Ticket #38969: main.log

File main.log, 48.4 KB (added by graceqy@…, 12 years ago)
Line 
1version:1
2:debug:main epoch: in tree: 0 installed: 0
3:debug:main zlib 1.2.7_0 exists in the ports tree
4:debug:main zlib 1.2.7_0  is the latest installed
5:debug:main zlib 1.2.7_0  is active
6:debug:main Merging existing variants '' into variants
7:debug:main new fully merged portvariants:
8:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/zlib
9:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
10:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
11:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
12:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
13:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
14:debug:main adding the default universal variant
15:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
16:debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
17:debug:main epoch: in tree: 0 installed: 0
18:debug:main samtools 0.1.18_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 org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
26:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
27:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
28:debug:main universal_variant is false, so not adding the default universal variant
29:debug:main No need to upgrade! samtools 0.1.18_0 >= samtools 0.1.18_0
30:debug:main epoch: in tree: 0 installed: 0
31:debug:main ncurses 5.9_2 exists in the ports tree
32:debug:main ncurses 5.9_2  is the latest installed
33:debug:main ncurses 5.9_2  is active
34:debug:main Merging existing variants '' into variants
35:debug:main new fully merged portvariants:
36:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/ncurses
37:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
38:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
39:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
40:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
41:debug:main adding the default universal variant
42:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
43:debug:main No need to upgrade! ncurses 5.9_2 >= ncurses 5.9_2
44:debug:main epoch: in tree: 0 installed: 0
45:debug:main boost 1.53.0_1 exists in the ports tree
46:debug:main boost 1.53.0_1 +no_single+no_static+python27 is the latest installed
47:debug:main boost 1.53.0_1 +no_single+no_static+python27 is active
48:debug:main Merging existing variants '+no_single+no_static+python27' into variants
49:debug:main new fully merged portvariants: no_static + no_single + python27 +
50:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/boost
51:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
52:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
53:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
54:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
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 No need to upgrade! boost 1.53.0_1 >= boost 1.53.0_1
61:debug:main epoch: in tree: 0 installed: 0
62:debug:main expat 2.1.0_0 exists in the ports tree
63:debug:main expat 2.1.0_0  is the latest installed
64:debug:main expat 2.1.0_0  is active
65:debug:main Merging existing variants '' into variants
66:debug:main new fully merged portvariants:
67:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/expat
68:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
69:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
70:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
71:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
72:debug:main adding the default universal variant
73:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
74:debug:main No need to upgrade! expat 2.1.0_0 >= expat 2.1.0_0
75:debug:main epoch: in tree: 0 installed: 0
76:debug:main bzip2 1.0.6_0 exists in the ports tree
77:debug:main bzip2 1.0.6_0  is the latest installed
78:debug:main bzip2 1.0.6_0  is active
79:debug:main Merging existing variants '' into variants
80:debug:main new fully merged portvariants:
81:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/bzip2
82:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
83:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
84:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
85:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
86:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
87:debug:main universal variant already exists, so not adding the default one
88:debug:main No need to upgrade! bzip2 1.0.6_0 >= bzip2 1.0.6_0
89:debug:main epoch: in tree: 0 installed: 0
90:debug:main libiconv 1.14_0 exists in the ports tree
91:debug:main libiconv 1.14_0  is the latest installed
92:debug:main libiconv 1.14_0  is active
93:debug:main Merging existing variants '' into variants
94:debug:main new fully merged portvariants:
95:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/textproc/libiconv
96:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
97:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
98:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
99:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
100:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
101:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
102:debug:main universal variant already exists, so not adding the default one
103:debug:main No need to upgrade! libiconv 1.14_0 >= libiconv 1.14_0
104:debug:main epoch: in tree: 0 installed: 0
105:debug:main icu 49.1.2_1 exists in the ports tree
106:debug:main icu 49.1.2_1  is the latest installed
107:debug:main icu 49.1.2_1  is active
108:debug:main Merging existing variants '' into variants
