Ticket #42119: main.log

File main.log, 57.2 KB (added by warren-mcgee@…, 11 years ago)

This is the full main log for the installation.

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/11.4.2 (Mac OS X 10.7) 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 0.1.18_0 exists in the ports tree
19:debug:main samtools 0.1.18_0  is the latest installed
20:debug:main samtools 0.1.18_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/11.4.2 (Mac OS X 10.7) 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 0.1.18_0 >= samtools 0.1.18_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/11.4.2 (Mac OS X 10.7) 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 boost 1.55.0_0 exists in the ports tree
48:debug:main boost 1.55.0_0 +no_single+no_static+python27 is the latest installed
49:debug:main boost 1.55.0_0 +no_single+no_static+python27 is active
50:debug:main Merging existing variants '+no_single+no_static+python27' into variants
51:debug:main new fully merged portvariants: no_static + no_single + python27 +
52:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/boost
53:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
54:debug:main compiler clang 421.0.57 not blacklisted because it doesn't match {clang < 421}
55:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
56:debug:main universal variant already exists, so not adding the default one
57:debug:main Executing variant python27 provides python27
58:debug:main Executing variant no_static provides no_static
59:debug:main Executing variant no_single provides no_single
60:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
61:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
62:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
63:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
64:debug:main No need to upgrade! boost 1.55.0_0 >= boost 1.55.0_0
65:debug:main epoch: in tree: 0 installed: 0
66:debug:main expat 2.1.0_0 exists in the ports tree
67:debug:main expat 2.1.0_0  is the latest installed
68:debug:main expat 2.1.0_0  is active
69:debug:main Merging existing variants '' into variants
70:debug:main new fully merged portvariants:
71:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/expat
72:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
73:debug:main adding the default universal variant
74:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
75:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
76:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
77:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
78:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
79:debug:main No need to upgrade! expat 2.1.0_0 >= expat 2.1.0_0
80:debug:main epoch: in tree: 0 installed: 0
81:debug:main bzip2 1.0.6_0 exists in the ports tree
82:debug:main bzip2 1.0.6_0  is the latest installed
83:debug:main bzip2 1.0.6_0  is active
84:debug:main Merging existing variants '' into variants
85:debug:main new fully merged portvariants:
86:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2
87:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
88:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
89:debug:main universal variant already exists, so not adding the default one
90:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
91:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
92:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
93:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
94:debug:main No need to upgrade! bzip2 1.0.6_0 >= bzip2 1.0.6_0
95:debug:main epoch: in tree: 0 installed: 0
96:debug:main libiconv 1.14_0 exists in the ports tree
97:debug:main libiconv 1.14_0  is the latest installed
98:debug:main libiconv 1.14_0  is active
99:debug:main Merging existing variants '' into variants
100:debug:main new fully merged portvariants:
101:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/libiconv
102:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
103:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
104:debug:main universal variant already exists, so not adding the default one
105:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
106:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
107:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
108:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
109:debug:main No need to upgrade! libiconv 1.14_0 >= libiconv 1.14_0
110:debug:main epoch: in tree: 0 installed: 0
111:debug:main icu 51.2_1 exists in the ports tree
112:debug:main icu 51.2_1  is the latest installed
113:debug:main icu 51.2_1  is active
114:debug:main Merging existing variants '' into variants
115:debug:main new fully merged portvariants:
116:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/icu
117:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
118:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
119:debug:main universal variant already exists, so not adding the default one
120:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
121:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
122:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
123:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
124:debug:main No need to upgrade! icu 51.2_1 >= icu 51.2_1
125:debug:main epoch: in tree: 2 installed: 2
126:debug:main python27 2.7.6_0 exists in the ports tree
127:debug:main python27 2.7.6_0  is the latest installed
128:debug:main python27 2.7.6_0  is active
129:debug:main Merging existing variants '' into variants
130:debug:main new fully merged portvariants:
131:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/lang/python27
132:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
133:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
134:debug:main universal variant already exists, so not adding the default one
135:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
136:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
137:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
138:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
139:debug:main No need to upgrade! python27 2.7.6_0 >= python27 2.7.6_0
140:debug:main epoch: in tree: 0 installed: 0
141:debug:main gettext 0.18.3.2_0 exists in the ports tree
142:debug:main gettext 0.18.3.2_0  is the latest installed
143:debug:main gettext 0.18.3.2_0  is active
144:debug:main Merging existing variants '' into variants
145:debug:main new fully merged portvariants:
146:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/gettext
147:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
148:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
149:debug:main compiler clang 421.0.57 not blacklisted because it doesn't match {clang < 211.10.1}
150:debug:main universal variant already exists, so not adding the default one
151:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
152:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
153:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
154:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
