Ticket #43382: main.log

File main.log, 37.6 KB (added by cpage@…, 11 years ago)
Line 
1version:1
2:debug:main epoch: in tree: 0 installed: 0
3:debug:main zlib 1.2.8_0 exists in the ports tree
4:debug:main zlib 1.2.8_0  is the latest installed
5:debug:main zlib 1.2.8_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/13.1.0 (Mac OS X 10.9) arch i386
10:debug:main adding the default universal variant
11:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
12:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
13:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
14:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
15:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
16:debug:main No need to upgrade! zlib 1.2.8_0 >= zlib 1.2.8_0
17:debug:main epoch: in tree: 0 installed: 0
18:debug:main samtools 0.1.19_0 exists in the ports tree
19:debug:main samtools 0.1.19_0  is the latest installed
20:debug:main samtools 0.1.19_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/13.1.0 (Mac OS X 10.9) arch i386
25:debug:main universal_variant is false, so not adding the default universal variant
26:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
27:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
28:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
29:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
30:debug:main No need to upgrade! samtools 0.1.19_0 >= samtools 0.1.19_0
31:debug:main epoch: in tree: 0 installed: 0
32:debug:main ncurses 5.9_2 exists in the ports tree
33:debug:main ncurses 5.9_2  is the latest installed
34:debug:main ncurses 5.9_2  is active
35:debug:main Merging existing variants '' into variants
36:debug:main new fully merged portvariants:
37:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/ncurses
38:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
39:debug:main adding the default universal variant
40:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
41:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
42:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
43:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
44:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
45:debug:main No need to upgrade! ncurses 5.9_2 >= ncurses 5.9_2
46:debug:main epoch: in tree: 0 installed: 0
47:debug:main bowtie 0.12.9_0 exists in the ports tree
48:debug:main bowtie 0.12.9_0  is the latest installed
49:debug:main bowtie 0.12.9_0  is active
50:debug:main Merging existing variants '' into variants
51:debug:main new fully merged portvariants:
52:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/bowtie
53:debug:main OS darwin/13.1.0 (Mac OS X 10.9) arch i386
54:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
55:debug:main universal variant already exists, so not adding the default one
56:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
57:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
58:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
59:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
60:debug:main No need to upgrade! bowtie 0.12.9_0 >= bowtie 0.12.9_0
61:msg:main --->  Computing dependencies for tophat:info:main .:debug:main tophat has no conflicts
62:debug:main Searching for dependency: zlib
63:debug:main Found Dependency: receipt exists for zlib
64:debug:main Searching for dependency: samtools
65:debug:main Found Dependency: receipt exists for samtools
66:debug:main Searching for dependency: bowtie
67:debug:main Found Dependency: receipt exists for bowtie
68:msg:main
69:debug:main Executing org.macports.main (tophat)
70:debug:main changing euid/egid - current euid: 0 - current egid: 0
71:debug:main egid changed to: 501
72:debug:main euid changed to: 502
73:debug:archivefetch archivefetch phase started at Wed Apr 16 12:43:30 EDT 2014
74:msg:archivefetch --->  Fetching archive for tophat
75:debug:archivefetch Executing org.macports.archivefetch (tophat)
76:debug:archivefetch euid/egid changed to: 0/0
77:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
78:debug:archivefetch euid/egid changed to: 502/501
79:info:archivefetch --->  tophat-1.2.0_0.darwin_13.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
80:msg:archivefetch --->  Attempting to fetch tophat-1.2.0_0.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/tophat
81:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
82:msg:archivefetch --->  Attempting to fetch tophat-1.2.0_0.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/tophat
83:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
84:msg:archivefetch --->  Attempting to fetch tophat-1.2.0_0.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/tophat
85:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 Not Found
86:debug:archivefetch Privilege de-escalation not attempted as not running as root.
87:debug:fetch fetch phase started at Wed Apr 16 12:43:30 EDT 2014
88:notice:fetch --->  Fetching distfiles for tophat
89:debug:fetch Executing org.macports.fetch (tophat)
90:debug:fetch Privilege de-escalation not attempted as not running as root.
