Ticket #37200: main.log

File main.log, 17.4 KB (added by mesh89@…, 11 years ago)
Line 
1version:1
2:debug:main Found Dependency: path: /usr/bin filename: unzip regex: ^unzip$
3:debug:main epoch: in tree: 0 installed: 0
4:debug:main md5sha1sum 0.9.5_1 exists in the ports tree
5:debug:main md5sha1sum 0.9.5_1  is the latest installed
6:debug:main md5sha1sum 0.9.5_1  is active
7:debug:main Merging existing variants '' into variants
8:debug:main new fully merged portvariants:
9:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/sysutils/md5sha1sum
10:debug:main OS darwin/12.2.0 (Mac OS X 10.8) arch i386
11:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
12:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
13:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
14:debug:main adding the default universal variant
15:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
16:debug:main No need to upgrade! md5sha1sum 0.9.5_1 >= md5sha1sum 0.9.5_1
17:debug:main epoch: in tree: 1 installed: 1
18:debug:main openssl 1.0.1c_0 exists in the ports tree
19:debug:main openssl 1.0.1c_0  is the latest installed
20:debug:main openssl 1.0.1c_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/ports/devel/openssl
24:debug:main OS darwin/12.2.0 (Mac OS X 10.8) 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 Using group file /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl
29:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
30:debug:main universal variant already exists, so not adding the default one
31:debug:main No need to upgrade! openssl 1.0.1c_0 >= openssl 1.0.1c_0
32:debug:main epoch: in tree: 0 installed: 0
33:debug:main zlib 1.2.7_0 exists in the ports tree
34:debug:main zlib 1.2.7_0  is the latest installed
35:debug:main zlib 1.2.7_0  is active
36:debug:main Merging existing variants '' into variants
37:debug:main new fully merged portvariants:
38:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/archivers/zlib
39:debug:main OS darwin/12.2.0 (Mac OS X 10.8) arch i386
40:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
41:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
42:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
43:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
44:debug:main adding the default universal variant
45:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
46:debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
47:msg:main --->  Computing dependencies for bowtie:info:main .:debug:main bowtie has no conflicts
48:debug:main Found Dependency: path: /usr/bin filename: unzip regex: ^unzip$
49:debug:main Searching for dependency: unzip
50:debug:main Didn't find receipt, going to depspec regex for: unzip
51:debug:main Found Dependency: path: /usr/bin filename: unzip regex: ^unzip$
52:debug:main Searching for dependency: md5sha1sum
53:debug:main Found Dependency: receipt exists for md5sha1sum
54:msg:main
55:debug:main Executing org.macports.main (bowtie)
56:debug:archivefetch archivefetch phase started at Tue Dec  4 14:34:18 CET 2012
57:msg:archivefetch --->  Fetching archive for bowtie
58:debug:archivefetch Executing org.macports.archivefetch (bowtie)
59:info:archivefetch --->  bowtie-0.12.7_0.darwin_12.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
60:msg:archivefetch --->  Attempting to fetch bowtie-0.12.7_0.darwin_12.x86_64.tbz2 from http://lil.fr.packages.macports.org/bowtie
61:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
62:msg:archivefetch --->  Attempting to fetch bowtie-0.12.7_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/bowtie
63:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
64:msg:archivefetch --->  Attempting to fetch bowtie-0.12.7_0.darwin_12.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/bowtie
65:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
66:debug:fetch fetch phase started at Tue Dec  4 14:34:20 CET 2012
67:notice:fetch --->  Fetching distfiles for bowtie
68:debug:fetch Executing org.macports.fetch (bowtie)
69:debug:checksum checksum phase started at Tue Dec  4 14:34:20 CET 2012
70:notice:checksum --->  Verifying checksum(s) for bowtie
71:debug:checksum Executing org.macports.checksum (bowtie)
72:info:checksum --->  Checksumming bowtie-0.12.7-src.zip
73:debug:checksum Correct (sha1) checksum for bowtie-0.12.7-src.zip
74:debug:checksum Correct (rmd160) checksum for bowtie-0.12.7-src.zip