155:debug:main No need to upgrade! gettext 0.18.3.2_0 >= gettext 0.18.3.2_0
156:debug:main epoch: in tree: 1 installed: 1
157:debug:main openssl 1.0.1f_0 exists in the ports tree
158:debug:main openssl 1.0.1f_0  is the latest installed
159:debug:main openssl 1.0.1f_0  is active
160:debug:main Merging existing variants '' into variants
161:debug:main new fully merged portvariants:
162:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/openssl
163:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
164:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
165:debug:main universal variant already exists, so not adding the default one
166:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
167:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
168:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
169:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
170:debug:main No need to upgrade! openssl 1.0.1f_0 >= openssl 1.0.1f_0
171:debug:main epoch: in tree: 0 installed: 0
172:debug:main sqlite3 3.8.2_0 exists in the ports tree
173:debug:main sqlite3 3.8.2_0  is the latest installed
174:debug:main sqlite3 3.8.2_0  is active
175:debug:main Merging existing variants '' into variants
176:debug:main new fully merged portvariants:
177:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/databases/sqlite3
178:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
179:debug:main adding the default universal variant
180:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
181:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
182:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
183:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
184:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
185:debug:main No need to upgrade! sqlite3 3.8.2_0 >= sqlite3 3.8.2_0
186:debug:main epoch: in tree: 20090923 installed: 20090923
187:debug:main libedit 20121213-3.0_0 exists in the ports tree
188:debug:main libedit 20121213-3.0_0  is the latest installed
189:debug:main libedit 20121213-3.0_0  is active
190:debug:main Merging existing variants '' into variants
191:debug:main new fully merged portvariants:
192:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/libedit
193:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
194:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
195:debug:main universal variant already exists, so not adding the default one
196:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
197:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
198:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
199:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
200:debug:main No need to upgrade! libedit 20121213-3.0_0 >= libedit 20121213-3.0_0
201:debug:main epoch: in tree: 0 installed: 0
202:debug:main db46 4.6.21_9 exists in the ports tree
203:debug:main db46 4.6.21_9  is the latest installed
204:debug:main db46 4.6.21_9  is active
205:debug:main Merging existing variants '' into variants
206:debug:main new fully merged portvariants:
207:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/databases/db46
208:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
209:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
210:debug:main universal variant already exists, so not adding the default one
211:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
212:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
213:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
214:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
215:debug:main No need to upgrade! db46 4.6.21_9 >= db46 4.6.21_9
216:debug:main epoch: in tree: 0 installed: 0
217:debug:main db_select 0.1_2 exists in the ports tree
218:debug:main db_select 0.1_2  is the latest installed
219:debug:main db_select 0.1_2  is active
220:debug:main Merging existing variants '' into variants
221:debug:main new fully merged portvariants:
222:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/sysutils/db_select
223:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
224:debug:main universal_variant is false, so not adding the default universal variant
225:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
226:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
227:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
228:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
229:debug:main No need to upgrade! db_select 0.1_2 >= db_select 0.1_2
230:debug:main epoch: in tree: 0 installed: 0
231:debug:main python_select 0.3_3 exists in the ports tree
232:debug:main python_select 0.3_3  is the latest installed
233:debug:main python_select 0.3_3  is active
234:debug:main Merging existing variants '' into variants
235:debug:main new fully merged portvariants:
236:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/sysutils/python_select
237:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
238:debug:main universal_variant is false, so not adding the default universal variant
239:debug:main Running callback portconfigure::add_automatic_compiler_dependencies
240:debug:main Finished running callback portconfigure::add_automatic_compiler_dependencies
241:debug:main Running callback portbuild::add_automatic_buildsystem_dependencies
242:debug:main Finished running callback portbuild::add_automatic_buildsystem_dependencies
243:debug:main No need to upgrade! python_select 0.3_3 >= python_select 0.3_3
244:msg:main --->  Computing dependencies for cufflinks:info:main .:debug:main cufflinks has no conflicts
245:debug:main Searching for dependency: zlib
246:debug:main Found Dependency: receipt exists for zlib
247:debug:main Searching for dependency: samtools
248:debug:main Found Dependency: receipt exists for samtools
249:debug:main Searching for dependency: boost
250:debug:main Found Dependency: receipt exists for boost
251:msg:main
252:debug:main Executing org.macports.main (cufflinks)
253:debug:main changing euid/egid - current euid: 0 - current egid: 0
254:debug:main egid changed to: 502
255:debug:main euid changed to: 502
256:debug:archivefetch archivefetch phase started at Mon Jan 13 19:05:27 CST 2014
257:msg:archivefetch --->  Fetching archive for cufflinks
258:debug:archivefetch Executing org.macports.archivefetch (cufflinks)
259:debug:archivefetch euid/egid changed to: 0/0
260:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
261:debug:archivefetch euid/egid changed to: 502/502
262:info:archivefetch --->  cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
263:msg:archivefetch --->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/cufflinks
264:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
265:msg:archivefetch --->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/cufflinks
266:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
267:msg:archivefetch --->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/cufflinks
268:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
269:debug:archivefetch Privilege de-escalation not attempted as not running as root.
