Ticket #57764: main.log

File main.log, 70.3 KB (added by emilioxavier (Emilio Xavier Esposito), 6 years ago)
Line 
1version:1
2:debug:sysinfo macOS 10.14 (darwin/18.2.0) arch i386
3:debug:sysinfo MacPorts 2.5.4
4:debug:sysinfo Xcode 10.1
5:debug:sysinfo SDK 10.14
6:debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.14
7:debug:main bowtie2 has no conflicts
8:debug:main Executing org.macports.main (bowtie2)
9:debug:main dropping privileges: euid changed to 502, egid changed to 501.
10:debug:archivefetch archivefetch phase started at Mon Jan 14 16:55:00 EST 2019
11:msg:archivefetch --->  Fetching archive for bowtie2
12:debug:archivefetch Executing org.macports.archivefetch (bowtie2)
13:debug:archivefetch euid/egid changed to: 0/0
14:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
15:debug:archivefetch euid/egid changed to: 502/501
16:info:archivefetch --->  bowtie2-2.2.9_0.darwin_18.x86_64.tbz2 doesn't seem to exist in /opt/local/var/macports/incoming/verified
17:msg:archivefetch --->  Attempting to fetch bowtie2-2.2.9_0.darwin_18.x86_64.tbz2 from https://packages.macports.org/bowtie2
18:debug:archivefetch Fetching archive failed: The requested URL returned error: 404 Not Found
19:msg:archivefetch --->  Attempting to fetch bowtie2-2.2.9_0.darwin_18.x86_64.tbz2 from http://ywg.ca.packages.macports.org/mirror/macports/packages/bowtie2
20:debug:archivefetch Fetching archive failed: The requested URL returned error: 404 Not Found
21:msg:archivefetch --->  Attempting to fetch bowtie2-2.2.9_0.darwin_18.x86_64.tbz2 from http://sea.us.packages.macports.org/macports/packages/bowtie2
22:debug:archivefetch Fetching archive failed: The requested URL returned error: 404 Not Found
23:debug:archivefetch Privilege de-escalation not attempted as not running as root.
24:debug:fetch fetch phase started at Mon Jan 14 16:55:01 EST 2019
25:notice:fetch --->  Fetching distfiles for bowtie2
26:debug:fetch elevating privileges for fetch: euid changed to 0, egid changed to 0.
27:debug:fetch dropping privileges: euid changed to 502, egid changed to 501.
28:debug:fetch Executing org.macports.fetch (bowtie2)
29:info:fetch --->  bowtie2-2.2.9.tar.gz does not exist in /opt/local/var/macports/distfiles/bowtie2
30:notice:fetch --->  Attempting to fetch bowtie2-2.2.9.tar.gz from https://distfiles.macports.org/bowtie2
31:debug:fetch Privilege de-escalation not attempted as not running as root.
32:debug:checksum checksum phase started at Mon Jan 14 16:55:02 EST 2019
33:notice:checksum --->  Verifying checksums for bowtie2
34:debug:checksum Executing org.macports.checksum (bowtie2)
35:info:checksum --->  Checksumming bowtie2-2.2.9.tar.gz
36:debug:checksum Calculated (rmd160) is 4d385888f4cc1dc465cdd74b2e735ca2baed90e8
37:debug:checksum Correct (rmd160) checksum for bowtie2-2.2.9.tar.gz
38:debug:checksum Calculated (sha256) is 435c27c33807be6227b5370f53146a3e7f890534db650d3d0f5e86570f9d5170
39:debug:checksum Correct (sha256) checksum for bowtie2-2.2.9.tar.gz
40:debug:checksum Privilege de-escalation not attempted as not running as root.
41:debug:extract extract phase started at Mon Jan 14 16:55:02 EST 2019
42:notice:extract --->  Extracting bowtie2
43:debug:extract Executing org.macports.extract (bowtie2)
44:info:extract --->  Extracting bowtie2-2.2.9.tar.gz
45:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/bowtie2/bowtie2-2.2.9.tar.gz'
46:debug:extract Environment:
47:debug:extract CC_PRINT_OPTIONS='YES'
48:debug:extract CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/.CC_PRINT_OPTIONS'
49:debug:extract CPATH='/opt/local/include'
50:debug:extract LIBRARY_PATH='/opt/local/lib'
51:debug:extract MACOSX_DEPLOYMENT_TARGET='10.14'
52:info:extract Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/bowtie2/bowtie2-2.2.9.tar.gz' | /usr/bin/tar -xf -
53:debug:extract system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/bowtie2/bowtie2-2.2.9.tar.gz' | /usr/bin/tar -xf -
54:debug:extract euid/egid changed to: 0/0
55:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work to macports
56:debug:extract euid/egid changed to: 502/501
57:debug:extract Executing proc-post-org.macports.extract-extract-0
58:debug:extract Privilege de-escalation not attempted as not running as root.