75:debug:extract extract phase started at Tue Dec  4 14:34:20 CET 2012
76:notice:extract --->  Extracting bowtie
77:debug:extract setting option extract.cmd to /usr/bin/unzip
78:debug:extract setting option extract.pre_args to -q
79:debug:extract setting option extract.post_args to {-d /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work}
80:debug:extract Executing org.macports.extract (bowtie)
81:info:extract --->  Extracting bowtie-0.12.7-src.zip
82:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/bowtie/bowtie-0.12.7-src.zip'
83:debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.8'
84:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work" && /usr/bin/unzip -q '/opt/local/var/macports/distfiles/bowtie/bowtie-0.12.7-src.zip' -d /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work'
85:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work" && /usr/bin/unzip -q '/opt/local/var/macports/distfiles/bowtie/bowtie-0.12.7-src.zip' -d /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work
86:debug:patch patch phase started at Tue Dec  4 14:34:21 CET 2012
87:debug:patch Executing org.macports.patch (bowtie)
88:debug:configure configure phase started at Tue Dec  4 14:34:21 CET 2012
89:notice:configure --->  Configuring bowtie
90:debug:configure Using compiler 'Mac OS X clang'
91:debug:configure Executing org.macports.configure (bowtie)
92:debug:build build phase started at Tue Dec  4 14:34:21 CET 2012
93:notice:build --->  Building bowtie
94:debug:build Executing org.macports.build (bowtie)
95: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_ports_science_bowtie/bowtie/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.8'
96:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/bowtie-0.12.7" && /usr/bin/make -j2 -w allall CC=/usr/bin/clang CXX=/usr/bin/clang++ EXTRA_FLAGS="-arch x86_64"'
97:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/bowtie-0.12.7" && /usr/bin/make -j2 -w allall CC=/usr/bin/clang CXX=/usr/bin/clang++ EXTRA_FLAGS="-arch x86_64"
98:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/bowtie-0.12.7'
99:info:build cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h | md5sum | awk '{print $1}' > .bowtie-build.md5
100:info:build cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h search_1mm_phase1.c search_1mm_phase2.c search_23mm_phase1.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase1.c search_seeded_phase2.c search_seeded_phase3.c search_seeded_phase4.c | md5sum | awk '{print $1}' > .bowtie.md5
101:info:build /usr/bin/clang++ -O3  -DCOMPILER_OPTIONS="\"-O3  -arch x86_64  \"" -arch x86_64   \
102:info:build             -DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
103:info:build             -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM  -DNDEBUG -Wall \
104:info:build             -I SeqAn-1.1 \
105:info:build             -o bowtie-build ebwt_build.cpp \
106:info:build             ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
107:info:build             
108:info:build /usr/bin/clang++ -O3  -DCOMPILER_OPTIONS="\"-O3  -arch x86_64  \"" -arch x86_64   \
109:info:build             -DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
110:info:build             -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM  -DNDEBUG -Wall \
111:info:build             -I SeqAn-1.1 \
112:info:build             -o bowtie ebwt_search.cpp \
113:info:build             ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
114:info:build              -lpthread
115:info:build clang: clang: warning: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
116:info:build treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
117:info:build In file included from ebwt_build.cpp:11:
118:info:build ./ebwt.h:1501:1: warning: 'SideLocus' defined as a struct here but previously declared as a class [-Wmismatched-tags]
119:info:build struct SideLocus {
120:info:build ^
121:info:build ./ebwt.h:306:1: note: did you mean struct here?
122:info:build class SideLocus;
123:info:build ^~~~~
124:info:build struct
125:info:build In file included from ebwt_search.cpp:15:
126:info:build ./ebwt.h:1501:1: warning: 'SideLocus' defined as a struct here but previously declared as a class [-Wmismatched-tags]
127:info:build struct SideLocus {
128:info:build ^
129:info:build ./ebwt.h:306:1: note: did you mean struct here?