91:debug:checksum checksum phase started at Wed Apr 16 12:43:30 EDT 2014
92:notice:checksum --->  Verifying checksums for tophat
93:debug:checksum Executing org.macports.checksum (tophat)
94:info:checksum --->  Checksumming tophat-1.2.0.tar.gz
95:debug:checksum Correct (sha1) checksum for tophat-1.2.0.tar.gz
96:debug:checksum Correct (rmd160) checksum for tophat-1.2.0.tar.gz
97:debug:checksum Privilege de-escalation not attempted as not running as root.
98:debug:extract extract phase started at Wed Apr 16 12:43:30 EDT 2014
99:notice:extract --->  Extracting tophat
100:debug:extract Executing org.macports.extract (tophat)
101:info:extract --->  Extracting tophat-1.2.0.tar.gz
102:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz'
103: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_tarballs_ports_science_tophat/tophat/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.9'
104:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz' | /usr/bin/tar -xf -'
105:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz' | /usr/bin/tar -xf -
106:debug:extract euid/egid changed to: 0/0
107:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work to macports
108:debug:extract euid/egid changed to: 502/501
109:debug:extract Privilege de-escalation not attempted as not running as root.
110:debug:patch patch phase started at Wed Apr 16 12:43:31 EDT 2014
111:debug:patch Executing org.macports.patch (tophat)
112:notice:patch --->  Applying patches to tophat
113:info:patch --->  Applying src_GList.hh.patch
114:debug:patch 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='10.9'
115:debug:patch 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/patch -p0'
116:debug:patch 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/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/tophat/files/src_GList.hh.patch'
117:info:patch patching file src/GList.hh
118:debug:patch Privilege de-escalation not attempted as not running as root.
119:debug:configure configure phase started at Wed Apr 16 12:43:31 EDT 2014
120:notice:configure --->  Configuring tophat
121:debug:configure Using compiler 'Xcode Clang'
122:debug:configure Executing org.macports.configure (tophat)
123:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -arch x86_64' CPPFLAGS='-I/opt/local/include -D_DARWIN_C_SOURCE' CXXFLAGS='-pipe -Os -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' CXX='/usr/bin/clang++' 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' F90FLAGS='-pipe -Os -m64' LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64' FCFLAGS='-pipe -Os -m64' OBJC='/usr/bin/clang' OBJCXX='/usr/bin/clang++' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -Os -arch x86_64' OBJCXXFLAGS='-pipe -Os -arch x86_64' FFLAGS='-pipe -Os -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
124:debug:configure 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" && ./configure --prefix=/opt/local'
125:debug:configure 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" && ./configure --prefix=/opt/local
126:info:configure checking for a BSD-compatible install... /usr/bin/install -c
127:info:configure checking whether build environment is sane... yes
128:info:configure checking for gawk... no
129:info:configure checking for mawk... no
130:info:configure checking for nawk... no
131:info:configure checking for awk... awk
132:info:configure checking whether make sets $(MAKE)... yes
133:info:configure checking build system type... i386-apple-darwin13.1.0
134:info:configure checking host system type... i386-apple-darwin13.1.0
135:info:configure checking for gcc... /usr/bin/clang
136:info:configure checking for C compiler default output file name... a.out
137:info:configure checking whether the C compiler works... yes
138:info:configure checking whether we are cross compiling... no
139:info:configure checking for suffix of executables...