59:debug:patch patch phase started at Mon Jan 14 16:55:02 EST 2019
60:debug:patch Executing org.macports.patch (bowtie2)
61:notice:patch --->  Applying patches to bowtie2
62:info:patch --->  Applying patch-src-Makefile.diff
63:debug:patch Environment:
64:debug:patch CC_PRINT_OPTIONS='YES'
65:debug:patch CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/.CC_PRINT_OPTIONS'
66:debug:patch CPATH='/opt/local/include'
67:debug:patch LIBRARY_PATH='/opt/local/lib'
68:debug:patch MACOSX_DEPLOYMENT_TARGET='10.14'
69:info:patch Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/ports/science/bowtie2/files/patch-src-Makefile.diff'
70:debug:patch system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9" && /usr/bin/patch -p0 < '/opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/ports/science/bowtie2/files/patch-src-Makefile.diff'
71:info:patch patching file Makefile
72:debug:patch Privilege de-escalation not attempted as not running as root.
73:debug:configure configure phase started at Mon Jan 14 16:55:02 EST 2019
74:notice:configure --->  Configuring bowtie2
75:debug:configure Preferred compilers: clang macports-clang-5.0 macports-clang-4.0
76:debug:configure Using compiler 'Xcode Clang'
77:debug:configure Executing org.macports.configure (bowtie2)
78:debug:configure Privilege de-escalation not attempted as not running as root.
79:debug:build build phase started at Mon Jan 14 16:55:02 EST 2019
80:notice:build --->  Building bowtie2
81:debug:build Executing org.macports.build (bowtie2)
82:debug:build Environment:
83:debug:build CC_PRINT_OPTIONS='YES'
84:debug:build CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/.CC_PRINT_OPTIONS'
85:debug:build CPATH='/opt/local/include'
86:debug:build LIBRARY_PATH='/opt/local/lib'
87:debug:build MACOSX_DEPLOYMENT_TARGET='10.14'
88:info:build Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9" && /usr/bin/make -j8 -w all CC=/usr/bin/clang CXX=/usr/bin/clang++ CPP=/usr/bin/cpp
89:debug:build system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9" && /usr/bin/make -j8 -w all CC=/usr/bin/clang CXX=/usr/bin/clang++ CPP=/usr/bin/cpp
90:info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9'
91:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
92:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
93:info:build              -I third_party \
94:info:build             -o bowtie2-build-s bt2_build.cpp \
95:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
96:info:build             -lpthread
97:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
98:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
99:info:build              -I third_party \
100:info:build             -o bowtie2-build-l bt2_build.cpp \
101:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
102:info:build             -lpthread
103:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
104:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
105:info:build              -I third_party \
106:info:build             -o bowtie2-align-s bt2_search.cpp \
107:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
108:info:build             -lpthread
109:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
110:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
111:info:build              -I third_party \
112:info:build             -o bowtie2-align-l bt2_search.cpp \
113:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
114:info:build             -lpthread
115:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 \
116:info:build             -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
117:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
118:info:build              -I third_party -I . \
119:info:build             -o bowtie2-inspect-s bt2_inspect.cpp \
120:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
121:info:build             -lpthread
122:info:build /usr/bin/clang++ -O3 -m64 -msse2  -funroll-loops -g3 \
123:info:build             -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -stdlib=libstdc++ -DPOPCNT_CAPABILITY\"" -stdlib=libstdc++ -DPOPCNT_CAPABILITY \
124:info:build             -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
125:info:build              -I third_party -I . \
126:info:build             -o bowtie2-inspect-l bt2_inspect.cpp \
127:info:build             ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
128:info:build             -lpthread
129:info:build clang: warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
130:info:build clang: clang: warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
131:info:build warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
132:info:build clangclang: : warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
133:info:build warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
134:info:build clang: warning: libstdc++ is deprecated; move to libc++ [-Wdeprecated]
135:info:build warningwarning: : include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
136:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
137:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
138:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
139:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
140:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
141:info:build bt2_inspect.cpp:22:10: fatal error: 'string' file not found
142:info:build bt2_inspect.cpp:22:10: fatal error: 'string' file not found
143:info:build #include <string>
144:info:build #include <string>
145:info:build          ^~~~~~~~
146:info:build          ^~~~~~~~
147:info:build bt2_build.cpp:20:10: fatal error: 'iostream' file not found
148:info:build #include <iostream>
149:info:build          ^~~~~~~~~~
150:info:build bt2_build.cpp:20:10: fatal error: 'iostream' file not found
151:info:build #include <iostream>
152:info:build          ^~~~~~~~~~
153:info:build bt2_search.cpp:21:10bt2_search.cpp:21::10:  fatal error: 'iostream' file not found
154:info:build fatal error: 'iostream' file not found
155:info:build #include <iostream>
156:info:build          ^~~~~~~~~~
157:info:build #include <iostream>
158:info:build          ^~~~~~~~~~
159:info:build 1 warning and 1 error generated.
160:info:build 1 warning and 1 error generated.
161:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
162:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
163:info:build 1 warning and 1 error generated.
164:info:build 1 warning generated.
165:info:build 1 warning generated.
166:info:build 1 warning and 1 error generated.
167:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
168:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
169:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
170:info:build In file included from ref_read.cpp:20:
171:info:build ./ref_read.h:23:10: fatal error: 'iostream' file not found
172:info:build In file included from ref_read.cpp:20:
173:info:build ./ref_read.h:23:10#include <iostream>:
174:info:build           ^~~~~~~~~~fatal error
175:info:build : 'iostream' file not found
176:info:build #include <iostream>
177:info:build          ^~~~~~~~~~
178:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
179:info:build 1 warning generated.
180:info:build 1 warning generated.
181:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
182:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
183:info:build In file included from ref_read.cpp:20:
184:info:build ./ref_read.h:23:10: fatal error: 'iostream' file not found
185:info:build #include <iostream>
186:info:build          ^~~~~~~~~~
187:info:build In file included from ref_read.cpp:20:
188:info:build ./ref_read.h:23:10: fatal error: 'iostream' file not found
189:info:build #include <iostream>
190:info:build          ^~~~~~~~~~
191:info:build 1 warning and 1 error generated.
192:info:build 1 warning and 1 error generated.
193:info:build 1 warning and 1 error generated.
194:info:build 1 warning and 1 error generated.
195:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
196:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
197:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
198:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
199:info:build alphabet.cpp:21:10: fatal error: 'cassert' file not found
200:info:build alphabet.cpp:21:10: fatal error: 'cassert' file not found
201:info:build #include <cassert>
202:info:build          ^~~~~~~~~
203:info:build #include <cassert>
204:info:build          ^~~~~~~~~
205:info:build 1 warning and 1 error generated.
206:info:build 1 warning and 1 error generated.
207:info:build 1 warning generated.
208:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
209:info:build 1 warning generated.
210:info:build 1 warning generated.
211:info:build 1 warning generated.
212:info:build 1 warning and 1 error generated.
213:info:build 1 warning and 1 error generated.
214:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
215:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
216:info:build In file included from ref_read.cpp:20:
217:info:build ./ref_read.h:23:10: fatal error: 'iostream' file not found
218:info:build #include <iostream>
219:info:build          ^~~~~~~~~~
220:info:build In file included from ref_read.cpp:20:
221:info:build ./ref_read.h:23:10: fatal error: 'iostream' file not found
222:info:build #include <iostream>
223:info:build          ^~~~~~~~~~
224:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning
225:info:build : include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
226:info:build edit.cpp:20:10: fatal error: 'iostream' file not found
227:info:build edit.cpp:20:10: fatal error: 'iostream' file not found
228:info:build #include <iostream>
229:info:build          ^~~~~~~~~~
230:info:build #include <iostream>
231:info:build          ^~~~~~~~~~
232:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
233:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
234:info:build alphabet.cpp:21:10: fatal error: 'cassert' file not found
235:info:build #include <cassert>
236:info:build          ^~~~~~~~~
237:info:build alphabet.cpp:21:10: fatal error: 'cassert' file not found
238:info:build #include <cassert>
239:info:build          ^~~~~~~~~
240:info:build 1 warning and 1 error generated.
241:info:build 1 warning and 1 error generated.
242:info:build warning: warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
243:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
244:info:build 1 warning generated.
245:info:build 1 warning generated.
246:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
247:info:build edit.cpp:20:10: fatal error: 'iostream' file not found
248:info:build #include <iostream>
249:info:build          ^~~~~~~~~~
250:info:build edit.cpp:20:10: fatal error: 'iostream' file not found
251:info:build #include <iostream>
252:info:build          ^~~~~~~~~~
253:info:build 1 warning and 1 error generated.
254:info:build 1 warning and 1 error generated.
255:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
256:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
257:info:build 1 warning and 1 error generated.
258:info:build 1 warning and 1 error generated.
259:info:build alphabet.cpp:21:alphabet.cpp:1021:: 10fatal error::  fatal error'cassert' file not found:
260:info:build 'cassert' file not found
261:info:build #include <cassert>
262:info:build          ^~~~~~~~~
263:info:build #include <cassert>
264:info:build          ^~~~~~~~~
265:info:build 1 warning and 1 error generated.
266:info:build 1 warning and 1 error generated.
267:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning
268:info:build : include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
269:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
270:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
271:info:build #include <string>
272:info:build          ^~~~~~~~
273:info:build #include <string>
274:info:build          ^~~~~~~~
275:info:build warning: warninginclude path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
276:info:build 1 warning1 warning generated.
277:info:build  generated.
278:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
279:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
280:info:build edit.cpp:20:10: fatal error: 'iostream' file not found
281:info:build #include <iostream>
282:info:build          ^~~~~~~~~~edit.cpp:20:10
283:info:build : fatal error: 'iostream' file not found
284:info:build #include <iostream>
285:info:build          ^~~~~~~~~~
286:info:build 1 warning and 1 error generated.
287:info:build 1 warning and 1 error generated.
288:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
289:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
290:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
291:info:build #include <string>
292:info:build          ^~~~~~~~
293:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
294:info:build #include <string>
295:info:build          ^~~~~~~~
296:info:build 1 warning and 1 error generated.
297:info:build 1 warning and 1 error generated.
298:info:build warningwarning: : include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
299:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
300:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
301:info:build #include <string>
302:info:build          ^~~~~~~~
303:info:build bt2_idx.cpp:20:10: fatal error: 'string' file not found
304:info:build #include <string>
305:info:build          ^~~~~~~~
306:info:build 1 warning and 1 error generated.
307:info:build 1 warning and 1 error generated.
308:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
309:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
310:info:build #include <string>
311:info:build          ^~~~~~~~
312:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
313:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
314:info:build #include <string>
315:info:build          ^~~~~~~~
316:info:build 1 warning and 1 error generated.
317:info:build 1 warning and 1 error generated.
318:info:build 1 warning and 1 error generated.
319:info:build 1 warning and 1 error generated.
320:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
321:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
322:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
323:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
324:info:build #include <string>
325:info:build          ^~~~~~~~
326:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
327:info:build #include <string>
328:info:build          ^~~~~~~~
329:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
330:info:build #include <string>
331:info:build          ^~~~~~~~
332:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
333:info:build bt2_io.cpp:20:10: fatal error: 'string' file not found
334:info:build #include <string>
335:info:build          ^~~~~~~~
336:info:build 1 warning and 1 error generated.
337:info:build 1 warning and 1 error generated.
338:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
339:info:build bt2_util.cpp:20:10: fatal error: 'string' file not found
340:info:build #include <string>
341:info:build          ^~~~~~~~
342:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
343:info:build bt2_util.cpp:20:10: fatal error: 'string' file not found
344:info:build #include <string>
345:info:build          ^~~~~~~~
346:info:build 1 warning and 1 error generated.
347:info:build 1 warning and 1 error generated.
348:info:build 1 warning and 1 error generated.
349:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
350:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
351:info:build bt2_util.cpp:20:10bt2_util.cpp:: 20fatal error: 'string' file not found
352:info:build :10: fatal error: 'string' file not found
353:info:build #include <string>
354:info:build          ^~~~~~~~
355:info:build #include <string>
356:info:build          ^~~~~~~~
357:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
358:info:build reference.cpp:20:10: fatal error: 'string' file not found
359:info:build #include <string>
360:info:build          ^~~~~~~~
361:info:build 1 warning and 1 error generated.
362:info:build 1 warning and 1 error generated.
363:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
364:info:build 1 warning and 1 error generated.
365:info:build reference.cpp:20:10: fatal error: 'string' file not found
366:info:build #include <string>
367:info:build          ^~~~~~~~
368:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
369:info:build bt2_util.cpp:20:10: fatal error: 'string' file not found
370:info:build #include <string>
371:info:build          ^~~~~~~~
372:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
373:info:build bt2_util.cpp:20:10: fatal error: 'string' file not found
374:info:build #include <string>
375:info:build          ^~~~~~~~
376:info:build 1 warning and 1 error generated.
377:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
378:info:build In file included from ds.cpp:20:
379:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
380:info:build #include <algorithm>
381:info:build          ^~~~~~~~~~~
382:info:build 1 warning and 1 error generated.
383:info:build 1 warning and 1 error generated.
384:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
385:info:build 1 warning and 1 error generated.
386:info:build In file included from ds.cpp:20:
387:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
388:info:build #include <algorithm>
389:info:build          ^~~~~~~~~~~
390:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
391:info:build reference.cpp:20:10warning: :include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] fatal error:
392:info:build 'string' file not found
393:info:build #include <string>
394:info:build          ^~~~~~~~
395:info:build reference.cpp:20:10: fatal error: 'string' file not found
396:info:build #include <string>
397:info:build          ^~~~~~~~
398:info:build 1 warning and 1 error generated.
399:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
400:info:build In file included from multikey_qsort.cpp:20:
401:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
402:info:build #include <iostream>
403:info:build          ^~~~~~~~~~
404:info:build 1 warning and 1 error generated.
405:info:build 1 warning and 1 error generated.
406:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
407:info:build In file included from multikey_qsort.cpp:20:
408:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
409:info:build #include <iostream>
410:info:build          ^~~~~~~~~~
411:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
412:info:build reference.cpp:20:10: fatal error: 'string' file not found
413:info:build #include <string>
414:info:build          ^~~~~~~~
415:info:build 1 warning and 1 error generated.
416:info:build 1 warning and 1 error generated.
417:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
418:info:build 1 warning and 1 error generated.
419:info:build reference.cpp:20:10: fatal error: 'string' file not found
420:info:build #include <string>
421:info:build          ^~~~~~~~
422:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
423:info:build In file included from ds.cpp:20:
424:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
425:info:build #include <algorithm>
426:info:build          ^~~~~~~~~~~
427:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
428:info:build In file included from ds.cpp:20:
429:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
430:info:build #include <algorithm>
431:info:build          ^~~~~~~~~~~
432:info:build 1 warning and 1 error generated.
433:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
434:info:build limit.cpp:20:10: fatal error: 'limits' file not found
435:info:build #include <limits>
436:info:build          ^~~~~~~~
437:info:build 1 warning and 1 error generated.
438:info:build 1 warning and 1 error generated.
439:info:build 1 warning and 1 error generated.
440:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
441:info:build 1 warning and 1 error generated.
442:info:build In file included from random_source.cpp:20:
443:info:build In file included from ./random_source.h:24:
444:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
445:info:build #include <stdexcept>
446:info:build          ^~~~~~~~~~~
447:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
448:info:build limit.cpp:20:10: fatal error: 'limits' file not found
449:info:build #include <limits>
450:info:build          ^~~~~~~~
451:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
452:info:build In file included from multikey_qsort.cpp:20:
453:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
454:info:build #include <iostream>
455:info:build          ^~~~~~~~~~
456:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
457:info:build 1 warning and 1 error generated.
458:info:build In file included from multikey_qsort.cpp:20:
459:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
460:info:build #include <iostream>
461:info:build          ^~~~~~~~~~
462:info:build 1 warning and 1 error generated.
463:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
464:info:build In file included from random_source.cpp:20:
465:info:build In file included from ./random_source.h:24:
466:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
467:info:build #include <stdexcept>
468:info:build          ^~~~~~~~~~~
469:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
470:info:build In file included from ds.cpp:20:
471:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
472:info:build #include <algorithm>
473:info:build          ^~~~~~~~~~~
474:info:build 1 warning and 1 error generated.
475:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
476:info:build 1 warning and 1 error generated.
477:info:build In file included from ds.cpp:20:
478:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
479:info:build #include <algorithm>
480:info:build          ^~~~~~~~~~~
481:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
482:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
483:info:build #include <exception>
484:info:build          ^~~~~~~~~~~
485:info:build 1 warning and 1 error generated.
486:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
487:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
488:info:build #include <exception>
489:info:build          ^~~~~~~~~~~
490:info:build 1 warning and 1 error generated.
491:info:build 1 warning and 1 error generated.
492:info:build 1 warning and 1 error generated.
493:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
494:info:build 1 warning and 1 error generated.
495:info:build In file included from multikey_qsort.cpp:20:
496:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
497:info:build #include <iostream>
498:info:build          ^~~~~~~~~~
499:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
500:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
501:info:build limit.cpp:20:10: fatal error: 'limits' file not found
502:info:build #include <limits>
503:info:build          ^~~~~~~~
504:info:build limit.cpp:20:10: fatal error: 'limits' file not found
505:info:build #include <limits>
506:info:build          ^~~~~~~~
507:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
508:info:build 1 warning and 1 error generated.
509:info:build 1 warning and 1 error generated.
510:info:build 1 warning and 1 error generated.
511:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
512:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
513:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
514:info:build In file included from multikey_qsort.cpp:20:
515:info:build ./multikey_qsort.h:23:10: fatal error: 'iostream' file not found
516:info:build #include <iostream>
517:info:build          ^~~~~~~~~~
518:info:build 1 warning and 1 error generated.
519:info:build In file included from random_source.cpp:20:
520:info:build In file included from ./random_source.h:24:
521:info:build ./assert_helpers.h:23:In file included from random_source.cpp10::20 fatal error: 'stdexcept' file not found:
522:info:build In file included from
523:info:build ./random_source.h:24:
524:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
525:info:build #include <stdexcept>
526:info:build          ^~~~~~~~~~~
527:info:build #include <stdexcept>
528:info:build          ^~~~~~~~~~~
529:info:build In file included from diff_sample.cpp:20:
530:info:build In file included from ./diff_sample.h:30:
531:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
532:info:build #include <stdexcept>
533:info:build          ^~~~~~~~~~~
534:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
535:info:build In file included from diff_sample.cpp:20:
536:info:build In file included from ./diff_sample.h:30:
537:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
538:info:build #include <stdexcept>
539:info:build          ^~~~~~~~~~~
540:info:build 1 warning and 11 warning error and 1 error generated generated.
541:info:build .
542:info:build warning: warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
543:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
544:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
545:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
546:info:build #include <exception>
547:info:build          ^~~~~~~~~~~
548:info:build #include <exception>
549:info:build          ^~~~~~~~~~~
550:info:build 1 warning and 1 error generated.
551:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
552:info:build bowtie_build_main.cpp:20:10: fatal error: 'iostream' file not found
553:info:build #include <iostream>
554:info:build          ^~~~~~~~~~
555:info:build 1 warning and 1 error generated.
556:info:build 1 warning and 1 error generated.
557:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
558:info:build limit.cpp:20:10: fatal error: 'limits' file not found
559:info:build #include <limits>
560:info:build          ^~~~~~~~
561:info:build 1 warning and 1 error generated.
562:info:build 1 warning and 1 error generated.
563:info:build 1 warning and 1 error generated.
564:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
565:info:build bowtie_build_main.cpp:20:10: fatal error: 'iostream' file not found
566:info:build #include <iostream>
567:info:build          ^~~~~~~~~~
568:info:build 1 warning and 1 error generated.
569:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
570:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
571:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
572:info:build In file included from random_source.cpp:20:
573:info:build In file included from ./random_source.h:24:
574:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
575:info:build #include <stdexcept>
576:info:build          ^~~~~~~~~~~
577:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
578:info:build 1 warning generated.
579:info:build limit.cpp:20:10: fatal error: 'limits' file not found
580:info:build #include <limits>
581:info:build          ^~~~~~~~
582:info:build 1 warning generated.
583:info:build 1 warning and 1 error generated.
584:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
585:info:build pat.cpp:20:10: fatal error: 'cmath' file not found
586:info:build #include <cmath>
587:info:build          ^~~~~~~
588:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
589:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
590:info:build pat.cpp:20:10: fatal error: 'cmath' file not found
591:info:build #include <cmath>
592:info:build          ^~~~~~~
593:info:build In file included from random_source.cpp:20:
594:info:build In file included from ./random_source.h:24:
595:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
596:info:build #include <stdexcept>
597:info:build          ^~~~~~~~~~~
598:info:build 1 warning and 1 error generated.
599:info:build make: *** [bowtie2-build-l] Error 1
600:info:build make: *** Waiting for unfinished jobs....
601:info:build 1 warning and 1 error generated.
602:info:build make: *** [bowtie2-build-s] Error 1
603:info:build 1 warning and 1 error generated.
604:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
605:info:build 1 warning and 1 error generated.
606:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
607:info:build #include <exception>
608:info:build          ^~~~~~~~~~~
609:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
610:info:build tinythread.cpp:24:10: fatal error: 'exception' file not found
611:info:build #include <exception>
612:info:build          ^~~~~~~~~~~
613:info:build 1 warning and 1 error generated.
614:info:build 1 warning and 1 error generated.
615:info:build make: *** [bowtie2-inspect-l] Error 1
616:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
617:info:build 1 warning and 1 error generated.
618:info:build sam.cpp:20:10: fatal error: 'string' file not found
619:info:build #include <string>
620:info:build          ^~~~~~~~
621:info:build 1 warning and 1 error generated.
622:info:build make: *** [bowtie2-inspect-s] Error 1
623:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
624:info:build sam.cpp:20:10: fatal error: 'string' file not found
625:info:build #include <string>
626:info:build          ^~~~~~~~
627:info:build 1 warning and 1 error generated.
628:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
629:info:build 1 warning and 1 error generated.
630:info:build In file included from read_qseq.cpp:20:
631:info:build ./pat.h:23:10: fatal error: 'cassert' file not found
632:info:build #include <cassert>
633:info:build          ^~~~~~~~~
634:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
635:info:build In file included from read_qseq.cpp:20:
636:info:build ./pat.h:23:10: fatal error: 'cassert' file not found
637:info:build #include <cassert>
638:info:build          ^~~~~~~~~
639:info:build 1 warning and 1 error generated.
640:info:build 1 warning and 1 error generated.
641:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
642:info:build aligner_seed_policy.cpp:20:10: fatal error: 'string' file not found
643:info:build #include <string>
644:info:build          ^~~~~~~~
645:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
646:info:build aligner_seed_policy.cpp:20:10: fatal error: 'string' file not found
647:info:build #include <string>
648:info:build          ^~~~~~~~
649:info:build 1 warning and 1 error generated.
650:info:build 1 warning and 1 error generated.
651:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
652:info:build In file included from aligner_seed.cpp:20:
653:info:build ./aligner_cache.h:58:10: fatal error: 'iostream' file not found
654:info:build #include <iostream>
655:info:build          ^~~~~~~~~~
656:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
657:info:build In file included from aligner_seed.cpp:20:
658:info:build ./aligner_cache.h:58:10: fatal error: 'iostream' file not found
659:info:build #include <iostream>
660:info:build          ^~~~~~~~~~
661:info:build 1 warning and 1 error generated.
662:info:build 1 warning and 1 error generated.
663:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
664:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
665:info:build aligner_seed2.cppaligner_seed2.cpp::2020::1010::  fatal errorfatal error: : 'limits' file not found'limits' file not found
666:info:build #include <limits>#include <limits>
667:info:build          ^~~~~~~~
668:info:build          ^~~~~~~~
669:info:build 1 warning and 1 error generated.
670:info:build 1 warning and 1 error generated.
671:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
672:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
673:info:build aligner_sw.cpp:20:10aligner_sw.cpp:: 20:10fatal error::  'limits' file not found
674:info:build fatal error: 'limits' file not found
675:info:build #include <limits>
676:info:build          ^~~~~~~~
677:info:build #include <limits>
678:info:build          ^~~~~~~~
679:info:build 1 warning and 1 error generated.
680:info:build 1 warning and 1 error generated.
681:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
682:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
683:info:build aligner_sw_driver.cpp:45:10: fatal error: 'iostream' file not found
684:info:build #include <iostream>
685:info:build          ^~~~~~~~~~
686:info:build aligner_sw_driver.cpp:45:10: fatal error: 'iostream' file not found
687:info:build #include <iostream>
688:info:build          ^~~~~~~~~~
689:info:build 1 warning and 1 error generated.
690:info:build 1 warning and 1 error generated.
691:info:build warning: warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
692:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
693:info:build In file included from aligner_cache.cpp:20:
694:info:build ./aligner_cache.h:58:10: fatal error: 'iostream' file not found
695:info:build #include <iostream>
696:info:build          ^~~~~~~~~~
697:info:build In file included from aligner_cache.cpp:20:
698:info:build ./aligner_cache.h:58:10: fatal error: 'iostream' file not found
699:info:build #include <iostream>
700:info:build          ^~~~~~~~~~
701:info:build 1 warning and 1 error generated.
702:info:build 1 warning and 1 error generated.
703:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
704:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
705:info:build aligner_result.cpp:20aligner_result.cpp::20:1010: fatal error::  fatal error: 'iostream' file not found
706:info:build 'iostream' file not found
707:info:build #include <iostream>#include <iostream>
708:info:build          ^~~~~~~~~~         ^~~~~~~~~~
709:info:build 1 warning and 1 error generated.
710:info:build 1 warning and 1 error generated.
711:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
712:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
713:info:build In file included from ref_coord.cpp:20:
714:info:build ./ref_coord.h:24:10: fatal error: 'iostream' file not found
715:info:build In file included from ref_coord.cpp:20:
716:info:build ./ref_coord.h:24:10: fatal error: 'iostream' file not found
717:info:build #include <iostream>
718:info:build          ^~~~~~~~~~
719:info:build #include <iostream>
720:info:build          ^~~~~~~~~~
721:info:build 1 warning and 1 error generated.
722:info:build 1 warning and 1 error generated.
723:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
724:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
725:info:build In file included from mask.cpp:20:
726:info:build ./mask.h:23:10: fatal error: 'iostream' file not found
727:info:build #include <iostream>
728:info:build          ^~~~~~~~~~
729:info:build In file included from mask.cpp:20:
730:info:build ./mask.h:23:10: fatal error: 'iostream' file not found
731:info:build #include <iostream>
732:info:build          ^~~~~~~~~~
733:info:build 1 warning and 1 error generated.
734:info:build 1 warning and 1 error generated.
735:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
736:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
737:info:build In file included from pe.cpp:In file included from 20pe.cpp:20:
738:info:build :
739:info:build ./assert_helpers.h./assert_helpers.h::2323::1010::  fatal errorfatal error: : 'stdexcept' file not found'stdexcept' file not found
740:info:build #include <stdexcept>#include <stdexcept>
741:info:build          ^~~~~~~~~~~         ^~~~~~~~~~~
742:info:build 1 warning and 1 error generated.
743:info:build 1 warning and 1 error generated.
744:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
745:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
746:info:build aln_sink.cpp:20:10: fatal error: 'iomanip' file not found
747:info:build aln_sink.cpp:20:10: fatal error: 'iomanip' file not found
748:info:build #include <iomanip>
749:info:build          ^~~~~~~~~
750:info:build #include <iomanip>
751:info:build          ^~~~~~~~~
752:info:build 1 warning and 1 error generated.
753:info:build 1 warning and 1 error generated.
754:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
755:info:build In file included from dp_framer.cpp:20:
756:info:build In file included from ./dp_framer.h:51:
757:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
758:info:build #include <algorithm>
759:info:build          ^~~~~~~~~~~
760:info:build In file included from dp_framer.cpp:20:
761:info:build In file included from ./dp_framer.h:51:
762:info:build ./ds.h:23:10: fatal error: 'algorithm' file not found
763:info:build #include <algorithm>
764:info:build          ^~~~~~~~~~~
765:info:build 1 warning and 1 error generated.
766:info:build 1 warning and 1 error generated.
767:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
768:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
769:info:build scoring.cpp:20:10: fatal error: 'iostream' file not found
770:info:build scoring.cpp:20:10: fatal error: 'iostream' file not found
771:info:build #include <iostream>
772:info:build          ^~~~~~~~~~
773:info:build #include <iostream>
774:info:build          ^~~~~~~~~~
775:info:build 1 warning and 1 error generated.
776:info:build 1 warning and 1 error generated.
777:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
778:info:build presets.cpp:20:10presets.cpp:: 20fatal error:: 'iostream' file not found
779:info:build 10: fatal error: 'iostream' file not found
780:info:build #include <iostream>
781:info:build          ^~~~~~~~~~
782:info:build #include <iostream>
783:info:build          ^~~~~~~~~~
784:info:build 1 warning and 1 error generated.
785:info:build 1 warning and 1 error generated.
786:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
787:info:build In file included from unique.cpp:20:
788:info:build ./unique.h:37:10: fatal error: 'string' file not found
789:info:build #include <string>
790:info:build          ^~~~~~~~
791:info:build In file included from unique.cpp:20:
792:info:build ./unique.h:37:10: fatal error: 'string' file not found
793:info:build #include <string>
794:info:build          ^~~~~~~~
795:info:build 1 warning and 1 error generated.
796:info:build 1 warning and 1 error generated.
797:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
798:info:build simple_func.cpp:20:10: fatal error: 'iostream' file not found
799:info:build simple_func.cpp:20:10: fatal error#include <iostream>:
800:info:build 'iostream' file not found         ^~~~~~~~~~
801:info:build #include <iostream>
802:info:build          ^~~~~~~~~~
803:info:build 1 warning and 1 error generated.
804:info:build 1 warning and 1 error generated.
805:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
806:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
807:info:build In file included from random_util.cpp:20:
808:info:build ./random_util.h:23:10: fatal error: 'algorithm' file not found
809:info:build #include <algorithm>
810:info:build          ^~~~~~~~~~~
811:info:build In file included from random_util.cpp:20:
812:info:build ./random_util.h:23:10: fatal error: 'algorithm' file not found
813:info:build #include <algorithm>
814:info:build          ^~~~~~~~~~~
815:info:build 1 warning and 1 error generated.
816:info:build 1 warning and 1 error generated.
817:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
818:info:build In file included from In file included from aligner_bt.cppaligner_bt.cpp::20:
819:info:build ./aligner_bt.h20::
820:info:build 23:./aligner_bt.h10::23 :fatal error10: :'utility' file not found
821:info:build fatal error: 'utility' file not found
822:info:build #include <utility>
823:info:build          ^~~~~~~~~
824:info:build #include <utility>
825:info:build          ^~~~~~~~~
826:info:build 1 warning and 1 error generated.
827:info:build 1 warning and 1 error generated.
828:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
829:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
830:info:build In file included from sse_util.cpp:20:
831:info:build In file included from ./sse_util.h:23:
832:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
833:info:build #include <stdexcept>
834:info:build          ^~~~~~~~~~~
835:info:build In file included from sse_util.cpp:20:
836:info:build In file included from ./sse_util.h:23:
837:info:build ./assert_helpers.h:23:10: fatal error: 'stdexcept' file not found
838:info:build #include <stdexcept>
839:info:build          ^~~~~~~~~~~
840:info:build 1 warning and 1 error generated.