270:debug:fetch fetch phase started at Mon Jan 13 19:05:28 CST 2014
271:notice:fetch --->  Fetching distfiles for cufflinks
272:debug:fetch Executing org.macports.fetch (cufflinks)
273:debug:fetch Privilege de-escalation not attempted as not running as root.
274:debug:checksum checksum phase started at Mon Jan 13 19:05:28 CST 2014
275:notice:checksum --->  Verifying checksums for cufflinks
276:debug:checksum Executing org.macports.checksum (cufflinks)
277:info:checksum --->  Checksumming cufflinks-0.9.3.tar.gz
278:debug:checksum Correct (sha1) checksum for cufflinks-0.9.3.tar.gz
279:debug:checksum Correct (rmd160) checksum for cufflinks-0.9.3.tar.gz
280:debug:checksum Privilege de-escalation not attempted as not running as root.
281:debug:extract extract phase started at Mon Jan 13 19:05:28 CST 2014
282:notice:extract --->  Extracting cufflinks
283:debug:extract Executing org.macports.extract (cufflinks)
284:info:extract --->  Extracting cufflinks-0.9.3.tar.gz
285:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/cufflinks/cufflinks-0.9.3.tar.gz'
286: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_cufflinks/cufflinks/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7'
287:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cufflinks/cufflinks-0.9.3.tar.gz' | /usr/bin/gnutar --no-same-owner -xf -'
288:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/cufflinks/cufflinks-0.9.3.tar.gz' | /usr/bin/gnutar --no-same-owner -xf -
289:debug:extract euid/egid changed to: 0/0
290:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work to macports
291:debug:extract euid/egid changed to: 502/502
292:debug:extract Privilege de-escalation not attempted as not running as root.
293:debug:patch patch phase started at Mon Jan 13 19:05:28 CST 2014
294:debug:patch Executing org.macports.patch (cufflinks)
295:debug:patch Privilege de-escalation not attempted as not running as root.
296:debug:configure configure phase started at Mon Jan 13 19:05:28 CST 2014
297:notice:configure --->  Configuring cufflinks
298:debug:configure Using compiler 'Xcode Clang'
299:debug:configure Executing org.macports.configure (cufflinks)
300:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -Os -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -Os -arch x86_64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.7' 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_cufflinks/cufflinks/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'
301:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3" && ./configure --prefix=/opt/local'
302:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3" && ./configure --prefix=/opt/local
303:info:configure checking for a BSD-compatible install... /usr/bin/install -c
304:info:configure checking whether build environment is sane... yes
305:info:configure checking for gawk... no
306:info:configure checking for mawk... no
307:info:configure checking for nawk... no
308:info:configure checking for awk... awk
309:info:configure checking whether make sets $(MAKE)... yes
310:info:configure checking for gawk... (cached) awk
311:info:configure checking for C++ compiler default output file name... a.out
312:info:configure checking whether the C++ compiler works... yes
313:info:configure checking whether we are cross compiling... no
314:info:configure checking for suffix of executables...
