| 1 | version:1 |
|---|
| 2 | :debug:main epoch: in tree: 0 installed: 0 |
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| 3 | :debug:main zlib 1.2.7_0 exists in the ports tree |
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| 4 | :debug:main zlib 1.2.7_0 is the latest installed |
|---|
| 5 | :debug:main zlib 1.2.7_0 is active |
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| 6 | :debug:main Merging existing variants '' into variants |
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| 7 | :debug:main new fully merged portvariants: |
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| 8 | :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/archivers/zlib |
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| 9 | :debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386 |
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| 10 | :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided |
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| 11 | :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided |
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| 12 | :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided |
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| 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 |
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| 14 | :debug:main adding the default universal variant |
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| 15 | :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf |
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| 16 | :debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0 |
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| 17 | :debug:main epoch: in tree: 0 installed: 0 |
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| 18 | :debug:main samtools 0.1.17_0 exists in the ports tree |
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| 19 | :debug:main samtools 0.1.17_0 is the latest installed |
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| 20 | :debug:main samtools 0.1.17_0 is active |
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| 21 | :debug:main Merging existing variants '' into variants |
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| 22 | :debug:main new fully merged portvariants: |
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| 23 | :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/samtools |
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| 24 | :debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386 |
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| 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 |
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| 27 | :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided |
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| 28 | :debug:main universal_variant is false, so not adding the default universal variant |
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| 29 | :debug:main No need to upgrade! samtools 0.1.17_0 >= samtools 0.1.17_0 |
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| 30 | :debug:main epoch: in tree: 0 installed: 0 |
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| 31 | :debug:main bowtie 0.12.7_0 exists in the ports tree |
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| 32 | :debug:main bowtie 0.12.7_0 is the latest installed |
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| 33 | :debug:main bowtie 0.12.7_0 is active |
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| 34 | :debug:main Merging existing variants '' into variants |
|---|
| 35 | :debug:main new fully merged portvariants: |
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| 36 | :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/science/bowtie |
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| 37 | :debug:main OS darwin/11.4.0 (Mac OS X 10.7) arch i386 |
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| 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 Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf |
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| 42 | :debug:main universal variant already exists, so not adding the default one |
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| 43 | :debug:main No need to upgrade! bowtie 0.12.7_0 >= bowtie 0.12.7_0 |
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| 44 | :msg:main ---> Computing dependencies for tophat:info:main .:debug:main tophat has no conflicts |
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| 45 | :debug:main Searching for dependency: zlib |
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| 46 | :debug:main Found Dependency: receipt exists for zlib |
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| 47 | :debug:main Searching for dependency: samtools |
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| 48 | :debug:main Found Dependency: receipt exists for samtools |
