Ticket #53228: main.log

File main.log, 43.7 KB (added by Morpheu5 (Andrea Franceschini), 7 years ago)

main.log

Line 
1version:1
2:msg:archivefetch --->  Computing dependencies for R:info:archivefetch .:debug:archivefetch Searching for dependency: pkgconfig
3:debug:archivefetch Found Dependency: receipt exists for pkgconfig
4:debug:archivefetch Searching for dependency: gcc5
5:debug:archivefetch Found Dependency: receipt exists for gcc5
6:debug:archivefetch Searching for dependency: readline
7:debug:archivefetch Found Dependency: receipt exists for readline
8:debug:archivefetch Searching for dependency: icu
9:debug:archivefetch Found Dependency: receipt exists for icu
10:debug:archivefetch Searching for dependency: libiconv
11:debug:archivefetch Found Dependency: receipt exists for libiconv
12:debug:archivefetch Searching for dependency: zlib
13:debug:archivefetch Found Dependency: receipt exists for zlib
14:debug:archivefetch Searching for dependency: xz
15:debug:archivefetch Found Dependency: receipt exists for xz
16:debug:archivefetch Searching for dependency: libgcc
17:debug:archivefetch Found Dependency: receipt exists for libgcc
18:debug:archivefetch Searching for dependency: cairo
19:debug:archivefetch Found Dependency: receipt exists for cairo
20:debug:archivefetch Searching for dependency: pango
21:debug:archivefetch Found Dependency: receipt exists for pango
22:debug:archivefetch Searching for dependency: glib2
23:debug:archivefetch Found Dependency: receipt exists for glib2
24:debug:archivefetch Searching for dependency: freetype
25:debug:archivefetch Found Dependency: receipt exists for freetype
26:debug:archivefetch Searching for dependency: fontconfig
27:debug:archivefetch Found Dependency: receipt exists for fontconfig
28:debug:archivefetch Searching for dependency: gettext
29:debug:archivefetch Found Dependency: receipt exists for gettext
30:debug:archivefetch Searching for dependency: libpng
31:debug:archivefetch Found Dependency: receipt exists for libpng
32:debug:archivefetch Searching for dependency: tiff
33:debug:archivefetch Found Dependency: receipt exists for tiff
34:debug:archivefetch Searching for dependency: jpeg
35:debug:archivefetch Found Dependency: receipt exists for jpeg
36:msg:archivefetch
37:debug:main Executing org.macports.main (R)
38:debug:main changing euid/egid - current euid: 0 - current egid: 0
39:debug:main egid changed to: 501
40:debug:main euid changed to: 502
41:debug:fetch fetch phase started at Thu Jan  5 17:04:32 CET 2017
42:notice:fetch --->  Fetching distfiles for R
43:debug:fetch Executing proc-pre-org.macports.fetch-fetch-0
44:debug:fetch compilers.enforce_c list:
45:debug:fetch compilers.enforce_fortran list:
46:debug:fetch compilers.enforce_some_fortran list:
47:debug:fetch Executing org.macports.fetch (R)
48:debug:fetch Privilege de-escalation not attempted as not running as root.
49:debug:checksum checksum phase started at Thu Jan  5 17:04:32 CET 2017
50:notice:checksum --->  Verifying checksums for R
51:debug:checksum Executing org.macports.checksum (R)
52:info:checksum --->  Checksumming R-3.3.2.tar.gz
53:debug:checksum Calculated (rmd160) is 99eb136e8ffb6f4a09943565af08f3dd4a5a7491
54:debug:checksum Correct (rmd160) checksum for R-3.3.2.tar.gz
55:debug:checksum Calculated (sha256) is d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c
56:debug:checksum Correct (sha256) checksum for R-3.3.2.tar.gz
57:debug:checksum Privilege de-escalation not attempted as not running as root.
58:debug:extract extract phase started at Thu Jan  5 17:04:32 CET 2017
59:notice:extract --->  Extracting R
60:debug:extract Executing org.macports.extract (R)
61:info:extract --->  Extracting R-3.3.2.tar.gz
62:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/R/R-3.3.2.tar.gz'
63:debug:extract Environment:
64CC_PRINT_OPTIONS='YES'
65CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/.CC_PRINT_OPTIONS'
66CPATH='/opt/local/include'
67LIBRARY_PATH='/opt/local/lib'
68MACOSX_DEPLOYMENT_TARGET='10.12'
69:debug:extract Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R/R-3.3.2.tar.gz' | /usr/bin/tar -xf -'
70:debug:extract Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R/R-3.3.2.tar.gz' | /usr/bin/tar -xf -
71:debug:extract euid/egid changed to: 0/0
72:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work to macports
73:debug:extract euid/egid changed to: 502/501
74:debug:extract Privilege de-escalation not attempted as not running as root.
