1 | version:1 |
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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 |
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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 |
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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 |
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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 |
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39 | :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided |
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40 | :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided |
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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:main Skipping completed org.macports.archivefetch (tophat) |
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57 | :debug:main Privilege de-escalation not attempted as not running as root. |
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58 | :debug:main Skipping completed org.macports.fetch (tophat) |
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59 | :debug:main Privilege de-escalation not attempted as not running as root. |
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60 | :debug:main Skipping completed org.macports.checksum (tophat) |
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61 | :debug:main Privilege de-escalation not attempted as not running as root. |
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62 | :debug:main Skipping completed org.macports.extract (tophat) |
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63 | :debug:main Privilege de-escalation not attempted as not running as root. |
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64 | :debug:main Skipping completed org.macports.patch (tophat) |
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65 | :debug:main Privilege de-escalation not attempted as not running as root. |
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66 | :debug:main Skipping completed org.macports.configure (tophat) |
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67 | :debug:main Privilege de-escalation not attempted as not running as root. |
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68 | :debug:build build phase started at Tue Jul 3 10:13:03 CEST 2012 |
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69 | :notice:build ---> Building tophat |
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70 | :debug:build Executing org.macports.build (tophat) |
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71 | :debug:build port disallows a parallel build |
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72 | :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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73 | :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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74 | :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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75 | :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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76 | :info:build /usr/bin/make all-recursive |
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77 | :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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78 | :info:build Making all in src |
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79 | :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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80 | :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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81 | :info:build then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi |
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82 | :info:build In file included from GFaSeqGet.cpp:1: |
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83 | :info:build In file included from ./GFaSeqGet.h:4: |
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84 | :info:build ./GList.hh:972:6: warning: unused variable 'result' [-Wunused-variable] |
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85 | :info:build int result=-1; |
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86 | :info:build ^ |
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87 | :info:build GFaSeqGet.cpp:62:17: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
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88 | :info:build if (fofs!=0) { fseeko(fh,fofs,SEEK_SET); } //e.g. for offsets provided by cdbyank |
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89 | :info:build ^~~~~~ |
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90 | :info:build fseek |
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91 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
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92 | :info:build int fseek(FILE *, long, int); |
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93 | :info:build ^ |
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94 | :info:build GFaSeqGet.cpp:128:2: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
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95 | :info:build fseeko(fh,fseqstart,SEEK_SET); |
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96 | :info:build ^~~~~~ |
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97 | :info:build fseek |
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98 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
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99 | :info:build int fseek(FILE *, long, int); |
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100 | :info:build ^ |
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101 | :info:build GFaSeqGet.cpp:261:3: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
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102 | :info:build fseeko(fh, fstart, SEEK_SET); |
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103 | :info:build ^~~~~~ |
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104 | :info:build fseek |
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105 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
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106 | :info:build int fseek(FILE *, long, int); |
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107 | :info:build ^ |
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108 | :info:build GFaSeqGet.cpp:280:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
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109 | :info:build fseeko(fh, lendlen, SEEK_CUR); |
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110 | :info:build ^~~~~~ |
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111 | :info:build fseek |
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112 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
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113 | :info:build int fseek(FILE *, long, int); |
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114 | :info:build ^ |
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115 | :info:build GFaSeqGet.cpp:300:5: error: use of undeclared identifier 'fseeko'; did you mean 'fseek'? |
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116 | :info:build fseeko(fh, lendlen, SEEK_CUR); |
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117 | :info:build ^~~~~~ |
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118 | :info:build fseek |
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119 | :info:build /usr/include/stdio.h:259:6: note: 'fseek' declared here |
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120 | :info:build int fseek(FILE *, long, int); |
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121 | :info:build ^ |
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122 | :info:build 1 warning and 5 errors generated. |
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123 | :info:build make[2]: *** [GFaSeqGet.o] Error 1 |
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124 | :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' |
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125 | :info:build make[1]: *** [all-recursive] Error 1 |
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126 | :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' |
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127 | :info:build make: *** [all] Error 2 |
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128 | :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' |
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129 | :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 |
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130 | :info:build Exit code: 2 |
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131 | :error:build org.macports.build for port tophat returned: command execution failed |
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132 | :debug:build Error code: CHILDSTATUS 38890 2 |
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133 | :debug:build Backtrace: command execution failed |
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134 | while executing |
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135 | "system -nice 0 $fullcmdstring" |
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136 | ("eval" body line 1) |
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137 | invoked from within |
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138 | "eval system $notty $nice \$fullcmdstring" |
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139 | invoked from within |
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140 | "command_exec build" |
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141 | (procedure "portbuild::build_main" line 8) |
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142 | invoked from within |
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143 | "$procedure $targetname" |
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144 | :info:build Warning: targets not executed for tophat: org.macports.activate org.macports.build org.macports.destroot org.macports.install |
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145 | :notice:build Please see the log file for port tophat for details: |
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146 | /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_tophat/tophat/main.log |
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