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| 49 | :debug:main Searching for dependency: bowtie |
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| 50 | :debug:main Found Dependency: receipt exists for bowtie |
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| 51 | :msg:main |
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| 52 | :debug:main Executing org.macports.main (tophat) |
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| 53 | :debug:main changing euid/egid - current euid: 0 - current egid: 0 |
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| 54 | :debug:main egid changed to: 501 |
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| 55 | :debug:main euid changed to: 502 |
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| 56 | :debug:archivefetch archivefetch phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 57 | :msg:archivefetch ---> Fetching archive for tophat |
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| 58 | :debug:archivefetch Executing org.macports.archivefetch (tophat) |
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| 59 | :debug:archivefetch euid/egid changed to: 0/0 |
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| 60 | :debug:archivefetch chowned /opt/local/var/macports/incoming to macports |
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| 61 | :debug:archivefetch euid/egid changed to: 502/501 |
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| 62 | :info:archivefetch ---> tophat-1.2.0_0.darwin_11.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified |
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| 63 | :msg:archivefetch ---> Attempting to fetch tophat-1.2.0_0.darwin_11.x86_64.tbz2 from http://packages.macports.org/tophat |
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| 64 | :debug:archivefetch Fetching archive failed:: The requested URL returned error: 404 |
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| 65 | :debug:archivefetch Privilege de-escalation not attempted as not running as root. |
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| 66 | :debug:fetch fetch phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 67 | :notice:fetch ---> Fetching distfiles for tophat |
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| 68 | :debug:fetch Executing org.macports.fetch (tophat) |
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| 69 | :debug:fetch Privilege de-escalation not attempted as not running as root. |
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| 70 | :debug:checksum checksum phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 71 | :notice:checksum ---> Verifying checksum(s) for tophat |
|---|
| 72 | :debug:checksum Executing org.macports.checksum (tophat) |
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| 73 | :info:checksum ---> Checksumming tophat-1.2.0.tar.gz |
|---|
| 74 | :debug:checksum Correct (sha1) checksum for tophat-1.2.0.tar.gz |
|---|
| 75 | :debug:checksum Correct (rmd160) checksum for tophat-1.2.0.tar.gz |
|---|
| 76 | :debug:checksum Privilege de-escalation not attempted as not running as root. |
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| 77 | :debug:extract extract phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 78 | :notice:extract ---> Extracting tophat |
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| 79 | :debug:extract Executing org.macports.extract (tophat) |
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| 80 | :info:extract ---> Extracting tophat-1.2.0.tar.gz |
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| 81 | :debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz' |
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| 82 | :debug:extract Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7' |
|---|
| 83 | :debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz' | /usr/bin/gnutar --no-same-owner -xf -' |
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| 84 | :debug:extract Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/tophat/tophat-1.2.0.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - |
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| 85 | :debug:extract euid/egid changed to: 0/0 |
|---|
| 86 | :debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work to macports |
|---|
| 87 | :debug:extract euid/egid changed to: 502/501 |
|---|
| 88 | :debug:extract Privilege de-escalation not attempted as not running as root. |
|---|
| 89 | :debug:patch patch phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 90 | :debug:patch Executing org.macports.patch (tophat) |
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| 91 | :debug:patch Privilege de-escalation not attempted as not running as root. |
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| 92 | :debug:configure configure phase started at Tue Jul 3 13:19:16 CEST 2012 |
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| 93 | :notice:configure ---> Configuring tophat |