109:debug:main new fully merged portvariants:
110:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/icu
111:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
112:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
113:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
114:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
115:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
116:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
117:debug:main universal variant already exists, so not adding the default one
118:debug:main No need to upgrade! icu 49.1.2_1 >= icu 49.1.2_1
119:debug:main epoch: in tree: 2 installed: 2
120:debug:main python27 2.7.3_1 exists in the ports tree
121:debug:main python27 2.7.3_1  is the latest installed
122:debug:main python27 2.7.3_1  is active
123:debug:main Merging existing variants '' into variants
124:debug:main new fully merged portvariants:
125:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/lang/python27
126:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
127:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
128:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
129:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
130:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/select-1.0.tcl
131:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
132:debug:main universal variant already exists, so not adding the default one
133:debug:main No need to upgrade! python27 2.7.3_1 >= python27 2.7.3_1
134:debug:main epoch: in tree: 0 installed: 0
135:debug:main gettext 0.18.2.1_0 exists in the ports tree
136:debug:main gettext 0.18.2.1_0  is the latest installed
137:debug:main gettext 0.18.2.1_0  is active
138:debug:main Merging existing variants '' into variants
139:debug:main new fully merged portvariants:
140:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/gettext
141:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
142:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
143:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
144:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
145:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/compiler_blacklist_versions-1.0.tcl
146:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
147:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
148:debug:main compiler clang 318.0.54 not blacklisted because does not match {clang < 211.10.1}
149:debug:main universal variant already exists, so not adding the default one
150:debug:main No need to upgrade! gettext 0.18.2.1_0 >= gettext 0.18.2.1_0
151:debug:main epoch: in tree: 1 installed: 1
152:debug:main openssl 1.0.1e_1 exists in the ports tree
153:debug:main openssl 1.0.1e_1  is the latest installed
154:debug:main openssl 1.0.1e_1  is active
155:debug:main Merging existing variants '' into variants
156:debug:main new fully merged portvariants:
157:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/openssl
158:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
159:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
160:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
161:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
162:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
163:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
164:debug:main universal variant already exists, so not adding the default one
165:debug:main No need to upgrade! openssl 1.0.1e_1 >= openssl 1.0.1e_1
166:debug:main epoch: in tree: 0 installed: 0
167:debug:main sqlite3 3.7.16.1_0 exists in the ports tree
168:debug:main sqlite3 3.7.16.1_0  is the latest installed
169:debug:main sqlite3 3.7.16.1_0  is active
170:debug:main Merging existing variants '' into variants
171:debug:main new fully merged portvariants:
172:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/databases/sqlite3
173:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
174:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
175:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
176:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
177:debug:main adding the default universal variant
178:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
179:debug:main No need to upgrade! sqlite3 3.7.16.1_0 >= sqlite3 3.7.16.1_0
180:debug:main epoch: in tree: 20090923 installed: 20090923
181:debug:main libedit 20121213-3.0_0 exists in the ports tree
182:debug:main libedit 20121213-3.0_0  is the latest installed
183:debug:main libedit 20121213-3.0_0  is active
184:debug:main Merging existing variants '' into variants
185:debug:main new fully merged portvariants:
186:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/devel/libedit
187:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
188:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
189:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
190:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
191:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
192:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
193:debug:main universal variant already exists, so not adding the default one
194:debug:main No need to upgrade! libedit 20121213-3.0_0 >= libedit 20121213-3.0_0
195:debug:main epoch: in tree: 0 installed: 0
196:debug:main db46 4.6.21_8 exists in the ports tree
197:debug:main db46 4.6.21_8  is the latest installed
198:debug:main db46 4.6.21_8  is active
199:debug:main Merging existing variants '' into variants
200:debug:main new fully merged portvariants:
201:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/databases/db46
202:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
203:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
204:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
205:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
206:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/muniversal-1.0.tcl
207:debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
208:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/select-1.0.tcl
209:debug:main universal variant already exists, so not adding the default one
210:debug:main No need to upgrade! db46 4.6.21_8 >= db46 4.6.21_8
211:debug:main epoch: in tree: 0 installed: 0
212:debug:main db_select 0.1_2 exists in the ports tree
213:debug:main db_select 0.1_2  is the latest installed
214:debug:main db_select 0.1_2  is active
215:debug:main Merging existing variants '' into variants
216:debug:main new fully merged portvariants:
217:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/sysutils/db_select
218:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
219:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
220:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
221:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
222:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/select-1.0.tcl
223:debug:main universal_variant is false, so not adding the default universal variant
224:debug:main No need to upgrade! db_select 0.1_2 >= db_select 0.1_2
225:debug:main epoch: in tree: 0 installed: 0
226:debug:main python_select 0.3_2 exists in the ports tree
227:debug:main python_select 0.3_2  is the latest installed
228:debug:main python_select 0.3_2  is active
229:debug:main Merging existing variants '' into variants
230:debug:main new fully merged portvariants:
231:debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/sysutils/python_select
232:debug:main OS darwin/11.4.2 (Mac OS X 10.7) arch i386
233:debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided
234:debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided
235:debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided
236:debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/select-1.0.tcl
237:debug:main universal_variant is false, so not adding the default universal variant
238:debug:main No need to upgrade! python_select 0.3_2 >= python_select 0.3_2
239:msg:main --->  Computing dependencies for cufflinks:info:main .:debug:main cufflinks has no conflicts
240:debug:main Searching for dependency: zlib
241:debug:main Found Dependency: receipt exists for zlib
242:debug:main Searching for dependency: samtools
243:debug:main Found Dependency: receipt exists for samtools
244:debug:main Searching for dependency: boost
245:debug:main Found Dependency: receipt exists for boost
246:msg:main
247:debug:main Executing org.macports.main (cufflinks)
248:debug:main changing euid/egid - current euid: 0 - current egid: 0
249:debug:main egid changed to: 501
250:debug:main euid changed to: 502
251:debug:archivefetch archivefetch phase started at Tue Apr 30 15:40:03 EDT 2013
252:msg:archivefetch --->  Fetching archive for cufflinks
253:debug:archivefetch Executing org.macports.archivefetch (cufflinks)
254:debug:archivefetch euid/egid changed to: 0/0
255:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
256:debug:archivefetch euid/egid changed to: 502/501
257:info:archivefetch --->  cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
258:msg:archivefetch --->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/cufflinks
259:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
260:msg:archivefetch --->  Attempting to fetch cufflinks-0.9.3_0.darwin_11.x86_64.tbz2 from http://lil.fr.packages.macports.org/cufflinks
261:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
262: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
263:debug:archivefetch Fetching archive failed:: The requested URL returned error: 404
264:debug:archivefetch Privilege de-escalation not attempted as not running as root.
265:debug:fetch fetch phase started at Tue Apr 30 15:40:06 EDT 2013
266:notice:fetch --->  Fetching distfiles for cufflinks
267:debug:fetch Executing org.macports.fetch (cufflinks)
268:debug:fetch Privilege de-escalation not attempted as not running as root.
269:debug:checksum checksum phase started at Tue Apr 30 15:40:06 EDT 2013
270:notice:checksum --->  Verifying checksum(s) for cufflinks
271:debug:checksum Executing org.macports.checksum (cufflinks)
272:info:checksum --->  Checksumming cufflinks-0.9.3.tar.gz
273:debug:checksum Correct (sha1) checksum for cufflinks-0.9.3.tar.gz
274:debug:checksum Correct (rmd160) checksum for cufflinks-0.9.3.tar.gz
275:debug:checksum Privilege de-escalation not attempted as not running as root.
276:debug:extract extract phase started at Tue Apr 30 15:40:06 EDT 2013
277:notice:extract --->  Extracting cufflinks
278:debug:extract Executing org.macports.extract (cufflinks)
279:info:extract --->  Extracting cufflinks-0.9.3.tar.gz
280:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/cufflinks/cufflinks-0.9.3.tar.gz'
281: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'
282: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 -'
283: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 -
284:debug:extract euid/egid changed to: 0/0
285: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
286:debug:extract euid/egid changed to: 502/501
287:debug:extract Privilege de-escalation not attempted as not running as root.
288:debug:patch patch phase started at Tue Apr 30 15:40:06 EDT 2013
289:debug:patch Executing org.macports.patch (cufflinks)
290:debug:patch Privilege de-escalation not attempted as not running as root.