140:info:configure checking for suffix of object files... o
141:info:configure checking whether we are using the GNU C compiler... yes
142:info:configure checking whether /usr/bin/clang accepts -g... yes
143:info:configure checking for /usr/bin/clang option to accept ANSI C... none needed
144:info:configure checking for style of include used by make... GNU
145:info:configure checking dependency style of /usr/bin/clang... gcc3
146:info:configure checking whether we are using the GNU C++ compiler... yes
147:info:configure checking whether /usr/bin/clang++ accepts -g... yes
148:info:configure checking dependency style of /usr/bin/clang++... gcc3
149:info:configure checking for gawk... (cached) awk
150:info:configure checking for a BSD-compatible install... /usr/bin/install -c
151:info:configure checking for ranlib... ranlib
152:info:configure checking for ar... ar
153:info:configure checking for perl... /opt/local/bin/perl
154:info:configure checking for bash... /opt/local/bin/bash
155:info:configure checking for a Python interpreter with version >= 2.4... python
156:info:configure checking for python... /usr/bin/python
157:info:configure checking for python version... 2.7
158:info:configure checking for python platform... darwin
159:info:configure checking for python script directory... ${prefix}/lib/python2.7/site-packages
160:info:configure checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
161:info:configure checking for bamlib... yes
162:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
163:info:configure checking for egrep... grep -E
164:info:configure checking for ANSI C header files... yes
165:info:configure checking for sys/types.h... yes
166:info:configure checking for sys/stat.h... yes
167:info:configure checking for stdlib.h... yes
168:info:configure checking for string.h... yes
169:info:configure checking for memory.h... yes
170:info:configure checking for strings.h... yes
171:info:configure checking for inttypes.h... yes
172:info:configure checking for stdint.h... yes
173:info:configure checking for unistd.h... yes
174:info:configure checking if zlib is wanted... yes
175:info:configure checking for inflateEnd in -lz... yes
176:info:configure checking zlib.h usability... yes
177:info:configure checking zlib.h presence... yes
178:info:configure checking for zlib.h... yes
179:info:configure checking for inflateEnd in -lz... (cached) yes
180:info:configure checking zlib in /usr... ok
181:info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E
182:info:configure checking for stdlib.h... (cached) yes
183:info:configure checking for string.h... (cached) yes
184:info:configure checking for unistd.h... (cached) yes
185:info:configure checking for ANSI C header files... (cached) yes
186:info:configure checking for stdlib.h... (cached) yes
187:info:configure checking for string.h... (cached) yes
188:info:configure checking for unistd.h... (cached) yes
189:info:configure checking for stdbool.h that conforms to C99... yes
190:info:configure checking for _Bool... no
191:info:configure checking for an ANSI C-conforming const... yes
192:info:configure checking for special C compiler options needed for large files... no
193:info:configure checking for _FILE_OFFSET_BITS value needed for large files... no
194:info:configure checking for _LARGE_FILES value needed for large files... no
195:info:configure checking for gzread in -lz... yes
196:info:configure checking for stdlib.h... (cached) yes
197:info:configure checking for GNU libc compatible malloc... yes
198:info:configure checking for memset... yes
199:info:configure checking for strdup... yes
200:info:configure checking for strrchr... yes
201:info:configure checking for strtol... yes
202:info:configure checking for strsep... yes
203:info:configure checking how to create a pax tar archive... gnutar
204:info:configure checking dependency style of /usr/bin/clang... (cached) gcc3
205:info:configure checking dependency style of /usr/bin/clang++... (cached) gcc3
206:info:configure configure: creating ./config.status
207:info:configure config.status: creating Makefile
208:info:configure config.status: creating src/Makefile
209:info:configure config.status: creating config.h
210:info:configure config.status: executing depfiles commands
211:info:configure
212:info:configure -- tophat 1.2.0 Configuration Results --
213:info:configure   C compiler:          /usr/bin/clang -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG
214:info:configure   C++ compiler:        /usr/bin/clang++ -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include
215:info:configure   GCC version:         Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn)
216:info:configure   Host System type:    i386-apple-darwin13.1.0
217:info:configure   Install prefix:      /opt/local
218:info:configure   Install eprefix:     ${prefix}
219:info:configure
220:info:configure   See config.h for further configuration information.
221:info:configure   Email <cole@cs.umd.edu> with questions and bug reports.
222:info:configure
223:debug:configure Privilege de-escalation not attempted as not running as root.
224:debug:build build phase started at Wed Apr 16 12:43:36 EDT 2014
225:notice:build --->  Building tophat
226:debug:build Executing org.macports.build (tophat)
227:debug:build port disallows a parallel build
228: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='10.9'
229: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'
230: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
231: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'
232:info:build /Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
233: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'
234:info:build Making all in src
235: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'
236:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
237:info:build     then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
238:info:build reads.cpp:434:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
239:info:build               char base_prev_prev = "ACGTN"[ptr[(i-1)*4 + k]];
240:info:build                                            ^~~~~~~~~~~~~~~~~
241:info:build In file included from reads.cpp:26:
242:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
243:info:build         bool _spliced;
244:info:build              ^
245:info:build 2 warnings generated.