75:debug:patch patch phase started at Thu Jan  5 17:04:33 CET 2017
76:debug:patch Executing org.macports.patch (R)
77:debug:patch Executing proc-post-org.macports.patch-patch-0
78:info:patch --->  Patching Rscript.c: s|R_HOME|"/opt/local/Library/Frameworks/R.framework/Versions/3.3/Resources"|
79:debug:patch Executing reinplace: /usr/bin/sed s|R_HOME|\"/opt/local/Library/Frameworks/R.framework/Versions/3.3/Resources\"| < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/unix/Rscript.c >@ file25 2>@stderr
80:debug:patch euid/egid changed to: 0/0
81:debug:patch chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/unix/Rscript.c to macports
82:debug:patch euid/egid changed to: 502/501
83:debug:patch euid/egid changed to: 0/0
84:debug:patch setting attributes on /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/unix/Rscript.c
85:debug:patch euid/egid changed to: 502/501
86:info:patch --->  Patching Defn.h: s|<libintl.h>|"libintl.h"|
87:debug:patch Executing reinplace: /usr/bin/sed s|<libintl.h>|\"libintl.h\"| < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/include/Defn.h >@ file25 2>@stderr
88:debug:patch euid/egid changed to: 0/0
89:debug:patch chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/include/Defn.h to macports
90:debug:patch euid/egid changed to: 502/501
91:debug:patch euid/egid changed to: 0/0
92:debug:patch setting attributes on /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/src/include/Defn.h
93:debug:patch euid/egid changed to: 502/501
94:debug:patch Privilege de-escalation not attempted as not running as root.
95:debug:configure configure phase started at Thu Jan  5 17:04:33 CET 2017
96:notice:configure --->  Configuring R
97:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
98:debug:configure Using compiler 'Xcode Clang'
99:debug:configure Executing proc-pre-org.macports.configure-configure-0
100:debug:configure Active variants check for source-type install considers depends_fetch depends_extract depends_lib depends_build depends_run: readline icu libiconv zlib xz libgcc cairo pango glib2 freetype fontconfig gettext libpng tiff jpeg pkgconfig gcc5
101:debug:configure Executing proc-pre-org.macports.configure-configure-1
102:debug:configure Active variants check for source-type install considers depends_fetch depends_extract depends_lib depends_build depends_run: readline icu libiconv zlib xz libgcc cairo pango glib2 freetype fontconfig gettext libpng tiff jpeg pkgconfig gcc5
103:debug:configure Executing org.macports.configure (R)
104:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
105:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
106:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
107:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
108:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
109:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
110:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
111:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
112:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
113:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
114:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
115:debug:configure Preferred compilers: clang macports-clang-3.8 macports-clang-3.7
116:debug:configure Environment:
117CC='/usr/bin/clang'
118CC_PRINT_OPTIONS='YES'
119CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/.CC_PRINT_OPTIONS'
120CFLAGS='-pipe -Os -arch x86_64'
121CPATH='/opt/local/include'
122CPPFLAGS='-I/opt/local/include'
123CXX='/usr/bin/clang++'
124CXXFLAGS='-pipe -Os -arch x86_64 -stdlib=libc++'
125F77='/opt/local/bin/gfortran-mp-5'
126F90FLAGS='-pipe -Os -m64'
127FC='/opt/local/bin/gfortran-mp-5'
128FCFLAGS='-pipe -Os'
129FFLAGS='-pipe -Os'
130INSTALL='/usr/bin/install -c'
131LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names'
132LIBRARY_PATH='/opt/local/lib'
133MACOSX_DEPLOYMENT_TARGET='10.12'
134OBJC='/usr/bin/clang'
135OBJCFLAGS='-pipe -Os -arch x86_64'
136OBJCXX='/usr/bin/clang++'
137OBJCXXFLAGS='-pipe -Os -arch x86_64 -stdlib=libc++'
138:debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --without-tcltk --with-system-zlib --without-internal-tzcode --without-x --with-included-gettext --with-blas="-framework Accelerate" --with-lapack --with-cairo --with-recommended-packages'
139:debug:configure Executing command line:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --without-tcltk --with-system-zlib --without-internal-tzcode --without-x --with-included-gettext --with-blas="-framework Accelerate" --with-lapack --with-cairo --with-recommended-packages
140:info:configure configure: WARNING: unrecognized options: --with-system-zlib
141:info:configure checking build system type... x86_64-apple-darwin16.3.0
142:info:configure checking host system type... x86_64-apple-darwin16.3.0
143:info:configure loading site script './config.site'
144:info:configure loading build-specific script './config.site'
145:info:configure checking for pwd... /bin/pwd
146:info:configure checking whether builddir is srcdir... yes
147:info:configure checking for working aclocal... found
148:info:configure checking for working autoconf... found
149:info:configure checking for working automake... found
150:info:configure checking for working autoheader... found
151:info:configure checking whether ln -s works... yes
152:info:configure checking for bison... bison -y
153:info:configure checking for ar... ar
154:info:configure checking for a BSD-compatible install... /usr/bin/install -c
155:info:configure checking for sed... /usr/bin/sed
156:info:configure checking for which... /usr/bin/which
157:info:configure checking for less... /opt/local/bin/less
158:info:configure checking for gtar... no
159:info:configure checking for gnutar... no
160:info:configure checking for tar... /usr/bin/tar
161:info:configure checking for tex... /opt/local/bin/tex
162:info:configure checking for pdftex... /opt/local/bin/pdftex
163:info:configure checking for pdflatex... /opt/local/bin/pdflatex
164:info:configure checking for makeindex... /opt/local/bin/makeindex
165:info:configure checking for texi2any... /opt/local/bin/texi2any
166:info:configure checking whether texi2any version is at least 5.1... yes
167:info:configure checking for ginstall-info... no
168:info:configure checking for install-info... /opt/local/bin/install-info
169:info:configure checking for texi2dvi... /opt/local/bin/texi2dvi
170:info:configure checking for kpsewhich... /opt/local/bin/kpsewhich
171:info:configure checking for latex inconsolata package... found zi4.sty
172:info:configure checking for unzip... /usr/bin/unzip
173:info:configure checking for zip... /usr/bin/zip
174:info:configure checking for gzip... /usr/bin/gzip
175:info:configure checking for bzip2... /opt/local/bin/bzip2
176:info:configure checking for firefox... no
177:info:configure checking for mozilla... no
178:info:configure checking for galeon... no
179:info:configure checking for opera... no
180:info:configure checking for xdg-open... no
181:info:configure checking for kfmclient... no
182:info:configure checking for gnome-moz-remote... no
183:info:configure checking for open... /usr/bin/open
184:info:configure using default browser ... /usr/bin/open
185:info:configure checking for acroread... no
186:info:configure checking for acroread4... no
187:info:configure checking for xdg-open... no
188:info:configure checking for evince... no
189:info:configure checking for xpdf... no
190:info:configure checking for gv... no
191:info:configure checking for gnome-gv... no
192:info:configure checking for ggv... no
193:info:configure checking for okular... no
194:info:configure checking for kpdf... no
195:info:configure checking for open... /usr/bin/open
196:info:configure checking for notangle... false
197:info:configure checking for realpath... false
198:info:configure checking for pkg-config... /opt/local/bin/pkg-config
199:info:configure checking for gcc... /usr/bin/clang
200:info:configure checking whether the C compiler works... yes
201:info:configure checking for C compiler default output file name... a.out
202:info:configure checking for suffix of executables...
