| 1 | version: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 | |
|---|