130:info:build class SideLocus;
131:info:build ^~~~~
132:info:build struct
133:info:build ./ebwt.h:3938:11: error: default arguments cannot be added to an out-of-line definition of a member of a class template
134:info:build         uint32_t seed = 0)
135:info:build                  ^      ~
136:info:build ebwt_build.cpp:344:31: warning: unused variable 'sztot2' [-Wunused-variable]
137:info:build                                 std::pair<size_t, size_t> sztot2 =
138:info:build                                                           ^
139:info:build ./ebwt.h:3938:11: error: default arguments cannot be added to an out-of-line definition of a member of a class template
140:info:build         uint32_t seed = 0)
141:info:build                  ^      ~
142:info:build In file included from ebwt_search.cpp:32:
143:info:build ./sam.h:152:15: warning: 'SAMHitSink::reportHits' hides overloaded virtual functions [-Woverloaded-virtual]
144:info:build         virtual void reportHits(vector<Hit>& hs,
145:info:build                      ^
146:info:build ./hit.h:481:15: note: hidden overloaded virtual function 'HitSink::reportHits' declared here
147:info:build         virtual void reportHits(vector<Hit>& hs) {
148:info:build                      ^
149:info:build ./hit.h:488:15: note: hidden overloaded virtual function 'HitSink::reportHits' declared here
150:info:build         virtual void reportHits(vector<Hit>& hs, size_t start, size_t end) {
151:info:build                      ^
152:info:build In file included from ebwt_build.cpp:11:
153:info:build In file included from ./ebwt.h:24:
154:info:build ./alphabet.h:48:3: error: call to function 'reverseInPlace' that is neither visible in the template definition nor found by argument-dependent lookup
155:info:build                 reverseInPlace(s);
156:info:build                 ^
157:info:build ./hit.h:97:4: note: in instantiation of function template specialization 'reverseComplementInPlace<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>> >' requested here
158:info:build                         reverseComplementInPlace(hs.seq, hs.color);
159:info:build                         ^
160:info:build ./alphabet.h:74:20: note: 'reverseInPlace' should be declared prior to the call site or in namespace 'seqan'
161:info:build static inline void reverseInPlace(TStr& s) {
162:info:build                    ^
163:info:build In file included from ebwt_search.cpp:12:
164:info:build ./alphabet.h:48:3: error: call to function 'reverseInPlace' that is neither visible in the template definition nor found by argument-dependent lookup
165:info:build                 reverseInPlace(s);
166:info:build                 ^
167:info:build ./hit.h:97:4: note: in instantiation of function template specialization 'reverseComplementInPlace<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void>> >' requested here
168:info:build                         reverseComplementInPlace(hs.seq, hs.color);
169:info:build                         ^
170:info:build ./alphabet.h:74:20: note: 'reverseInPlace' should be declared prior to the call site or in namespace 'seqan'
171:info:build static inline void reverseInPlace(TStr& s) {
172:info:build                    ^
173:info:build 2 warnings and 2 errors generated.
174:info:build make: *** [bowtie] Error 1
175:info:build make: *** Waiting for unfinished jobs....
176:info:build 2 warnings and 2 errors generated.
177:info:build make: *** [bowtie-build] Error 1
178:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/bowtie-0.12.7'
179:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/work/bowtie-0.12.7" && /usr/bin/make -j2 -w allall CC=/usr/bin/clang CXX=/usr/bin/clang++ EXTRA_FLAGS="-arch x86_64"
180:info:build Exit code: 2
181:error:build org.macports.build for port bowtie returned: command execution failed
182:debug:build Error code: CHILDSTATUS 1151 2
183:debug:build Backtrace: command execution failed
184    while executing
185"system -nice 0 $fullcmdstring"
186    ("eval" body line 1)
187    invoked from within
188"eval system $notty $nice \$fullcmdstring"
189    invoked from within
190"command_exec build"
191    (procedure "portbuild::build_main" line 8)
192    invoked from within
193"$procedure $targetname"
194:info:build Warning: targets not executed for bowtie: org.macports.activate org.macports.build org.macports.destroot org.macports.install
195:notice:build Please see the log file for port bowtie for details:
196    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_bowtie/bowtie/main.log