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| 94 | :debug:configure Using compiler 'Mac OS X clang' |
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| 95 | :debug:configure Executing org.macports.configure (tophat) |
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| 96 | :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_tophat/tophat/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' |
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| 97 | :debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && ./configure --prefix=/opt/local' |
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| 98 | :debug:configure Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && ./configure --prefix=/opt/local |
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| 99 | :info:configure checking for a BSD-compatible install... /usr/bin/install -c |
|---|
| 100 | :info:configure checking whether build environment is sane... yes |
|---|
| 101 | :info:configure checking for gawk... no |
|---|
| 102 | :info:configure checking for mawk... no |
|---|
| 103 | :info:configure checking for nawk... no |
|---|
| 104 | :info:configure checking for awk... awk |
|---|
| 105 | :info:configure checking whether make sets $(MAKE)... yes |
|---|
| 106 | :info:configure checking build system type... i386-apple-darwin11.4.0 |
|---|
| 107 | :info:configure checking host system type... i386-apple-darwin11.4.0 |
|---|
| 108 | :info:configure checking for gcc... /usr/bin/clang |
|---|
| 109 | :info:configure checking for C compiler default output file name... a.out |
|---|
| 110 | :info:configure checking whether the C compiler works... yes |
|---|
| 111 | :info:configure checking whether we are cross compiling... no |
|---|
| 112 | :info:configure checking for suffix of executables... |
|---|
| 113 | :info:configure checking for suffix of object files... o |
|---|
| 114 | :info:configure checking whether we are using the GNU C compiler... yes |
|---|
| 115 | :info:configure checking whether /usr/bin/clang accepts -g... yes |
|---|
| 116 | :info:configure checking for /usr/bin/clang option to accept ANSI C... none needed |
|---|
| 117 | :info:configure checking for style of include used by make... GNU |
|---|
| 118 | :info:configure checking dependency style of /usr/bin/clang... gcc3 |
|---|
| 119 | :info:configure checking whether we are using the GNU C++ compiler... yes |
|---|
| 120 | :info:configure checking whether /usr/bin/clang++ accepts -g... yes |
|---|
| 121 | :info:configure checking dependency style of /usr/bin/clang++... gcc3 |
|---|
| 122 | :info:configure checking for gawk... (cached) awk |
|---|
| 123 | :info:configure checking for a BSD-compatible install... /usr/bin/install -c |
|---|
| 124 | :info:configure checking for ranlib... ranlib |
|---|
| 125 | :info:configure checking for ar... ar |
|---|
| 126 | :info:configure checking for perl... /usr/bin/perl |
|---|
| 127 | :info:configure checking for bash... /bin/bash |
|---|
| 128 | :info:configure checking for a Python interpreter with version >= 2.4... python |
|---|
| 129 | :info:configure checking for python... /usr/bin/python |
|---|
| 130 | :info:configure checking for python version... 2.7 |
|---|
| 131 | :info:configure checking for python platform... darwin |
|---|
| 132 | :info:configure checking for python script directory... ${prefix}/lib/python2.7/site-packages |
|---|
| 133 | :info:configure checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages |
|---|
| 134 | :info:configure checking for bamlib... yes |
|---|
| 135 | :info:configure checking how to run the C preprocessor... /usr/bin/clang -E |
|---|
| 136 | :info:configure checking for egrep... grep -E |
|---|
| 137 | :info:configure checking for ANSI C header files... yes |
|---|
| 138 | :info:configure checking for sys/types.h... yes |
|---|
| 139 | :info:configure checking for sys/stat.h... yes |
|---|
| 140 | :info:configure checking for stdlib.h... yes |
|---|
| 141 | :info:configure checking for string.h... yes |
|---|
| 142 | :info:configure checking for memory.h... yes |
|---|
| 143 | :info:configure checking for strings.h... yes |
|---|
| 144 | :info:configure checking for inttypes.h... yes |
|---|
| 145 | :info:configure checking for stdint.h... yes |
|---|
| 146 | :info:configure checking for unistd.h... yes |
|---|
| 147 | :info:configure checking if zlib is wanted... yes |
|---|
| 148 | :info:configure checking for inflateEnd in -lz... yes |
|---|
| 149 | :info:configure checking zlib.h usability... yes |
|---|
| 150 | :info:configure checking zlib.h presence... yes |
|---|
| 151 | :info:configure checking for zlib.h... yes |
|---|
| 152 | :info:configure checking for inflateEnd in -lz... (cached) yes |
|---|
| 153 | :info:configure checking zlib in /usr... ok |
|---|
| 154 | :info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E |
|---|
| 155 | :info:configure checking for stdlib.h... (cached) yes |
|---|