203:info:configure checking whether we are cross compiling... no
204:info:configure checking for suffix of object files... o
205:info:configure checking whether we are using the GNU C compiler... yes
206:info:configure checking whether /usr/bin/clang accepts -g... yes
207:info:configure checking for /usr/bin/clang option to accept ISO C89... none needed
208:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
209:info:configure checking for grep that handles long lines and -e... /opt/local/bin/grep
210:info:configure checking for egrep... /opt/local/bin/grep -E
211:info:configure checking whether /usr/bin/clang needs -traditional... no
212:info:configure checking for ANSI C header files... yes
213:info:configure checking for sys/types.h... yes
214:info:configure checking for sys/stat.h... yes
215:info:configure checking for stdlib.h... yes
216:info:configure checking for string.h... yes
217:info:configure checking for memory.h... yes
218:info:configure checking for strings.h... yes
219:info:configure checking for inttypes.h... yes
220:info:configure checking for stdint.h... yes
221:info:configure checking for unistd.h... yes
222:info:configure checking minix/config.h usability... no
223:info:configure checking minix/config.h presence... no
224:info:configure checking for minix/config.h... no
225:info:configure checking whether it is safe to define __EXTENSIONS__... yes
226:info:configure checking how to run the C preprocessor... /usr/bin/clang -E
227:info:configure defining F77 to be /opt/local/bin/gfortran-mp-5
228:info:configure checking whether we are using the GNU Fortran 77 compiler... yes
229:info:configure checking whether /opt/local/bin/gfortran-mp-5 accepts -g... yes
230:info:configure checking whether we are using the GNU C++ compiler... yes
231:info:configure checking whether /usr/bin/clang++ accepts -g... yes
232:info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E
233:info:configure checking whether __attribute__((visibility())) is supported... no
234:info:configure checking whether /usr/bin/clang accepts -fvisibility... yes
235:info:configure checking whether /opt/local/bin/gfortran-mp-5 accepts -fvisibility... yes
236:info:configure checking whether we are using the GNU Objective C compiler... yes
237:info:configure checking whether /usr/bin/clang accepts -g... yes
238:info:configure checking for Objective C++ compiler... trying some possibilities
239:info:configure checking whether /usr/bin/clang++ can compile ObjC++... yes
240:info:configure /usr/bin/clang++
241:info:configure checking how to print strings... printf
242:info:configure checking for a sed that does not truncate output... (cached) /usr/bin/sed
243:info:configure checking for fgrep... /opt/local/bin/grep -F
244:info:configure checking for ld used by /usr/bin/clang... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
245:info:configure checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
246:info:configure checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm -B
247:info:configure checking the name lister (/opt/local/bin/nm -B) interface... BSD nm
248:info:configure checking the maximum length of command line arguments... 196608
249:info:configure checking how to convert x86_64-apple-darwin16.3.0 file names to x86_64-apple-darwin16.3.0 format... func_convert_file_noop
250:info:configure checking how to convert x86_64-apple-darwin16.3.0 file names to toolchain format... func_convert_file_noop
251:info:configure checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r
252:info:configure checking for objdump... objdump
253:info:configure checking how to recognize dependent libraries... pass_all
254:info:configure checking for dlltool... no
255:info:configure checking how to associate runtime and link libraries... printf %s\n
256:info:configure checking for archiver @FILE support... no
257:info:configure checking for strip... strip
258:info:configure checking for ranlib... ranlib
259:info:configure checking for gawk... gawk
260:info:configure checking command to parse /opt/local/bin/nm -B output from /usr/bin/clang object... ok
261:info:configure checking for sysroot... no
262:info:configure checking for a working dd... /bin/dd
263:info:configure checking how to truncate binary pipes... /bin/dd bs=4096 count=1
264:info:configure checking for mt... no
265:info:configure checking if : is a manifest tool... no
266:info:configure checking for dsymutil... dsymutil
267:info:configure checking for nmedit... nmedit
268:info:configure checking for lipo... lipo
269:info:configure checking for otool... otool
270:info:configure checking for otool64... no
271:info:configure checking for -single_module linker flag... yes
272:info:configure checking for -exported_symbols_list linker flag... yes
273:info:configure checking for -force_load linker flag... yes
274:info:configure checking for dlfcn.h... yes
275:info:configure checking for objdir... .libs
276:info:configure checking if /usr/bin/clang supports -fno-rtti -fno-exceptions... yes
277:info:configure checking for /usr/bin/clang option to produce PIC... -fno-common -DPIC
278:info:configure checking if /usr/bin/clang PIC flag -fno-common -DPIC works... yes
279:info:configure checking if /usr/bin/clang static flag -static works... no
280:info:configure checking if /usr/bin/clang supports -c -o file.o... yes
281:info:configure checking if /usr/bin/clang supports -c -o file.o... (cached) yes
282:info:configure checking whether the /usr/bin/clang linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