315:info:configure checking for suffix of object files... o
316:info:configure checking whether we are using the GNU C++ compiler... yes
317:info:configure checking whether /usr/bin/clang++ accepts -g... yes
318:info:configure checking for style of include used by make... GNU
319:info:configure checking dependency style of /usr/bin/clang++... gcc3
320:info:configure checking for gcc... /usr/bin/clang
321:info:configure checking whether we are using the GNU C compiler... yes
322:info:configure checking whether /usr/bin/clang accepts -g... yes
323:info:configure checking for /usr/bin/clang option to accept ANSI C... none needed
324:info:configure checking dependency style of /usr/bin/clang... gcc3
325:info:configure checking whether make sets $(MAKE)... (cached) yes
326:info:configure checking for ranlib... ranlib
327:info:configure checking for a BSD-compatible install... /usr/bin/install -c
328:info:configure checking for boostlib >= 1.38.0... yes
329:info:configure checking for bamlib... yes
330:info:configure checking build system type... i686-apple-darwin11.4.2
331:info:configure checking whether the Boost::Thread library is available... yes
332:info:configure checking for exit in -lboost_thread-mt... yes
333:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
334:info:configure checking for egrep... grep -E
335:info:configure checking for ANSI C header files... yes
336:info:configure checking for sys/types.h... yes
337:info:configure checking for sys/stat.h... yes
338:info:configure checking for stdlib.h... yes
339:info:configure checking for string.h... yes
340:info:configure checking for memory.h... yes
341:info:configure checking for strings.h... yes
342:info:configure checking for inttypes.h... yes
343:info:configure checking for stdint.h... yes
344:info:configure checking for unistd.h... yes
345:info:configure checking if zlib is wanted... yes
346:info:configure checking for inflateEnd in -lz... yes
347:info:configure checking zlib.h usability... yes
348:info:configure checking zlib.h presence... yes
349:info:configure checking for zlib.h... yes
350:info:configure checking for inflateEnd in -lz... (cached) yes
351:info:configure checking zlib in /usr... ok
352:info:configure checking for stdlib.h... (cached) yes
353:info:configure checking for string.h... (cached) yes
354:info:configure checking for unistd.h... (cached) yes
355:info:configure checking for stdbool.h that conforms to C99... yes
356:info:configure checking for _Bool... yes
357:info:configure checking for inline... inline
358:info:configure checking for pid_t... yes
359:info:configure checking for size_t... yes
360:info:configure checking for ptrdiff_t... yes
361:info:configure checking host system type... i686-apple-darwin11.4.2
362:info:configure checking for struct sysinfo.totalram... no
363:info:configure checking whether sysctl is declared... yes
364:info:configure checking whether CTL_HW is declared... yes
365:info:configure checking whether HW_PHYSMEM is declared... yes
366:info:configure checking how to create a pax tar archive... gnutar
367:info:configure checking dependency style of /usr/bin/clang... (cached) gcc3
368:info:configure checking dependency style of /usr/bin/clang++... (cached) gcc3
369:info:configure configure: creating ./config.status
370:info:configure config.status: creating Makefile
371:info:configure config.status: creating src/Makefile
372:info:configure config.status: creating config.h
373:info:configure config.status: executing depfiles commands
374:info:configure
375:info:configure -- cufflinks 0.9.3 Configuration Results --
376:info:configure   C++ compiler:        /usr/bin/clang++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include
377:info:configure   GCC version:         Apple clang version 4.0 (tags/Apple/clang-421.0.57) (based on LLVM 3.1svn)
378:info:configure   Host System type:    i686-apple-darwin11.4.2
379:info:configure   Install prefix:      /opt/local
380:info:configure   Install eprefix:     ${prefix}
381:info:configure
382:info:configure   See config.h for further configuration information.
383:info:configure   Email <cole@cs.umd.edu> with questions and bug reports.
384:info:configure
385:debug:configure Privilege de-escalation not attempted as not running as root.