291:debug:configure configure phase started at Tue Apr 30 15:40:06 EDT 2013
292:notice:configure --->  Configuring cufflinks
293:debug:configure Using compiler 'Mac OS X clang'
294:debug:configure Executing org.macports.configure (cufflinks)
295:debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -arch x86_64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -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 -O2 -m64' LDFLAGS='-L/opt/local/lib -arch x86_64' OBJC='/usr/bin/clang' FCFLAGS='-pipe -O2 -m64' INSTALL='/usr/bin/install -c' OBJCFLAGS='-pipe -O2 -arch x86_64' FFLAGS='-pipe -O2 -m64' CC_PRINT_OPTIONS='YES' CC='/usr/bin/clang'
296: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'
297: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
298:info:configure checking for a BSD-compatible install... /usr/bin/install -c
299:info:configure checking whether build environment is sane... yes
300:info:configure checking for gawk... no
301:info:configure checking for mawk... no
302:info:configure checking for nawk... no
303:info:configure checking for awk... awk
304:info:configure checking whether make sets $(MAKE)... yes
305:info:configure checking for gawk... (cached) awk
306:info:configure checking for C++ compiler default output file name... a.out
307:info:configure checking whether the C++ compiler works... yes
308:info:configure checking whether we are cross compiling... no
309:info:configure checking for suffix of executables...
310:info:configure checking for suffix of object files... o
311:info:configure checking whether we are using the GNU C++ compiler... yes
312:info:configure checking whether /usr/bin/clang++ accepts -g... yes
313:info:configure checking for style of include used by make... GNU
314:info:configure checking dependency style of /usr/bin/clang++... gcc3
315:info:configure checking for gcc... /usr/bin/clang
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 /usr/bin/clang option to accept ANSI C... none needed
319:info:configure checking dependency style of /usr/bin/clang... gcc3
320:info:configure checking whether make sets $(MAKE)... (cached) yes
321:info:configure checking for ranlib... ranlib
322:info:configure checking for a BSD-compatible install... /usr/bin/install -c
323:info:configure checking for boostlib >= 1.38.0... yes
324:info:configure checking for bamlib... yes
325:info:configure checking build system type... i686-apple-darwin11.4.2
326:info:configure checking whether the Boost::Thread library is available... yes
327:info:configure checking for exit in -lboost_thread-mt... yes
328:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
329:info:configure checking for egrep... grep -E
330:info:configure checking for ANSI C header files... yes
331:info:configure checking for sys/types.h... yes
332:info:configure checking for sys/stat.h... yes
333:info:configure checking for stdlib.h... yes
334:info:configure checking for string.h... yes
335:info:configure checking for memory.h... yes
336:info:configure checking for strings.h... yes
337:info:configure checking for inttypes.h... yes
338:info:configure checking for stdint.h... yes
339:info:configure checking for unistd.h... yes
340:info:configure checking if zlib is wanted... yes
341:info:configure checking for inflateEnd in -lz... yes
342:info:configure checking zlib.h usability... yes
343:info:configure checking zlib.h presence... yes
344:info:configure checking for zlib.h... yes
345:info:configure checking for inflateEnd in -lz... (cached) yes
346:info:configure checking zlib in /usr... ok
347:info:configure checking for stdlib.h... (cached) yes
348:info:configure checking for string.h... (cached) yes
349:info:configure checking for unistd.h... (cached) yes
350:info:configure checking for stdbool.h that conforms to C99... yes
351:info:configure checking for _Bool... yes
352:info:configure checking for inline... inline
353:info:configure checking for pid_t... yes
354:info:configure checking for size_t... yes
355:info:configure checking for ptrdiff_t... yes
356:info:configure checking host system type... i686-apple-darwin11.4.2
357:info:configure checking for struct sysinfo.totalram... no
358:info:configure checking whether sysctl is declared... yes
359:info:configure checking whether CTL_HW is declared... yes
360:info:configure checking whether HW_PHYSMEM is declared... yes
361:info:configure checking how to create a pax tar archive... gnutar
362:info:configure checking dependency style of /usr/bin/clang... (cached) gcc3
363:info:configure checking dependency style of /usr/bin/clang++... (cached) gcc3
364:info:configure configure: creating ./config.status
365:info:configure config.status: creating Makefile
366:info:configure config.status: creating src/Makefile
367:info:configure config.status: creating config.h
368:info:configure config.status: executing depfiles commands
369:info:configure
370:info:configure -- cufflinks 0.9.3 Configuration Results --
371:info:configure   C++ compiler:        /usr/bin/clang++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG  -pthread -I/opt/local/include -I/opt/local/include
372:info:configure   GCC version:         Apple clang version 3.1 (tags/Apple/clang-318.0.54) (based on LLVM 3.1svn)
373:info:configure   Host System type:    i686-apple-darwin11.4.2
374:info:configure   Install prefix:      /opt/local
375:info:configure   Install eprefix:     ${prefix}
376:info:configure
377:info:configure   See config.h for further configuration information.