246:info:build if /usr/bin/clang -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include  -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -MT alphabet.o -MD -MP -MF ".deps/alphabet.Tpo" -c -o alphabet.o alphabet.c; \
247:info:build     then mv -f ".deps/alphabet.Tpo" ".deps/alphabet.Po"; else rm -f ".deps/alphabet.Tpo"; exit 1; fi
248:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT bwt_map.o -MD -MP -MF ".deps/bwt_map.Tpo" -c -o bwt_map.o bwt_map.cpp; \
249:info:build     then mv -f ".deps/bwt_map.Tpo" ".deps/bwt_map.Po"; else rm -f ".deps/bwt_map.Tpo"; exit 1; fi
250:info:build In file included from bwt_map.cpp:21:
251:info:build ./bwt_map.h:595:6: warning: private field '_seg_offset' is not used [-Wunused-private-field]
252:info:build         int _seg_offset;
253:info:build             ^
254:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
255:info:build         bool _spliced;
256:info:build              ^
257:info:build 2 warnings generated.
258:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
259:info:build     then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
260:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT junctions.o -MD -MP -MF ".deps/junctions.Tpo" -c -o junctions.o junctions.cpp; \
261:info:build     then mv -f ".deps/junctions.Tpo" ".deps/junctions.Po"; else rm -f ".deps/junctions.Tpo"; exit 1; fi
262:info:build In file included from junctions.cpp:16:
263:info:build In file included from ./junctions.h:23:
264:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
265:info:build         bool _spliced;
266:info:build              ^
267:info:build 1 warning generated.
268:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT insertions.o -MD -MP -MF ".deps/insertions.Tpo" -c -o insertions.o insertions.cpp; \
269:info:build     then mv -f ".deps/insertions.Tpo" ".deps/insertions.Po"; else rm -f ".deps/insertions.Tpo"; exit 1; fi
270:info:build In file included from insertions.cpp:34:
271:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
272:info:build         bool _spliced;
273:info:build              ^
274:info:build 1 warning generated.
275:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT deletions.o -MD -MP -MF ".deps/deletions.Tpo" -c -o deletions.o deletions.cpp; \
276:info:build     then mv -f ".deps/deletions.Tpo" ".deps/deletions.Po"; else rm -f ".deps/deletions.Tpo"; exit 1; fi
277:info:build In file included from deletions.cpp:15:
278:info:build In file included from ./deletions.h:22:
279:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
280:info:build         bool _spliced;
281:info:build              ^
282:info:build 1 warning generated.
283:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT align_status.o -MD -MP -MF ".deps/align_status.Tpo" -c -o align_status.o align_status.cpp; \
284:info:build     then mv -f ".deps/align_status.Tpo" ".deps/align_status.Po"; else rm -f ".deps/align_status.Tpo"; exit 1; fi
285:info:build In file included from align_status.cpp:20:
286:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
287:info:build         bool _spliced;
288:info:build              ^
289:info:build 1 warning generated.
290:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..   -I/opt/local/include -D_DARWIN_C_SOURCE -I/usr/include -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG -I/opt/local/include -MT fragments.o -MD -MP -MF ".deps/fragments.Tpo" -c -o fragments.o fragments.cpp; \
291:info:build     then mv -f ".deps/fragments.Tpo" ".deps/fragments.Po"; else rm -f ".deps/fragments.Tpo"; exit 1; fi
292:info:build In file included from fragments.cpp:15:
293:info:build In file included from ./bwt_map.h:16:
294:info:build In file included from ./SeqAn-1.1/seqan/sequence.h:27:
295:info:build In file included from ./SeqAn-1.1/seqan/basic.h:113:
296:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:149:7: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char [3]')
297:info:build                 out << "< " << getValueI1(p) << " , " << getValueI2(p) << " >";
298:info:build                 ~~~ ^  ~~~~
299:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:5269:1: note: candidate template ignored: failed template argument deduction
300:info:build operator<<(basic_ostream<_CharT, _Traits>& __os, shared_ptr<_Yp> const& __p);
301:info:build ^
302:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:4058:1: note: candidate template ignored: failed template argument deduction
303:info:build operator<<(basic_ostream<_CharT, _Traits>& __os,
304:info:build ^
305:info:build ./SeqAn-1.1/seqan/basic/basic_generated_forwards.h:1727:93: note: candidate template ignored: failed template argument deduction
306:info:build template <typename TTT1, typename TTT2, typename TTT3, typename TCompression> std::ostream& operator<<(std::ostream &out, Triple<TTT1,TTT2,TTT3,TCompression> const &t);        // "projects/library/seqan/basic/basic_aggregates.h"(267)
307:info:build                                                                                             ^
308:info:build ./SeqAn-1.1/seqan/basic/basic_generated_forwards.h:1728:78: note: candidate template ignored: failed template argument deduction
309:info:build template <typename TTT, unsigned _size, typename TCompression> std::ostream& operator<<(std::ostream& out, Tuple<TTT,_size,TCompression> const &a);             // "projects/library/seqan/basic/basic_aggregates.h"(548)
310:info:build                                                                              ^
311:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:589:1: note: candidate template ignored: failed template argument deduction
312:info:build operator << (TStream & strm,
313:info:build ^
314:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:596:1: note: candidate template ignored: failed template argument deduction
315:info:build operator << (TStream & strm,
316:info:build ^
317:info:build ./SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:260:1: note: candidate template ignored: failed template argument deduction
318:info:build operator << (TStream & stream,
319:info:build ^
320:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:148:16: note: candidate template ignored: failed template argument deduction
321:info:build         std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
322:info:build                       ^
323:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:268:7: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char [3]')
324:info:build                 out << "< " << getValueI1(t) << " , " << getValueI2(t) << " , " << getValueI3(t) << " >";
325:info:build                 ~~~ ^  ~~~~
326:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:5269:1: note: candidate template ignored: failed template argument deduction
327:info:build operator<<(basic_ostream<_CharT, _Traits>& __os, shared_ptr<_Yp> const& __p);
328:info:build ^
329:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:4058:1: note: candidate template ignored: failed template argument deduction
330:info:build operator<<(basic_ostream<_CharT, _Traits>& __os,
331:info:build ^
332:info:build ./SeqAn-1.1/seqan/basic/basic_generated_forwards.h:1728:78: note: candidate template ignored: failed template argument deduction
333:info:build template <typename TTT, unsigned _size, typename TCompression> std::ostream& operator<<(std::ostream& out, Tuple<TTT,_size,TCompression> const &a);             // "projects/library/seqan/basic/basic_aggregates.h"(548)
334:info:build                                                                              ^
335:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:589:1: note: candidate template ignored: failed template argument deduction
336:info:build operator << (TStream & strm,
337:info:build ^
338:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:596:1: note: candidate template ignored: failed template argument deduction
339:info:build operator << (TStream & strm,
340:info:build ^
341:info:build ./SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:260:1: note: candidate template ignored: failed template argument deduction
342:info:build operator << (TStream & stream,
343:info:build ^
344:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:148:16: note: candidate template ignored: failed template argument deduction
345:info:build         std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
346:info:build                       ^
347:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:267:16: note: candidate template ignored: failed template argument deduction
348:info:build         std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
349:info:build                       ^
350:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:549:7: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char [2]')
351:info:build                 out << "[";
352:info:build                 ~~~ ^  ~~~
353:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:5269:1: note: candidate template ignored: failed template argument deduction
354:info:build operator<<(basic_ostream<_CharT, _Traits>& __os, shared_ptr<_Yp> const& __p);
355:info:build ^
356:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:4058:1: note: candidate template ignored: failed template argument deduction
357:info:build operator<<(basic_ostream<_CharT, _Traits>& __os,
358:info:build ^
359:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:589:1: note: candidate template ignored: failed template argument deduction
360:info:build operator << (TStream & strm,
361:info:build ^
362:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:596:1: note: candidate template ignored: failed template argument deduction
363:info:build operator << (TStream & strm,
364:info:build ^
365:info:build ./SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:260:1: note: candidate template ignored: failed template argument deduction
366:info:build operator << (TStream & stream,
367:info:build ^
368:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:148:16: note: candidate template ignored: failed template argument deduction
369:info:build         std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
370:info:build                       ^
371:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:267:16: note: candidate template ignored: failed template argument deduction
372:info:build         std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
373:info:build                       ^
374:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:548:16: note: candidate template ignored: failed template argument deduction
375:info:build         std::ostream& operator<<(std::ostream& out, Tuple<_T,_size,TCompression> const &a) {
376:info:build                       ^
377:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:553:8: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char [2]')
378:info:build                         out << " " << a[j];