386:debug:build build phase started at Mon Jan 13 19:05:47 CST 2014
387:notice:build --->  Building cufflinks
388:debug:build Executing org.macports.build (cufflinks)
389: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_cufflinks/cufflinks/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7'
390:debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3" && /usr/bin/make -j8 -w all'
391:debug:build Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3" && /usr/bin/make -j8 -w all
392:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
393:info:build /usr/bin/make  all-recursive
394:info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
395:info:build Making all in src
396:info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3/src'
397:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
398:info:build     then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
399:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \
400:info:build     then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
401:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
402:info:build     then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
403:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT assemble.o -MD -MP -MF ".deps/assemble.Tpo" -c -o assemble.o assemble.cpp; \
404:info:build     then mv -f ".deps/assemble.Tpo" ".deps/assemble.Po"; else rm -f ".deps/assemble.Tpo"; exit 1; fi
405:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \
406:info:build     then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi
407:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT abundances.o -MD -MP -MF ".deps/abundances.Tpo" -c -o abundances.o abundances.cpp; \
408:info:build     then mv -f ".deps/abundances.Tpo" ".deps/abundances.Po"; else rm -f ".deps/abundances.Tpo"; exit 1; fi
409:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT scaffolds.o -MD -MP -MF ".deps/scaffolds.Tpo" -c -o scaffolds.o scaffolds.cpp; \
410:info:build     then mv -f ".deps/scaffolds.Tpo" ".deps/scaffolds.Po"; else rm -f ".deps/scaffolds.Tpo"; exit 1; fi
411:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT hits.o -MD -MP -MF ".deps/hits.Tpo" -c -o hits.o hits.cpp; \
412:info:build     then mv -f ".deps/hits.Tpo" ".deps/hits.Po"; else rm -f ".deps/hits.Tpo"; exit 1; fi
413:info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/opt/local/include -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -Os -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include -MT genes.o -MD -MP -MF ".deps/genes.Tpo" -c -o genes.o genes.cpp; \
414:info:build     then mv -f ".deps/genes.Tpo" ".deps/genes.Po"; else rm -f ".deps/genes.Tpo"; exit 1; fi
415:info:build In file included from genes.cpp:10:
416:info:build In file included from ./genes.h:17:
417:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
418:info:build         foreach(AugmentedCuffOp& op, aug_ops)
419:info:build                                  ^
420:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
421:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
422:info:build              ^
423:info:build In file included from genes.cpp:10:
424:info:build In file included from ./genes.h:18:
425:info:build In file included from ./abundances.h:22:
426:info:build In file included from ./bundles.h:21:
427:info:build In file included from ./gtf_tracking.h:12:
428:info:build In file included from ./gff.h:7:
429:info:build In file included from ./GFaSeqGet.h:4:
430:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
431:info:build  int result=-1;
432:info:build      ^
433:info:build In file included from differential.cpp:14:
434:info:build In file included from ./abundances.h:21:
435:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
436:info:build         foreach(AugmentedCuffOp& op, aug_ops)
437:info:build                                  ^
438:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
439:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
440:info:build              ^
441:info:build In file included from abundances.cpp:11:
442:info:build In file included from ./abundances.h:21:
443:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
444:info:build         foreach(AugmentedCuffOp& op, aug_ops)
445:info:build                                  ^
446:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
447:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
448:info:build              ^
449:info:build In file included from differential.cpp:14:
450:info:build In file included from ./abundances.h:22:
451:info:build In file included from ./bundles.h:21:
452:info:build In file included from ./gtf_tracking.h:12:
453:info:build In file included from ./gff.h:7:
454:info:build In file included from ./GFaSeqGet.h:4:
455:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
456:info:build  int result=-1;
457:info:build      ^
458:info:build In file included from abundances.cpp:11:
459:info:build In file included from ./abundances.h:22:
460:info:build In file included from ./bundles.h:21:
461:info:build In file included from ./gtf_tracking.h:12:
462:info:build In file included from ./gff.h:7:
463:info:build In file included from ./GFaSeqGet.h:4:
464:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
465:info:build  int result=-1;
466:info:build      ^
467:info:build In file included from scaffolds.cpp:13:
468:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
469:info:build         foreach(AugmentedCuffOp& op, aug_ops)
470:info:build                                  ^
471:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
472:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
473:info:build              ^
474:info:build scaffolds.cpp:1144:47: warning: '&&' within '||' [-Wlogical-op-parentheses]
475:info:build                 if (hit.left_alignment()->antisense_align() && strand() != CUFF_REV
476:info:build                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
477:info:build scaffolds.cpp:1144:47: note: place parentheses around the '&&' expression to silence this warning
478:info:build                 if (hit.left_alignment()->antisense_align() && strand() != CUFF_REV
479:info:build                                                             ^
480:info:build                     (                                                              )
481:info:build scaffolds.cpp:1145:50: warning: '&&' within '||' [-Wlogical-op-parentheses]
482:info:build                         || !(hit.left_alignment()->antisense_align()) && strand() == CUFF_REV)
483:info:build                         ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
484:info:build scaffolds.cpp:1145:50: note: place parentheses around the '&&' expression to silence this warning
485:info:build                         || !(hit.left_alignment()->antisense_align()) && strand() == CUFF_REV)
486:info:build                                                                       ^
487:info:build                            (                                                                 )
488:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
489:info:build    idxInsert(result, *item);
490:info:build    ^
491:info:build    this->
492:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
493:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
494:info:build                                 ^
495:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
496:info:build                                 uexons.Add(seg);
497:info:build                                        ^
498:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
499:info:build     void idxInsert(int idx, OBJ& item);
500:info:build          ^
501:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
502:info:build     setCapacity(this->fCapacity+list.fCount);
503:info:build     ^
504:info:build     this->
505:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
506:info:build                 qmrnas.Add(loc.mrnas);
507:info:build                        ^
508:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
509:info:build     void setCapacity(int NewCapacity);
510:info:build          ^
511:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
512:info:build     setCapacity(this->fCapacity+list.fCount);
513:info:build     ^
514:info:build     this->
515:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
516:info:build                 qmexons.Add(loc.mexons);
517:info:build                         ^
518:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
519:info:build     void setCapacity(int NewCapacity);
520:info:build          ^
521:info:build 2 warnings and 3 errors generated.