378:info:configure   Email <cole@cs.umd.edu> with questions and bug reports.
379:info:configure
380:debug:configure Privilege de-escalation not attempted as not running as root.
381:debug:build build phase started at Tue Apr 30 15:40:16 EDT 2013
382:notice:build --->  Building cufflinks
383:debug:build Executing org.macports.build (cufflinks)
384: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'
385: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 -j4 -w all'
386: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 -j4 -w all
387: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'
388:info:build /usr/bin/make  all-recursive
389: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'
390:info:build Making all in src
391: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'
392: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 -O2 -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; \
393:info:build     then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
394: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 -O2 -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; \
395:info:build     then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
396: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 -O2 -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; \
397:info:build     then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
398: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 -O2 -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; \
399:info:build     then mv -f ".deps/assemble.Tpo" ".deps/assemble.Po"; else rm -f ".deps/assemble.Tpo"; exit 1; fi
400:info:build In file included from differential.cpp:14:
401:info:build In file included from ./abundances.h:21:
402:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
403:info:build         foreach(AugmentedCuffOp& op, aug_ops)
404:info:build                                  ^
405:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
406:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
407:info:build              ^
408:info:build In file included from clustering.cpp:10:
409:info:build In file included from ./clustering.h:38:
410:info:build In file included from ./abundances.h:21:
411:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
412:info:build         foreach(AugmentedCuffOp& op, aug_ops)
413:info:build                                  ^
414:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
415:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
416:info:build              ^
417:info:build In file included from assemble.cpp:48:
418:info:build In file included from ./assemble.h:26:
419:info:build In file included from ./bundles.h:20:
420:info:build ./scaffolds.h:247:34: warning: unused variable 'op' [-Wunused-variable]
421:info:build         foreach(AugmentedCuffOp& op, aug_ops)
422:info:build                                  ^
423:info:build /opt/local/include/boost/foreach.hpp:1108:14: note: expanded from macro 'BOOST_FOREACH'
424:info:build         for (VAR = BOOST_FOREACH_DEREF(COL); !BOOST_FOREACH_ID(_foreach_continue); BOOST_FOREACH_ID(_foreach_continue) = true)
425:info:build              ^
426:info:build In file included from differential.cpp:14:
427:info:build In file included from ./abundances.h:22:
428:info:build In file included from ./bundles.h:21:
429:info:build In file included from ./gtf_tracking.h:12:
430:info:build In file included from ./gff.h:7:
431:info:build In file included from ./GFaSeqGet.h:4:
432:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
433:info:build  int result=-1;
434:info:build      ^
435:info:build In file included from clustering.cpp:10:
436:info:build In file included from ./clustering.h:38:
437:info:build In file included from ./abundances.h:22:
438:info:build In file included from ./bundles.h:21:
439:info:build In file included from ./gtf_tracking.h:12:
440:info:build In file included from ./gff.h:7:
441:info:build In file included from ./GFaSeqGet.h:4:
442:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
443:info:build  int result=-1;
444:info:build      ^
445:info:build In file included from assemble.cpp:48:
446:info:build In file included from ./assemble.h:26:
447:info:build In file included from ./bundles.h:21:
448:info:build In file included from ./gtf_tracking.h:12:
449:info:build In file included from ./gff.h:7:
450:info:build In file included from ./GFaSeqGet.h:4:
451:info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable]
452:info:build  int result=-1;
453:info:build      ^
454:info:build In file included from differential.cpp:15:
455:info:build In file included from ./differential.h:23:
456:info:build In file included from /opt/local/include/boost/graph/adjacency_list.hpp:45:
457:info:build In file included from /opt/local/include/boost/graph/named_graph.hpp:17:
458:info:build /opt/local/include/boost/multi_index/hashed_index.hpp:1254:10: error: no member named 'BOOST_FOREACH' in namespace 'boost'
459:info:build   boost::foreach::tag)
460:info:build   ~~~~~~~^
461:info:build ./common.h:26:25: note: expanded from macro 'foreach'
462:info:build #define foreach         BOOST_FOREACH
463:info:build                         ^
464:info:build In file included from differential.cpp:15:
465:info:build In file included from ./differential.h:23:
466:info:build In file included from /opt/local/include/boost/graph/adjacency_list.hpp:45:
467:info:build In file included from /opt/local/include/boost/graph/named_graph.hpp:17:
468:info:build /opt/local/include/boost/multi_index/hashed_index.hpp:1254:19: error: C++ requires a type specifier for all declarations
469:info:build   boost::foreach::tag)
470:info:build   ~~~~~           ^
471:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
472:info:build    idxInsert(result, *item);
473:info:build    ^
474:info:build    this->
475:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
476:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
477:info:build                                 ^
478:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
479:info:build                                 uexons.Add(seg);
480:info:build                                        ^
481:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
482:info:build     void idxInsert(int idx, OBJ& item);
483:info:build          ^
484:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
485:info:build     setCapacity(this->fCapacity+list.fCount);
486:info:build     ^
487:info:build     this->
488:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
489:info:build                 qmrnas.Add(loc.mrnas);
490:info:build                        ^
491:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
492:info:build     void setCapacity(int NewCapacity);
493:info:build          ^
494:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
495:info:build     setCapacity(this->fCapacity+list.fCount);
496:info:build     ^
497:info:build     this->
498:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
499:info:build                 qmexons.Add(loc.mexons);
500:info:build                         ^
501:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
502:info:build     void setCapacity(int NewCapacity);
503:info:build          ^
504:info:build 2 warnings and 3 errors generated.
505:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
506:info:build    idxInsert(result, *item);
507:info:build    ^
508:info:build    this->
509:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
510:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
511:info:build                                 ^
512:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
513:info:build                                 uexons.Add(seg);
514:info:build                                        ^
515:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
516:info:build     void idxInsert(int idx, OBJ& item);
517:info:build          ^
518:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
519:info:build     setCapacity(this->fCapacity+list.fCount);
520:info:build     ^
521:info:build     this->
522:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
523:info:build                 qmrnas.Add(loc.mrnas);
524:info:build                        ^
525:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
526:info:build     void setCapacity(int NewCapacity);
527:info:build          ^
528:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
529:info:build     setCapacity(this->fCapacity+list.fCount);
530:info:build     ^
531:info:build     this->
532:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
533:info:build                 qmexons.Add(loc.mexons);
534:info:build                         ^
535:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
536:info:build     void setCapacity(int NewCapacity);
537:info:build          ^
538:info:build make[2]: *** [clustering.o] Error 1
539:info:build make[2]: *** Waiting for unfinished jobs....
540:info:build In file included from differential.cpp:15:
541:info:build ./differential.h:176:50: warning: unused variable 's2' [-Wunused-variable]
542:info:build             const vector<shared_ptr<Scaffold> >& s2 =  bundles[i-1]->ref_scaffolds();
543:info:build                                                  ^
544:info:build In file included from assemble.cpp:19:
545:info:build In file included from ./lemon/topology.h:22:
546:info:build In file included from ./lemon/dfs.h:26:
547:info:build In file included from ./lemon/list_graph.h:26:
548:info:build ./lemon/bits/base_extender.h:362:11: error: use of undeclared identifier 'aNode'
549:info:build                         return aNode(edge);
550:info:build                                ^
551:info:build                                this->
552:info:build assemble.cpp:258:28: note: in instantiation of member function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::source' requested here
553:info:build                 ReachGraph::ANode a = bp.source(i);
554:info:build                                          ^
555:info:build ./lemon/smart_graph.h:912:8: note: must qualify identifier to find this declaration in dependent base class
556:info:build                 Node aNode(const UEdge& edge) const {
557:info:build                      ^
558:info:build ./lemon/smart_graph.h:919:15: note: must qualify identifier to find this declaration in dependent base class
559:info:build                 static bool aNode(const Node& node) {
560:info:build                             ^
561:info:build In file included from assemble.cpp:19:
562:info:build In file included from ./lemon/topology.h:22:
563:info:build In file included from ./lemon/dfs.h:26:
564:info:build In file included from ./lemon/list_graph.h:26:
565:info:build ./lemon/bits/base_extender.h:365:11: error: use of undeclared identifier 'bNode'
566:info:build                         return bNode(edge);
567:info:build                                ^
568:info:build                                this->
569:info:build assemble.cpp:259:28: note: in instantiation of member function 'lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::target' requested here
570:info:build                 ReachGraph::BNode b = bp.target(i);
571:info:build                                          ^
572:info:build ./lemon/smart_graph.h:915:8: note: must qualify identifier to find this declaration in dependent base class
573:info:build                 Node bNode(const UEdge& edge) const {
574:info:build                      ^
575:info:build ./lemon/smart_graph.h:923:15: note: must qualify identifier to find this declaration in dependent base class
576:info:build                 static bool bNode(const Node& node) {
577:info:build                             ^
578:info:build 2 warnings and 5 errors generated.
