpp:280:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?
109:info:build     fseeko(fh, lendlen, SEEK_CUR);
110:info:build     ^~~~~~
111:info:build     fseek
112:info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
113:info:build int      fseek(FILE *, long, int);
114:info:build          ^
115:info:build GFaSeqGet.cpp:300:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'?
116:info:build     fseeko(fh, lendlen, SEEK_CUR);
117:info:build     ^~~~~~
118:info:build     fseek
119:info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here
120:info:build int      fseek(FILE *, long, int);
121:info:build          ^
122:info:build 1 warning and 5 errors generated.
123:info:build make[2]: *** [GFaSeqGet.o] Error 1
124:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0/src'
125:info:build make[1]: *** [all-recursive] Error 1
126:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0'
127:info:build make: *** [all] Error 2
128:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0'
129:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all
130:info:build Exit code: 2
131:error:build org.macports.build for port tophat returned: command execution failed
132:debug:build Error code: CHILDSTATUS 38890 2
133:debug:build Backtrace: command execution failed
134    while executing
135"system -nice 0 $fullcmdstring"
136    ("eval" body line 1)
137    invoked from within
138"eval system $notty $nice \$fullcmdstring"
139    invoked from within
140"command_exec build"
141    (procedure "portbuild::build_main" line 8)
142    invoked from within
143"$procedure $targetname"
144:info:build Warning: targets not executed for tophat: org.macports.activate org.macports.build org.macports.destroot org.macports.install
145:notice:build Please see the log file for port tophat for details:
146    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/main.log