1. * Package: sci-biology/mothur-1.13.0-r1
2. * Repository: gentoo
3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux multilib readline test userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. >>> Unpacking source...
7. >>> Unpacking mothur-1.13.0.zip to /tmp/portage/sci-biology/mothur-1.13.0-r1/work
8. >>> Source unpacked in /tmp/portage/sci-biology/mothur-1.13.0-r1/work
9. >>> Preparing source in /tmp/portage/sci-biology/mothur-1.13.0-r1/work/Mothur.source ...
10. * Applying mothur-1.13.0-makefile.patch ...
11. [ ok ]
12. * Applying mothur-1.13.0-overflows.patch ...
13. [ ok ]
14. >>> Source prepared.
15. >>> Configuring source in /tmp/portage/sci-biology/mothur-1.13.0-r1/work/Mothur.source ...
16. >>> Source configured.
17. >>> Compiling source in /tmp/portage/sci-biology/mothur-1.13.0-r1/work/Mothur.source ...
18. make -j24 USEMPI=no USEREADLINE=yes
19. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o makegroupcommand.o makegroupcommand.cpp
20. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o alignment.o alignment.cpp
21. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o commandfactory.o commandfactory.cpp
22. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o ace.o ace.cpp
23. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sensspeccommand.o sensspeccommand.cpp
24. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o classifyseqscommand.o classifyseqscommand.cpp
25. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o progress.o progress.cpp
26. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o whittaker.o whittaker.cpp
27. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o parsesffcommand.o parsesffcommand.cpp
28. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o alignmentcell.o alignmentcell.cpp
29. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimerabellerophoncommand.o chimerabellerophoncommand.cpp
30. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedrabundvector.o sharedrabundvector.cpp
31. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o unifracweightedcommand.o unifracweightedcommand.cpp
32. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o suffixdb.o suffixdb.cpp
33. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o pintail.o pintail.cpp
34. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o shannon.o shannon.cpp
35. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o validcalculator.o validcalculator.cpp
36. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedrabundfloatvector.o sharedrabundfloatvector.cpp
37. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o kmerdb.o kmerdb.cpp
38. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o parselistscommand.o parselistscommand.cpp
39. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getlistcountcommand.o getlistcountcommand.cpp
40. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sequence.o sequence.cpp
41. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o listseqscommand.o listseqscommand.cpp
42. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o heatmapsimcommand.o heatmapsimcommand.cpp
43. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o clustercommand.o clustercommand.cpp
44. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o degapseqscommand.o degapseqscommand.cpp
45. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedchao1.o sharedchao1.cpp
46. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o qstat.o qstat.cpp
47. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o mothur.o mothur.cpp
48. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o unifracunweightedcommand.o unifracunweightedcommand.cpp
49. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o simpsoneven.o simpsoneven.cpp
50. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o dlibshuff.o dlibshuff.cpp
51. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o distancedb.o distancedb.cpp
52. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o phylodiversity.o phylodiversity.cpp
53. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o npshannon.o npshannon.cpp
54. mothur.cpp: In function 'int main(int, char**)':
55. mothur.cpp:53:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
56. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sequencedb.o sequencedb.cpp
57. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getrelabundcommand.o getrelabundcommand.cpp
58. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeraseqscommand.o chimeraseqscommand.cpp
59. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o shannoneven.o shannoneven.cpp
60. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o slayer.o slayer.cpp
61. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o raredisplay.o raredisplay.cpp
62. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getsharedotucommand.o getsharedotucommand.cpp
63. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o solow.o solow.cpp
64. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o commandoptionparser.o commandoptionparser.cpp
65. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o clearcutcommand.o clearcutcommand.cpp
66. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedjest.o sharedjest.cpp
67. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o screenseqscommand.o screenseqscommand.cpp
68. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o parsimonycommand.o parsimonycommand.cpp
69. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bayesian.o bayesian.cpp
70. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o slibshuff.o slibshuff.cpp
71. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o reversecommand.o reversecommand.cpp
72. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o database.o database.cpp
73. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o mgclustercommand.o mgclustercommand.cpp
74. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bstick.o bstick.cpp
75. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o splitabundcommand.o splitabundcommand.cpp
76. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedlennon.o sharedlennon.cpp
77. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o classify.o classify.cpp
78. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o noalign.o noalign.cpp
79. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedjabund.o sharedjabund.cpp
80. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o heatmapcommand.o heatmapcommand.cpp