379:info:build                         ~~~ ^  ~~~
380:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:5269:1: note: candidate template ignored: failed template argument deduction
381:info:build operator<<(basic_ostream<_CharT, _Traits>& __os, shared_ptr<_Yp> const& __p);
382:info:build ^
383:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:4058:1: note: candidate template ignored: failed template argument deduction
384:info:build operator<<(basic_ostream<_CharT, _Traits>& __os,
385:info:build ^
386:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:589:1: note: candidate template ignored: failed template argument deduction
387:info:build operator << (TStream & strm,
388:info:build ^
389:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:596:1: note: candidate template ignored: failed template argument deduction
390:info:build operator << (TStream & strm,
391:info:build ^
392:info:build ./SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:260:1: note: candidate template ignored: failed template argument deduction
393:info:build operator << (TStream & stream,
394:info:build ^
395:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:148:16: note: candidate template ignored: failed template argument deduction
396:info:build         std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
397:info:build                       ^
398:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:267:16: note: candidate template ignored: failed template argument deduction
399:info:build         std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
400:info:build                       ^
401:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:548:16: note: candidate template ignored: failed template argument deduction
402:info:build         std::ostream& operator<<(std::ostream& out, Tuple<_T,_size,TCompression> const &a) {
403:info:build                       ^
404:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:554:7: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const char [2]')
405:info:build                 out << "]";
406:info:build                 ~~~ ^  ~~~
407:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/memory:5269:1: note: candidate template ignored: failed template argument deduction
408:info:build operator<<(basic_ostream<_CharT, _Traits>& __os, shared_ptr<_Yp> const& __p);
409:info:build ^
410:info:build /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/string:4058:1: note: candidate template ignored: failed template argument deduction
411:info:build operator<<(basic_ostream<_CharT, _Traits>& __os,
412:info:build ^
413:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:589:1: note: candidate template ignored: failed template argument deduction
414:info:build operator << (TStream & strm,
415:info:build ^
416:info:build ./SeqAn-1.1/seqan/basic/basic_proxy.h:596:1: note: candidate template ignored: failed template argument deduction
417:info:build operator << (TStream & strm,
418:info:build ^
419:info:build ./SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:260:1: note: candidate template ignored: failed template argument deduction
420:info:build operator << (TStream & stream,
421:info:build ^
422:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:148:16: note: candidate template ignored: failed template argument deduction
423:info:build         std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
424:info:build                       ^
425:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:267:16: note: candidate template ignored: failed template argument deduction
426:info:build         std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
427:info:build                       ^
428:info:build ./SeqAn-1.1/seqan/basic/basic_aggregates.h:548:16: note: candidate template ignored: failed template argument deduction
429:info:build         std::ostream& operator<<(std::ostream& out, Tuple<_T,_size,TCompression> const &a) {
430:info:build                       ^
431:info:build In file included from fragments.cpp:15:
432:info:build ./bwt_map.h:746:7: warning: private field '_spliced' is not used [-Wunused-private-field]
433:info:build         bool _spliced;
434:info:build              ^
435:info:build 1 warning and 5 errors generated.
436:info:build make[2]: *** [fragments.o] Error 1
437: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'
438:info:build make[1]: *** [all-recursive] Error 1
439: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'
440:info:build make: *** [all] Error 2
441: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'
442: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
443:info:build Exit code: 2
444:error:build org.macports.build for port tophat returned: command execution failed
445:debug:build Error code: CHILDSTATUS 32793 2
446:debug:build Backtrace: command execution failed
447    while executing
448"system -nice 0 $fullcmdstring"
449    ("eval" body line 1)
450    invoked from within
451"eval system $notty $nice \$fullcmdstring"
452    invoked from within
453"command_exec build"
454    (procedure "portbuild::build_main" line 8)
455    invoked from within
456"$procedure $targetname"
457:info:build Warning: targets not executed for tophat: org.macports.activate org.macports.build org.macports.destroot org.macports.install
458:notice:build Please see the log file for port tophat for details:
459    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/main.log