841:info:build 1 warning and 1 error generated.
842:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
843:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
844:info:build In file included from aligner_swsse.cpp:21:
845:info:build In file included from In file included from ./aligner_sw_common.h:23aligner_swsse.cpp:
846:info:build :./aligner_result.h21:
847:info:build In file included from ./aligner_sw_common.h:23:
848:info:build ./aligner_result.h::23:23:1010::  fatal error: fatal error: 'utility' file not found
849:info:build 'utility' file not found
850:info:build #include <utility>
851:info:build          ^~~~~~~~~#include <utility>
852:info:build          ^~~~~~~~~
853:info:build 1 warning and 1 error generated.
854:info:build 1 warning and 1 error generated.
855:info:build warning: warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
856:info:build In file included from In file included from outq.cpp:outq.cpp20::
857:info:build 20In file included from :
858:info:build ./outq.hIn file included from ./outq.h:23:
859:info:build :./assert_helpers.h:2323:
860:info:build :./assert_helpers.h10::23 :fatal error10: :'stdexcept' file not found
861:info:build fatal error: 'stdexcept' file not found
862:info:build #include <stdexcept>#include <stdexcept>
863:info:build          ^~~~~~~~~~~         ^~~~~~~~~~~
864:info:build 1 warning and 1 error generated.
865:info:build 1 warning and 1 error generated.
866:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning:
867:info:build include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
868:info:build aligner_swsse_loc_i16.cppaligner_swsse_loc_i16.cpp::5555::1010::  fatal errorfatal error: 'limits' file not found
869:info:build : 'limits' file not found
870:info:build #include <limits>
871:info:build #include <limits>         ^~~~~~~~
872:info:build          ^~~~~~~~
873:info:build 1 warning and 1 error generated.
874:info:build 1 warning and 1 error generated.
875:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
876:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
877:info:build aligner_swsse_ee_i16.cpp:55:10: fatal error: 'limits' file not found
878:info:build #include <limits>
879:info:build          ^~~~~~~~
880:info:build aligner_swsse_ee_i16.cpp:55:10: fatal error: 'limits' file not found
881:info:build #include <limits>
882:info:build          ^~~~~~~~
883:info:build 1 warning and 1 error generated.
884:info:build 1 warning and 1 error generated.
885:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
886:info:build aligner_swsse_loc_u8.cpp:55:10aligner_swsse_loc_u8.cpp:55:: fatal error: 10'limits' file not found
887:info:build : fatal error: 'limits' file not found
888:info:build #include <limits>
889:info:build          ^~~~~~~~
890:info:build #include <limits>
891:info:build          ^~~~~~~~
892:info:build 1 warning and 1 error generated.
893:info:build 1 warning and 1 error generated.
894:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
895:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
896:info:build aligner_swsse_ee_u8.cpp:55:10: fatal error: 'limits' file not foundaligner_swsse_ee_u8.cpp:55:10
897:info:build : fatal error: 'limits' file not found
898:info:build #include <limits>
899:info:build          ^~~~~~~~
900:info:build #include <limits>
901:info:build          ^~~~~~~~
902:info:build 1 warning and 1 error generated.
903:info:build 1 warning and 1 error generated.
904:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
905:info:build warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
906:info:build In file included from aligner_driver.cpp:20:
907:info:build In file included from ./aligner_driver.h:78:
908:info:build ./aligner_seed2.h:98:10: fatal error: 'utility' file not found
909:info:build #include <utility>
910:info:build          ^~~~~~~~~
911:info:build In file included from aligner_driver.cpp:20:
912:info:build In file included from ./aligner_driver.h:78:
913:info:build ./aligner_seed2.h:98:10: fatal error: 'utility' file not found
914:info:build #include <utility>
915:info:build          ^~~~~~~~~
916:info:build 1 warning and 1 error generated.
917:info:build 1 warning and 1 error generated.
918:info:build warning: warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
919:info:build bowtie_main.cpp:20:10: fatal error: 'iostream' file not found
920:info:build #include <iostream>
921:info:build          ^~~~~~~~~~
922:info:build bowtie_main.cpp:20:10: fatal error: 'iostream' file not found
923:info:build #include <iostream>
924:info:build          ^~~~~~~~~~
925:info:build 1 warning and 1 error generated.
926:info:build 1 warning and 1 error generated.
927:info:build make: *** [bowtie2-align-l] Error 1
928:info:build make: *** [bowtie2-align-s] Error 1
929:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9'
930:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/work/bowtie2-2.2.9" && /usr/bin/make -j8 -w all CC=/usr/bin/clang CXX=/usr/bin/clang++ CPP=/usr/bin/cpp
931:info:build Exit code: 2
932:error:build Failed to build bowtie2: command execution failed
933:debug:build Error code: CHILDSTATUS 10317 2
934:debug:build Backtrace: command execution failed
935:debug:build     while executing
936:debug:build "system {*}$notty {*}$nice $fullcmdstring"
937:debug:build     invoked from within
938:debug:build "command_exec build"
939:debug:build     (procedure "portbuild::build_main" line 8)
940:debug:build     invoked from within
941:debug:build "$procedure $targetname"
942:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_bowtie2/bowtie2/main.log for details.