81. In file included from /usr/include/string.h:638:0,
82. from /usr/include/readline/chardefs.h:38,
83. from /usr/include/readline/keymaps.h:35,
84. from /usr/include/readline/readline.h:37,
85. from mothur.h:62,
86. from command.hpp:16,
87. from clearcutcommand.h:13,
88. from clearcutcommand.cpp:10:
89. In function 'char* strcpy(char*, const char*)',
90. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:183:70:
91. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
92. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
93. In function 'char* strcpy(char*, const char*)',
94. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:186:82:
95. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
96. In function 'char* strcpy(char*, const char*)',
97. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:189:81:
98. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
99. In function 'char* strcpy(char*, const char*)',
100. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:191:73:
101. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
102. In function 'char* strcpy(char*, const char*)',
103. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:192:73:
104. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
105. In function 'char* strcpy(char*, const char*)',
106. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:193:70:
107. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
108. In function 'char* strcpy(char*, const char*)',
109. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:200:76:
110. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
111. In function 'char* strcpy(char*, const char*)',
112. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:201:73:
113. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
114. In function 'char* strcpy(char*, const char*)',
115. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:202:76:
116. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
117. In function 'char* strcpy(char*, const char*)',
118. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:209:76:
119. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
120. In function 'char* strcpy(char*, const char*)',
121. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:218:66:
122. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
123. In function 'char* strcpy(char*, const char*)',
124. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:219:73:
125. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
126. In function 'char* strcpy(char*, const char*)',
127. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:220:70:
128. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
129. In function 'char* strcpy(char*, const char*)',
130. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:221:71:
131. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
132. In function 'char* strcpy(char*, const char*)',
133. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:236:72:
134. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
135. In function 'char* strcpy(char*, const char*)',
136. inlined from 'virtual int ClearcutCommand::execute()' at clearcutcommand.cpp:237:72:
137. /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
138. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o libshuff.o libshuff.cpp
139. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsorest.o sharedsorest.cpp
140. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeraccodecommand.o chimeraccodecommand.cpp
141. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedjclass.o sharedjclass.cpp
142. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedordervector.o sharedordervector.cpp
143. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o hclustercommand.o hclustercommand.cpp
144. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o mothurout.o mothurout.cpp
145. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sffinfocommand.o sffinfocommand.cpp
146. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readtreecommand.o readtreecommand.cpp
147. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o dmat.o dmat.cpp
148. dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
149. dmat.cpp:476:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
150. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getopt_long.o getopt_long.cpp
151. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o shen.o shen.cpp
152. mothurout.cpp: In member function 'std::string MothurOut::sortFile(std::string, std::string)':
153. mothurout.cpp:812:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
154. mothurout.cpp: In member function 'int MothurOut::renameFile(std::string, std::string)':
155. mothurout.cpp:714:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
156. mothurout.cpp:718:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
157. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o nameassignment.o nameassignment.cpp
158. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o geom.o geom.cpp
159. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o preclustercommand.o preclustercommand.cpp
160. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o setdircommand.o setdircommand.cpp
161. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o jackknife.o jackknife.cpp
162. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o weighted.o weighted.cpp
163. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o formatcolumn.o formatcolumn.cpp
164. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o deconvolutecommand.o deconvolutecommand.cpp
165. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bellerophon.o bellerophon.cpp
166. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getseqscommand.o getseqscommand.cpp
167. formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)':
168. formatcolumn.cpp:87:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
169. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedkstest.o sharedkstest.cpp
170. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chopseqscommand.o chopseqscommand.cpp
171. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimerarealigner.o chimerarealigner.cpp
172. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readotucommand.o readotucommand.cpp
173. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o mergefilecommand.o mergefilecommand.cpp
174. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeracheckrdp.o chimeracheckrdp.cpp
175. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o distclearcut.o distclearcut.cpp
176. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o treenode.o treenode.cpp
177. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o engine.o engine.cpp
178. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o kmer.o kmer.cpp
179. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedjackknife.o sharedjackknife.cpp
180. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedcommand.o sharedcommand.cpp
181. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o splitmatrix.o splitmatrix.cpp
182. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o hcluster.o hcluster.cpp
183. engine.cpp: In member function 'virtual std::string Engine::getCommand()':
184. engine.cpp:184:20: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
185. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o otuhierarchycommand.o otuhierarchycommand.cpp
186. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o suffixnodes.o suffixnodes.cpp
187. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o singlelinkage.o singlelinkage.cpp
188. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o consensuscommand.o consensuscommand.cpp
189. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o heatmapsim.o heatmapsim.cpp
190. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o knn.o knn.cpp
191. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o tree.o tree.cpp
192. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o inputdata.o inputdata.cpp
193. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o maligner.o maligner.cpp
194. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsabundvector.o sharedsabundvector.cpp
195. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getgroupcommand.o getgroupcommand.cpp
196. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readcluster.o readcluster.cpp
197. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o calculator.o calculator.cpp
198. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o efron.o efron.cpp
199. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o needlemanoverlap.o needlemanoverlap.cpp
200. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsobscollectsummary.o sharedsobscollectsummary.cpp
201. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o blastalign.o blastalign.cpp
202. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getsabundcommand.o getsabundcommand.cpp
203. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o systemcommand.o systemcommand.cpp
204. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o averagelinkage.o averagelinkage.cpp
205. blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string)':
206. blastalign.cpp:64:30: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
207. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o helpcommand.o helpcommand.cpp
208. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedutilities.o sharedutilities.cpp
209. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getoturepcommand.o getoturepcommand.cpp
210. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readotu.o readotu.cpp
211. systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
212. systemcommand.cpp:64:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
213. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o collectcommand.o collectcommand.cpp
214. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o unweighted.o unweighted.cpp
215. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sparsematrix.o sparsematrix.cpp
216. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o nastreport.o nastreport.cpp
217. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o alignmentdb.o alignmentdb.cpp
218. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o cmdargs.o cmdargs.cpp
219. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o fullmatrix.o fullmatrix.cpp
220. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimerapintailcommand.o chimerapintailcommand.cpp
221. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o fileoutput.o fileoutput.cpp
222. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o libshuffcommand.o libshuffcommand.cpp
223. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o overlap.o overlap.cpp
224. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o cluster.o cluster.cpp
225. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o filterseqscommand.o filterseqscommand.cpp
226. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bergerparker.o bergerparker.cpp
227. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sabundvector.o sabundvector.cpp
228. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedthetan.o sharedthetan.cpp
229. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeracheckcommand.o chimeracheckcommand.cpp
230. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o uvest.o uvest.cpp
231. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o nocommands.o nocommands.cpp
232. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o ccode.o ccode.cpp
233. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o setlogfilecommand.o setlogfilecommand.cpp
234. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o suffixtree.o suffixtree.cpp
235. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o collect.o collect.cpp
236. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedkulczynskicody.o sharedkulczynskicody.cpp
237. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o phylotypecommand.o phylotypecommand.cpp
238. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o rarefactsharedcommand.o rarefactsharedcommand.cpp
239. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsorabund.o sharedsorabund.cpp
240. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o fasta.o fasta.cpp
241. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o blastdb.o blastdb.cpp
242. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedbraycurtis.o sharedbraycurtis.cpp
243. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o summarycommand.o summarycommand.cpp
244. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o formatphylip.o formatphylip.cpp
245. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o phylosummary.o phylosummary.cpp
246. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chao1.o chao1.cpp
247. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o ordervector.o ordervector.cpp
248. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedkulczynski.o sharedkulczynski.cpp
249. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o aligncommand.o aligncommand.cpp
250. blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
251. blastdb.cpp:191:34: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
252. blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int)':
253. blastdb.cpp:132:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
254. blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int)':
255. blastdb.cpp:84:31: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
256. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o optionparser.o optionparser.cpp
257. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsorclass.o sharedsorclass.cpp
258. formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
259. formatphylip.cpp:96:29: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
260. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o prng.o prng.cpp
261. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeraslayercommand.o chimeraslayercommand.cpp
262. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o coverage.o coverage.cpp
263. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getrabundcommand.o getrabundcommand.cpp
264. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedlistvector.o sharedlistvector.cpp
265. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o qualityscores.o qualityscores.cpp
266. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimeraslayer.o chimeraslayer.cpp
267. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedace.o sharedace.cpp
268. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o distancecommand.o distancecommand.cpp
269. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedanderbergs.o sharedanderbergs.cpp
270. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o groupmap.o groupmap.cpp
271. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o quitcommand.o quitcommand.cpp
272. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o matrixoutputcommand.o matrixoutputcommand.cpp
273. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedsobs.o sharedsobs.cpp
274. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o classifyotucommand.o classifyotucommand.cpp
275. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readtree.o readtree.cpp
276. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o phylotree.o phylotree.cpp
277. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o binsequencecommand.o binsequencecommand.cpp
278. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o taxonomyequalizer.o taxonomyequalizer.cpp
279. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o validparameter.o validparameter.cpp
280. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readcolumn.o readcolumn.cpp
281. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o rarecalc.o rarecalc.cpp
282. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o parsimony.o parsimony.cpp
283. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o treegroupscommand.o treegroupscommand.cpp
284. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o boneh.o boneh.cpp
285. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o smithwilson.o smithwilson.cpp
286. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o simpson.o simpson.cpp
287. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o rarefact.o rarefact.cpp
288. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o removeseqscommand.o removeseqscommand.cpp
289. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o venncommand.o venncommand.cpp
290. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o logsd.o logsd.cpp
291. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readphylip.o readphylip.cpp
292. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o weightedlinkage.o weightedlinkage.cpp
293. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o listvector.o listvector.cpp
294. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o seqerrorcommand.o seqerrorcommand.cpp
295. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedmarczewski.o sharedmarczewski.cpp
296. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readblast.o readblast.cpp
297. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o rarefactcommand.o rarefactcommand.cpp
298. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o summarysharedcommand.o summarysharedcommand.cpp
299. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o venn.o venn.cpp
300. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o gotohoverlap.o gotohoverlap.cpp
301. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o trimseqscommand.o trimseqscommand.cpp
302. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o heip.o heip.cpp
303. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o collectsharedcommand.o collectsharedcommand.cpp
304. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o catchallcommand.o catchallcommand.cpp
305. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedochiai.o sharedochiai.cpp
306. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o readdistcommand.o readdistcommand.cpp
307. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o rabundvector.o rabundvector.cpp
308. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o treemap.o treemap.cpp
309. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedthetayc.o sharedthetayc.cpp
310. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o fastamap.o fastamap.cpp
311. catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()':
312. catchallcommand.cpp:154:37: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
313. catchallcommand.cpp:188:37: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
314. catchallcommand.cpp:242:35: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
315. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o phylodiversitycommand.o phylodiversitycommand.cpp
316. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o goodscoverage.o goodscoverage.cpp
317. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o getlabelcommand.o getlabelcommand.cpp
318. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o decalc.o decalc.cpp
319. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o invsimpson.o invsimpson.cpp
320. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o sharedmorisitahorn.o sharedmorisitahorn.cpp
321. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o chimera.o chimera.cpp
322. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o heatmap.o heatmap.cpp
323. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o nast.o nast.cpp
324. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bootstrapsharedcommand.o bootstrapsharedcommand.cpp
325. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o completelinkage.o completelinkage.cpp
326. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o clearcut.o clearcut.cpp
327. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o bootstrap.o bootstrap.cpp
328. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o secondarystructurecommand.o secondarystructurecommand.cpp
329. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o pcacommand.o pcacommand.cpp
330. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o seqsummarycommand.o seqsummarycommand.cpp
331. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o clustersplitcommand.o clustersplitcommand.cpp
332. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -DRELEASE_DATE="\"9/17/2010\"" -DVERSION="\"1.13.0\"" -DUSE_READLINE -I. -c -o globaldata.o globaldata.cpp
333. x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -o mothur engine.o npshannon.o weighted.o simpsoneven.o aligncommand.o dlibshuff.o chimerapintailcommand.o rarefact.o chimeraccodecommand.o solow.o rarefactcommand.o chimerarealigner.o globaldata.o ace.o sharedlennon.o sharedjabund.o sharedsorest.o trimseqscommand.o kmer.o validparameter.o sharedordervector.o clearcut.o pcacommand.o hclustercommand.o mothurout.o dmat.o summarysharedcommand.o preclustercommand.o jackknife.o readotucommand.o unweighted.o readcluster.o sparsematrix.o heatmapsim.o ccode.o sequence.o cmdargs.o libshuffcommand.o clustersplitcommand.o uvest.o sharedkulczynskicody.o sharedthetayc.o distancecommand.o binsequencecommand.o commandfactory.o sharedjclass.o taxonomyequalizer.o treegroupscommand.o treemap.o readphylip.o weightedlinkage.o optionparser.o maligner.o parselistscommand.o readcolumn.o shannon.o otuhierarchycommand.o raredisplay.o bstick.o classifyseqscommand.o commandoptionparser.o mgclustercommand.o sharedsabundvector.o noalign.o sharedbraycurtis.o chopseqscommand.o sharedkulczynski.o chimeraseqscommand.o sharedlistvector.o sharedanderbergs.o matrixoutputcommand.o collectsharedcommand.o fasta.o blastdb.o bayesian.o sharedrabundvector.o validcalculator.o bellerophon.o classify.o clustercommand.o hcluster.o phylotree.o sequencedb.o getrelabundcommand.o overlap.o slayer.o chimerabellerophoncommand.o suffixnodes.o parsimonycommand.o libshuff.o database.o gotohoverlap.o suffixdb.o sharedochiai.o alignmentdb.o sharedmorisitahorn.o chimera.o nast.o distancedb.o seqsummarycommand.o readtreecommand.o averagelinkage.o getrabundcommand.o efron.o boneh.o mergefilecommand.o knn.o systemcommand.o readotu.o smithwilson.o fullmatrix.o chimeracheckrdp.o prng.o clearcutcommand.o coverage.o setlogfilecommand.o collectcommand.o sharedace.o quitcommand.o listseqscommand.o simpson.o removeseqscommand.o venncommand.o logsd.o sensspeccommand.o sharedsobs.o pintail.o formatcolumn.o mothur.o readblast.o heatmapsimcommand.o degapseqscommand.o sharedchao1.o qstat.o unifracunweightedcommand.o chimeraslayer.o phylodiversity.o getopt_long.o shannoneven.o getsharedotucommand.o formatphylip.o sharedjest.o screenseqscommand.o sharedmarczewski.o getlistcountcommand.o catchallcommand.o deconvolutecommand.o listvector.o nameassignment.o phylotypecommand.o heip.o readdistcommand.o calculator.o decalc.o invsimpson.o sharedthetan.o alignment.o completelinkage.o sffinfocommand.o bergerparker.o goodscoverage.o setdircommand.o sharedjackknife.o singlelinkage.o ordervector.o parsesffcommand.o needlemanoverlap.o inputdata.o slibshuff.o helpcommand.o blastalign.o sharedsorabund.o venn.o cluster.o sabundvector.o rabundvector.o getgroupcommand.o summarycommand.o phylosummary.o sharedsorclass.o treenode.o qualityscores.o heatmapcommand.o groupmap.o readtree.o shen.o rarecalc.o parsimony.o kmerdb.o progress.o unifracweightedcommand.o sharedrabundfloatvector.o seqerrorcommand.o sharedkstest.o secondarystructurecommand.o fastamap.o phylodiversitycommand.o heatmap.o bootstrapsharedcommand.o chimeraslayercommand.o getlabelcommand.o geom.o splitabundcommand.o bootstrap.o getseqscommand.o splitmatrix.o suffixtree.o distclearcut.o makegroupcommand.o sharedcommand.o tree.o chao1.o whittaker.o consensuscommand.o reversecommand.o sharedsobscollectsummary.o getsabundcommand.o collect.o sharedutilities.o classifyotucommand.o fileoutput.o alignmentcell.o filterseqscommand.o nastreport.o nocommands.o chimeracheckcommand.o getoturepcommand.o rarefactsharedcommand.o -lreadline -lncurses
334. >>> Source compiled.
335. >>> Test phase [none]: sci-biology/mothur-1.13.0-r1
337. >>> Install mothur-1.13.0-r1 into /tmp/portage/sci-biology/mothur-1.13.0-r1/image/ category sci-biology
338. >>> Completed installing mothur-1.13.0-r1 into /tmp/portage/sci-biology/mothur-1.13.0-r1/image/
340. strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line
341. usr/bin/mothur
343. * QA Notice: Package triggers severe warnings which indicate that it
344. * may exhibit random runtime failures.
345. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
346. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
347. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
348. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
349. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
350. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
351. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
352. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
353. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
354. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
355. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
356. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
357. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
358. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
359. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
360. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
361. * /usr/include/bits/string3.h:104:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int) will always overflow destination buffer [enabled by default]
363. * Please do not file a Gentoo bug and instead report the above QA
364. * issues directly to the upstream developers of this software.
365. * Homepage: http://schloss.micro.umass.edu/wiki/Main_Page