522:info:build make[2]: *** [genes.o] Error 1
523:info:build make[2]: *** Waiting for unfinished jobs....
524:info:build In file included from differential.cpp:15:
525:info:build In file included from ./differential.h:23:
526:info:build In file included from /opt/local/include/boost/graph/adjacency_list.hpp:45:
527:info:build In file included from /opt/local/include/boost/graph/named_graph.hpp:18:
528:info:build /opt/local/include/boost/multi_index/hashed_index.hpp:1381:10: error: no member named 'BOOST_FOREACH' in namespace 'boost'
529:info:build   boost::foreach::tag)
530:info:build   ~~~~~~~^
531:info:build ./common.h:26:25: note: expanded from macro 'foreach'
532:info:build #define foreach         BOOST_FOREACH
533:info:build                         ^
534:info:build In file included from differential.cpp:15:
535:info:build In file included from ./differential.h:23:
536:info:build In file included from /opt/local/include/boost/graph/adjacency_list.hpp:45:
537:info:build In file included from /opt/local/include/boost/graph/named_graph.hpp:18:
538:info:build /opt/local/include/boost/multi_index/hashed_index.hpp:1381:19: error: C++ requires a type specifier for all declarations
539:info:build   boost::foreach::tag)
540:info:build   ~~~~~           ^
541:info:build In file included from differential.cpp:15:
542:info:build ./differential.h:176:50: warning: unused variable 's2' [-Wunused-variable]
543:info:build             const vector<shared_ptr<Scaffold> >& s2 =  bundles[i-1]->ref_scaffolds();
544:info:build                                                  ^
545:info:build differential.cpp:632:8: warning: unused variable 'multi_transcript_locus' [-Wunused-variable]
546:info:build                 bool multi_transcript_locus = samples[i]->transcripts.abundances().size() > 1;
547:info:build                      ^
548:info:build In file included from differential.cpp:14:
549:info:build In file included from ./abundances.h:22:
550:info:build In file included from ./bundles.h:21:
551:info:build In file included from ./gtf_tracking.h:12:
552:info:build In file included from ./gff.h:7:
553:info:build In file included from ./GFaSeqGet.h:4:
554:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
555:info:build    idxInsert(result, *item);
556:info:build    ^
557:info:build    this->
558:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
559:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
560:info:build                                 ^
561:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
562:info:build                                 uexons.Add(seg);
563:info:build                                        ^
564:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
565:info:build     void idxInsert(int idx, OBJ& item);
566:info:build          ^
567:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
568:info:build     setCapacity(this->fCapacity+list.fCount);
569:info:build     ^
570:info:build     this->
571:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
572:info:build                 qmrnas.Add(loc.mrnas);
573:info:build                        ^
574:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
575:info:build     void setCapacity(int NewCapacity);
576:info:build          ^
577:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
578:info:build     setCapacity(this->fCapacity+list.fCount);
579:info:build     ^
580:info:build     this->
581:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
582:info:build                 qmexons.Add(loc.mexons);
583:info:build                         ^
584:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
585:info:build     void setCapacity(int NewCapacity);
586:info:build          ^
587:info:build In file included from assemble.cpp:48:
588:info:build In file included from ./assemble.h:26:
589:info:build In file included from ./bundles.h:20:
590:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
591:info:build         foreach(AugmentedCuffOp& op, aug_ops)
592:info:build                                  ^
593:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
594:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
595:info:build              ^
596:info:build In file included from assemble.cpp:48:
597:info:build In file included from ./assemble.h:26:
598:info:build In file included from ./bundles.h:21:
599:info:build In file included from ./gtf_tracking.h:12:
600:info:build In file included from ./gff.h:7:
601:info:build In file included from ./GFaSeqGet.h:4:
602:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
603:info:build  int result=-1;
604:info:build      ^
605:info:build 4 warnings and 5 errors generated.