| 156 | :info:configure checking for string.h... (cached) yes |
|---|
| 157 | :info:configure checking for unistd.h... (cached) yes |
|---|
| 158 | :info:configure checking for ANSI C header files... (cached) yes |
|---|
| 159 | :info:configure checking for stdlib.h... (cached) yes |
|---|
| 160 | :info:configure checking for string.h... (cached) yes |
|---|
| 161 | :info:configure checking for unistd.h... (cached) yes |
|---|
| 162 | :info:configure checking for stdbool.h that conforms to C99... yes |
|---|
| 163 | :info:configure checking for _Bool... no |
|---|
| 164 | :info:configure checking for an ANSI C-conforming const... yes |
|---|
| 165 | :info:configure checking for special C compiler options needed for large files... no |
|---|
| 166 | :info:configure checking for _FILE_OFFSET_BITS value needed for large files... no |
|---|
| 167 | :info:configure checking for _LARGE_FILES value needed for large files... no |
|---|
| 168 | :info:configure checking for gzread in -lz... yes |
|---|
| 169 | :info:configure checking for stdlib.h... (cached) yes |
|---|
| 170 | :info:configure checking for GNU libc compatible malloc... yes |
|---|
| 171 | :info:configure checking for memset... yes |
|---|
| 172 | :info:configure checking for strdup... yes |
|---|
| 173 | :info:configure checking for strrchr... yes |
|---|
| 174 | :info:configure checking for strtol... yes |
|---|
| 175 | :info:configure checking for strsep... yes |
|---|
| 176 | :info:configure checking how to create a pax tar archive... gnutar |
|---|
| 177 | :info:configure checking dependency style of /usr/bin/clang... (cached) gcc3 |
|---|
| 178 | :info:configure checking dependency style of /usr/bin/clang++... (cached) gcc3 |
|---|
| 179 | :info:configure configure: creating ./config.status |
|---|
| 180 | :info:configure config.status: creating Makefile |
|---|
| 181 | :info:configure config.status: creating src/Makefile |
|---|
| 182 | :info:configure config.status: creating config.h |
|---|
| 183 | :info:configure config.status: executing depfiles commands |
|---|
| 184 | :info:configure |
|---|
| 185 | :info:configure -- tophat 1.2.0 Configuration Results -- |
|---|
| 186 | :info:configure C compiler: /usr/bin/clang -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG |
|---|
| 187 | :info:configure C++ compiler: /usr/bin/clang++ -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include |
|---|
| 188 | :info:configure GCC version: Apple clang version 3.0 (tags/Apple/clang-211.10.1) (based on LLVM 3.0svn) |
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| 189 | :info:configure Host System type: i386-apple-darwin11.4.0 |
|---|
| 190 | :info:configure Install prefix: /opt/local |
|---|
| 191 | :info:configure Install eprefix: ${prefix} |
|---|
| 192 | :info:configure |
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| 193 | :info:configure See config.h for further configuration information. |
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| 194 | :info:configure Email <cole@cs.umd.edu> with questions and bug reports. |
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| 195 | :info:configure |
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| 196 | :debug:configure Privilege de-escalation not attempted as not running as root. |
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| 197 | :debug:build build phase started at Tue Jul 3 13:19:23 CEST 2012 |
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| 198 | :notice:build ---> Building tophat |
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| 199 | :debug:build Executing org.macports.build (tophat) |
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| 200 | :debug:build port disallows a parallel build |
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| 201 | :debug:build Environment: CPATH='/opt/local/include' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/.CC_PRINT_OPTIONS' LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES' MACOSX_DEPLOYMENT_TARGET='10.7' |
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| 202 | :debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all' |
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| 203 | :debug:build Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all |
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| 204 | :info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0' |
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| 205 | :info:build /usr/bin/make all-recursive |
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| 206 | :info:build make[1]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0' |
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| 207 | :info:build Making all in src |
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| 208 | :info:build make[2]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0/src' |
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| 209 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \ |
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| 210 | :info:build then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi |
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| 211 | :info:build reads.cpp:434:37: warning: array subscript is of type 'char' [-Wchar-subscripts] |
|---|
| 212 | :info:build char base_prev_prev = "ACGTN"[ptr[(i-1)*4 + k]]; |
|---|
| 213 | :info:build ^~~~~~~~~~~~~~~~~ |
|---|
| 214 | :info:build 1 warning generated. |
|---|
| 215 | :info:build if /usr/bin/clang -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -MT alphabet.o -MD -MP -MF ".deps/alphabet.Tpo" -c -o alphabet.o alphabet.c; \ |
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| 216 | :info:build then mv -f ".deps/alphabet.Tpo" ".deps/alphabet.Po"; else rm -f ".deps/alphabet.Tpo"; exit 1; fi |
|---|
| 217 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT bwt_map.o -MD -MP -MF ".deps/bwt_map.Tpo" -c -o bwt_map.o bwt_map.cpp; \ |
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| 218 | :info:build then mv -f ".deps/bwt_map.Tpo" ".deps/bwt_map.Po"; else rm -f ".deps/bwt_map.Tpo"; exit 1; fi |
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| 219 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \ |
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| 220 | :info:build then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi |
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| 221 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT junctions.o -MD -MP -MF ".deps/junctions.Tpo" -c -o junctions.o junctions.cpp; \ |
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| 222 | :info:build then mv -f ".deps/junctions.Tpo" ".deps/junctions.Po"; else rm -f ".deps/junctions.Tpo"; exit 1; fi |
|---|
| 223 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT insertions.o -MD -MP -MF ".deps/insertions.Tpo" -c -o insertions.o insertions.cpp; \ |
|---|
| 224 | :info:build then mv -f ".deps/insertions.Tpo" ".deps/insertions.Po"; else rm -f ".deps/insertions.Tpo"; exit 1; fi |
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| 225 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT deletions.o -MD -MP -MF ".deps/deletions.Tpo" -c -o deletions.o deletions.cpp; \ |
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| 226 | :info:build then mv -f ".deps/deletions.Tpo" ".deps/deletions.Po"; else rm -f ".deps/deletions.Tpo"; exit 1; fi |
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| 227 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT align_status.o -MD -MP -MF ".deps/align_status.Tpo" -c -o align_status.o align_status.cpp; \ |
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| 228 | :info:build then mv -f ".deps/align_status.Tpo" ".deps/align_status.Po"; else rm -f ".deps/align_status.Tpo"; exit 1; fi |
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| 229 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT fragments.o -MD -MP -MF ".deps/fragments.Tpo" -c -o fragments.o fragments.cpp; \ |
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| 230 | :info:build then mv -f ".deps/fragments.Tpo" ".deps/fragments.Po"; else rm -f ".deps/fragments.Tpo"; exit 1; fi |
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| 231 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \ |
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| 232 | :info:build then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi |
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| 233 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT inserts.o -MD -MP -MF ".deps/inserts.Tpo" -c -o inserts.o inserts.cpp; \ |
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| 234 | :info:build then mv -f ".deps/inserts.Tpo" ".deps/inserts.Po"; else rm -f ".deps/inserts.Tpo"; exit 1; fi |
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| 235 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT qual.o -MD -MP -MF ".deps/qual.Tpo" -c -o qual.o qual.cpp; \ |
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| 236 | :info:build then mv -f ".deps/qual.Tpo" ".deps/qual.Po"; else rm -f ".deps/qual.Tpo"; exit 1; fi |
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| 237 | :info:build rm -f libtophat.a |
|---|
| 238 | :info:build ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o align_status.o fragments.o tokenize.o inserts.o qual.o |
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| 239 | :info:build ranlib libtophat.a |
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| 240 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT GBase.o -MD -MP -MF ".deps/GBase.Tpo" -c -o GBase.o GBase.cpp; \ |
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| 241 | :info:build then mv -f ".deps/GBase.Tpo" ".deps/GBase.Po"; else rm -f ".deps/GBase.Tpo"; exit 1; fi |
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| 242 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT codons.o -MD -MP -MF ".deps/codons.Tpo" -c -o codons.o codons.cpp; \ |