579:info:build make[2]: *** [assemble.o] Error 1
580:info:build differential.cpp:632:8: warning: unused variable 'multi_transcript_locus' [-Wunused-variable]
581:info:build                 bool multi_transcript_locus = samples[i]->transcripts.abundances().size() > 1;
582:info:build                      ^
583:info:build In file included from differential.cpp:14:
584:info:build In file included from ./abundances.h:22:
585:info:build In file included from ./bundles.h:21:
586:info:build In file included from ./gtf_tracking.h:12:
587:info:build In file included from ./gff.h:7:
588:info:build In file included from ./GFaSeqGet.h:4:
589:info:build ./GList.hh:507:4: error: use of undeclared identifier 'idxInsert'
590:info:build    idxInsert(result, *item);
591:info:build    ^
592:info:build    this->
593:info:build ./GList.hh:107:33: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
594:info:build     int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it
595:info:build                                 ^
596:info:build ./gtf_tracking.h:314:12: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
597:info:build                                 uexons.Add(seg);
598:info:build                                        ^
599:info:build ./GList.hh:52:10: note: must qualify identifier to find this declaration in dependent base class
600:info:build     void idxInsert(int idx, OBJ& item);
601:info:build          ^
602:info:build ./GList.hh:772:5: error: use of undeclared identifier 'setCapacity'
603:info:build     setCapacity(this->fCapacity+list.fCount);
604:info:build     ^
605:info:build     this->
606:info:build ./gtf_tracking.h:650:10: note: in instantiation of member function 'GList<GffObj>::Add' requested here
607:info:build                 qmrnas.Add(loc.mrnas);
608:info:build                        ^
609:info:build ./GList.hh:171:10: note: must qualify identifier to find this declaration in dependent base class
610:info:build     void setCapacity(int NewCapacity);
611:info:build          ^
612:info:build ./GList.hh:537:5: error: use of undeclared identifier 'setCapacity'
613:info:build     setCapacity(this->fCapacity+list.fCount);
614:info:build     ^
615:info:build     this->
616:info:build ./gtf_tracking.h:653:11: note: in instantiation of member function 'GArray<GSeg>::Add' requested here
617:info:build                 qmexons.Add(loc.mexons);
618:info:build                         ^
619:info:build ./GList.hh:76:10: note: must qualify identifier to find this declaration in dependent base class
620:info:build     void setCapacity(int NewCapacity);
621:info:build          ^
622:info:build 4 warnings and 5 errors generated.
623:info:build make[2]: *** [differential.o] Error 1
624: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'
625:info:build make[1]: *** [all-recursive] Error 1
626: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'
627:info:build make: *** [all] Error 2
628: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'
629: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 -j4 -w all
630:info:build Exit code: 2
631:error:build org.macports.build for port cufflinks returned: command execution failed
632:debug:build Error code: CHILDSTATUS 6186 2
633:debug:build Backtrace: command execution failed
634    while executing
635"system -nice 0 $fullcmdstring"
636    ("eval" body line 1)
637    invoked from within
638"eval system $notty $nice \$fullcmdstring"
639    invoked from within
640"command_exec build"
641    (procedure "portbuild::build_main" line 8)
642    invoked from within
643"$procedure $targetname"
644:info:build Warning: targets not executed for cufflinks: org.macports.activate org.macports.build org.macports.destroot org.macports.install
645:notice:build Please see the log file for port cufflinks for details:
646    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cufflinks/cufflinks/main.log
647