606:info:build In file included from clustering.cpp:10:
607:info:build In file included from ./clustering.h:38:
608:info:build In file included from ./abundances.h:21:
609:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
610:info:build         foreach(AugmentedCuffOp& op, aug_ops)
611:info:build                                  ^
612:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
613:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
614:info:build              ^
615:info:build 3 warnings generated.
616:info:build make[2]: *** [differential.o] Error 1
617:info:build In file included from clustering.cpp:10:
618:info:build In file included from ./clustering.h:38:
619:info:build In file included from ./abundances.h:22:
620:info:build In file included from ./bundles.h:21:
621:info:build In file included from ./gtf_tracking.h:12:
622:info:build In file included from ./gff.h:7:
623:info:build In file included from ./GFaSeqGet.h:4:
624:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
625:info:build  int result=-1;
626:info:build      ^
627:info:build assemble.cpp:188:21: warning: unused variable 'a_for_b' [-Wunused-variable]
628:info:build                 ReachGraph::ANode a_for_b = b_to_a[b_id];
629:info:build                                   ^
630:info:build assemble.cpp:123:17: warning: unused variable 'hits_for_node' [-Wunused-variable]
631:info:build         HitsForNodeMap hits_for_node = get(vertex_name, dag);
632:info:build                        ^
633:info:build assemble.cpp:262:21: warning: unused variable 'a_for_b' [-Wunused-variable]
634:info:build                 ReachGraph::ANode a_for_b = bp.nodeFromANodeId(a_id_for_b);
635:info:build                                   ^
636:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
637:info:build    idxInsert(result, *item);
638:info:build    ^
639:info:build    this->
640:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
641:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
642:info:build                                 ^
643:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
644:info:build                                 uexons.Add(seg);
645:info:build                                        ^
646:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
647:info:build     void idxInsert(int idx, OBJ& item);
648:info:build          ^
649:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
650:info:build     setCapacity(this->fCapacity+list.fCount);
651:info:build     ^
652:info:build     this->
653:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
654:info:build                 qmrnas.Add(loc.mrnas);
655:info:build                        ^
656:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
657:info:build     void setCapacity(int NewCapacity);
658:info:build          ^
659:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
660:info:build     setCapacity(this->fCapacity+list.fCount);
661:info:build     ^
662:info:build     this->
663:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
664:info:build                 qmexons.Add(loc.mexons);
665:info:build                         ^
666:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
667:info:build     void setCapacity(int NewCapacity);
668:info:build          ^
669:info:build 2 warnings and 3 errors generated.