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| 243 | :info:build then mv -f ".deps/codons.Tpo" ".deps/codons.Po"; else rm -f ".deps/codons.Tpo"; exit 1; fi |
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| 244 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT gdna.o -MD -MP -MF ".deps/gdna.Tpo" -c -o gdna.o gdna.cpp; \ |
|---|
| 245 | :info:build then mv -f ".deps/gdna.Tpo" ".deps/gdna.Po"; else rm -f ".deps/gdna.Tpo"; exit 1; fi |
|---|
| 246 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT GStr.o -MD -MP -MF ".deps/GStr.Tpo" -c -o GStr.o GStr.cpp; \ |
|---|
| 247 | :info:build then mv -f ".deps/GStr.Tpo" ".deps/GStr.Po"; else rm -f ".deps/GStr.Tpo"; exit 1; fi |
|---|
| 248 | :info:build if /usr/bin/clang++ -DHAVE_CONFIG_H -I. -I. -I.. -I/opt/local/include -I/usr/include -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -pipe -O2 -arch x86_64 -DNDEBUG -I/opt/local/include -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \ |
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| 249 | :info:build then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi |
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| 250 | :info:build In file included from GFaSeqGet.cpp:1: |
|---|
| 251 | :info:build In file included from ./GFaSeqGet.h:4: |
|---|
| 252 | :info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable] |
|---|
| 253 | :info:build int result=-1; |
|---|
| 254 | :info:build ^ |
|---|
| 255 | :info:build GFaSeqGet.cpp:62:17: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
|---|
| 256 | :info:build if (fofs!=0) { fseeko(fh,fofs,SEEK_SET); } //e.g. for offsets provided by cdbyank |
|---|
| 257 | :info:build ^~~~~~ |
|---|
| 258 | :info:build fseek |
|---|
| 259 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
|---|
| 260 | :info:build int fseek(FILE *, long, int); |
|---|
| 261 | :info:build ^ |
|---|
| 262 | :info:build GFaSeqGet.cpp:128:2: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
|---|
| 263 | :info:build fseeko(fh,fseqstart,SEEK_SET); |
|---|
| 264 | :info:build ^~~~~~ |
|---|
| 265 | :info:build fseek |
|---|
| 266 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
|---|
| 267 | :info:build int fseek(FILE *, long, int); |
|---|
| 268 | :info:build ^ |
|---|
| 269 | :info:build GFaSeqGet.cpp:261:3: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
|---|
| 270 | :info:build fseeko(fh, fstart, SEEK_SET); |
|---|
| 271 | :info:build ^~~~~~ |
|---|
| 272 | :info:build fseek |
|---|
| 273 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
|---|
| 274 | :info:build int fseek(FILE *, long, int); |
|---|
| 275 | :info:build ^ |
|---|
| 276 | :info:build GFaSeqGet.cpp:280:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
|---|
| 277 | :info:build fseeko(fh, lendlen, SEEK_CUR); |
|---|
| 278 | :info:build ^~~~~~ |
|---|
| 279 | :info:build fseek |
|---|
| 280 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
|---|
| 281 | :info:build int fseek(FILE *, long, int); |
|---|
| 282 | :info:build ^ |
|---|
| 283 | :info:build GFaSeqGet.cpp:300:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
|---|
| 284 | :info:build fseeko(fh, lendlen, SEEK_CUR); |
|---|
| 285 | :info:build ^~~~~~ |
|---|
| 286 | :info:build fseek |
|---|
| 287 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
|---|
| 288 | :info:build int fseek(FILE *, long, int); |
|---|
| 289 | :info:build ^ |
|---|
| 290 | :info:build 1 warning and 5 errors generated. |
|---|
| 291 | :info:build make[2]: *** [GFaSeqGet.o] Error 1 |
|---|
| 292 | :info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0/src' |
|---|
| 293 | :info:build make[1]: *** [all-recursive] Error 1 |
|---|
| 294 | :info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0' |
|---|
| 295 | :info:build make: *** [all] Error 2 |
|---|
| 296 | :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0' |
|---|
| 297 | :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/work/tophat-1.2.0" && /usr/bin/make -w all |
|---|
| 298 | :info:build Exit code: 2 |
|---|
| 299 | :error:build org.macports.build for port tophat returned: command execution failed |
|---|
| 300 | :debug:build Error code: CHILDSTATUS 41585 2 |
|---|
| 301 | :debug:build Backtrace: command execution failed |
|---|
| 302 | while executing |
|---|
| 303 | "system -nice 0 $fullcmdstring" |
|---|
| 304 | ("eval" body line 1) |
|---|
| 305 | invoked from within |
|---|
| 306 | "eval system $notty $nice \$fullcmdstring" |
|---|
| 307 | invoked from within |
|---|
| 308 | "command_exec build" |
|---|
| 309 | (procedure "portbuild::build_main" line 8) |
|---|
| 310 | invoked from within |
|---|
| 311 | "$procedure $targetname" |
|---|
| 312 | :info:build Warning: targets not executed for tophat: org.macports.activate org.macports.build org.macports.destroot org.macports.install |
|---|
| 313 | :notice:build Please see the log file for port tophat for details: |
|---|
| 314 | /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/main.log |
|---|