670:info:build make[2]: *** [clustering.o] Error 1
671:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
672:info:build    idxInsert(result, *item);
673:info:build    ^
674:info:build    this->
675:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
676:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
677:info:build                                 ^
678:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
679:info:build                                 uexons.Add(seg);
680:info:build                                        ^
681:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
682:info:build     void idxInsert(int idx, OBJ& item);
683:info:build          ^
684:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
685:info:build     setCapacity(this->fCapacity+list.fCount);
686:info:build     ^
687:info:build     this->
688:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
689:info:build                 qmrnas.Add(loc.mrnas);
690:info:build                        ^
691:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
692:info:build     void setCapacity(int NewCapacity);
693:info:build          ^
694:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
695:info:build     setCapacity(this->fCapacity+list.fCount);
696:info:build     ^
697:info:build     this->
698:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
699:info:build                 qmexons.Add(loc.mexons);
700:info:build                         ^
701:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
702:info:build     void setCapacity(int NewCapacity);
703:info:build          ^
704:info:build In file included from assemble.cpp:48:
705:info:build In file included from ./assemble.h:26:
706:info:build In file included from ./bundles.h:21:
707:info:build In file included from ./gtf_tracking.h:12:
708:info:build In file included from ./gff.h:7:
709:info:build In file included from ./GFaSeqGet.h:4:
710:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
711:info:build    idxInsert(result, *item);
712:info:build    ^
713:info:build    this->
714:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
715:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
716:info:build                                 ^
717:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
718:info:build                                 uexons.Add(seg);
719:info:build                                        ^
720:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
721:info:build     void idxInsert(int idx, OBJ& item);
722:info:build          ^
723:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
724:info:build     setCapacity(this->fCapacity+list.fCount);
725:info:build     ^
726:info:build     this->
727:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
728:info:build                 qmrnas.Add(loc.mrnas);
729:info:build                        ^
730:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
731:info:build     void setCapacity(int NewCapacity);
732:info:build          ^
733:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
734:info:build     setCapacity(this->fCapacity+list.fCount);
735:info:build     ^
736:info:build     this->
737:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
738:info:build                 qmexons.Add(loc.mexons);
739:info:build                         ^
740:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
741:info:build     void setCapacity(int NewCapacity);
742:info:build          ^
743:info:build 2 warnings and 3 errors generated.
744:info:build make[2]: *** [abundances.o] Error 1
745:info:build In file included from assemble.cpp:19:
746:info:build In file included from ./lemon/topology.h:22:
747:info:build In file included from ./lemon/dfs.h:26:
748:info:build In file included from ./lemon/list_graph.h:26:
749:info:build ./lemon/bits/base_extender.h:362:11: error: use of undeclared identifier 'aNode'
750:info:build                         return aNode(edge);
751:info:build                                ^
752:info:build                                this->
753:info:build assemble.cpp:258:28: note: in instantiation of member function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::source' requested here
754:info:build                 ReachGraph::ANode a = bp.source(i);
755:info:build                                          ^
756:info:build ./lemon/smart_graph.h:912:8: note: must qualify identifier to find this declaration in dependent base class
757:info:build                 Node aNode(const UEdge& edge) const {
758:info:build                      ^
759:info:build ./lemon/smart_graph.h:919:15: note: must qualify identifier to find this declaration in dependent base class
760:info:build                 static bool aNode(const Node& node) {
761:info:build                             ^
762:info:build In file included from assemble.cpp:19:
763:info:build In file included from ./lemon/topology.h:22:
764:info:build In file included from ./lemon/dfs.h:26:
765:info:build In file included from ./lemon/list_graph.h:26:
766:info:build ./lemon/bits/base_extender.h:365:11: error: use of undeclared identifier 'bNode'
767:info:build                         return bNode(edge);
768:info:build                                ^
769:info:build                                this->
770:info:build assemble.cpp:259:28: note: in instantiation of member function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::target' requested here
771:info:build                 ReachGraph::BNode b = bp.target(i);
772:info:build                                          ^
773:info:build ./lemon/smart_graph.h:915:8: note: must qualify identifier to find this declaration in dependent base class
774:info:build                 Node bNode(const UEdge& edge) const {
775:info:build                      ^
776:info:build ./lemon/smart_graph.h:923:15: note: must qualify identifier to find this declaration in dependent base class
777:info:build                 static bool bNode(const Node& node) {
778:info:build                             ^
779:info:build 5 warnings and 5 errors generated.
780:info:build make[2]: *** [assemble.o] Error 1
781:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3/src'
782:info:build make[1]: *** [all-recursive] Error 1
783:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
784:info:build make: *** [all] Error 2
785:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3'
786:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/work/cufflinks-0.9.3" && /usr/bin/make -j8 -w all
787:info:build Exit code: 2
788:error:build org.macports.build for port cufflinks returned: command execution failed
789:debug:build Error code: CHILDSTATUS 26040 2
790:debug:build Backtrace: command execution failed
791    while executing
792"system -nice 0 $fullcmdstring"
793    ("eval" body line 1)
794    invoked from within
795"eval system $notty $nice \$fullcmdstring"
796    invoked from within
797"command_exec build"
798    (procedure "portbuild::build_main" line 8)
799    invoked from within
800"$procedure $targetname"
801:info:build Warning: targets not executed for cufflinks: org.macports.activate org.macports.build org.macports.destroot org.macports.install
802:notice:build Please see the log file for port cufflinks for details:
803    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log