283:info:configure checking dynamic linker characteristics... darwin16.3.0 dyld
284:info:configure checking how to hardcode library paths into programs... immediate
285:info:configure checking whether stripping libraries is possible... yes
286:info:configure checking if libtool supports shared libraries... yes
287:info:configure checking whether to build shared libraries... yes
288:info:configure checking whether to build static libraries... no
289:info:configure checking how to run the C++ preprocessor... /usr/bin/clang++ -E
290:info:configure checking for ld used by /usr/bin/clang++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
291:info:configure checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
292:info:configure checking whether the /usr/bin/clang++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
293:info:configure checking for /usr/bin/clang++ option to produce PIC... -fno-common -DPIC
294:info:configure checking if /usr/bin/clang++ PIC flag -fno-common -DPIC works... yes
295:info:configure checking if /usr/bin/clang++ static flag -static works... no
296:info:configure checking if /usr/bin/clang++ supports -c -o file.o... yes
297:info:configure checking if /usr/bin/clang++ supports -c -o file.o... (cached) yes
298:info:configure checking whether the /usr/bin/clang++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
299:info:configure checking dynamic linker characteristics... darwin16.3.0 dyld
300:info:configure checking how to hardcode library paths into programs... immediate
301:info:configure checking if libtool supports shared libraries... yes
302:info:configure checking whether to build shared libraries... yes
303:info:configure checking whether to build static libraries... no
304:info:configure checking for /opt/local/bin/gfortran-mp-5 option to produce PIC... -fno-common
305:info:configure checking if /opt/local/bin/gfortran-mp-5 PIC flag -fno-common works... yes
306:info:configure checking if /opt/local/bin/gfortran-mp-5 static flag -static works... no
307:info:configure checking if /opt/local/bin/gfortran-mp-5 supports -c -o file.o... yes
308:info:configure checking if /opt/local/bin/gfortran-mp-5 supports -c -o file.o... (cached) yes
309:info:configure checking whether the /opt/local/bin/gfortran-mp-5 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
310:info:configure checking dynamic linker characteristics... darwin16.3.0 dyld
311:info:configure checking how to hardcode library paths into programs... immediate
312:info:configure checking for sin in -lm... yes
313:info:configure checking readline/history.h usability... yes
314:info:configure checking readline/history.h presence... yes
315:info:configure checking for readline/history.h... yes
316:info:configure checking readline/readline.h usability... yes
317:info:configure checking readline/readline.h presence... yes
318:info:configure checking for readline/readline.h... yes
319:info:configure checking for rl_callback_read_char in -lreadline... yes
320:info:configure checking for history_truncate_file... yes
321:info:configure checking whether rl_completion_matches exists and is declared... yes
322:info:configure checking for ANSI C header files... (cached) yes
323:info:configure checking for dirent.h that defines DIR... yes
324:info:configure checking for library containing opendir... none required
325:info:configure checking for sys/wait.h that is POSIX.1 compatible... yes
326:info:configure checking arpa/inet.h usability... yes
327:info:configure checking arpa/inet.h presence... yes
328:info:configure checking for arpa/inet.h... yes
329:info:configure checking dl.h usability... no
330:info:configure checking dl.h presence... no
331:info:configure checking for dl.h... no
332:info:configure checking for dlfcn.h... (cached) yes
333:info:configure checking elf.h usability... no
334:info:configure checking elf.h presence... no
335:info:configure checking for elf.h... no
336:info:configure checking features.h usability... no
337:info:configure checking features.h presence... no
338:info:configure checking for features.h... no
339:info:configure checking fcntl.h usability... yes
340:info:configure checking fcntl.h presence... yes
341:info:configure checking for fcntl.h... yes
342:info:configure checking floatingpoint.h usability... no
343:info:configure checking floatingpoint.h presence... no
344:info:configure checking for floatingpoint.h... no
345:info:configure checking fpu_control.h usability... no
346:info:configure checking fpu_control.h presence... no
347:info:configure checking for fpu_control.h... no
348:info:configure checking glob.h usability... yes
349:info:configure checking glob.h presence... yes
350:info:configure checking for glob.h... yes
351:info:configure checking grp.h usability... yes
352:info:configure checking grp.h presence... yes
353:info:configure checking for grp.h... yes
354:info:configure checking langinfo.h usability... yes
355:info:configure checking langinfo.h presence... yes
356:info:configure checking for langinfo.h... yes
357:info:configure checking netdb.h usability... yes
358:info:configure checking netdb.h presence... yes
359:info:configure checking for netdb.h... yes
360:info:configure checking netinet/in.h usability... yes
361:info:configure checking netinet/in.h presence... yes
362:info:configure checking for netinet/in.h... yes
363:info:configure checking pwd.h usability... yes
364:info:configure checking pwd.h presence... yes
365:info:configure checking for pwd.h... yes
366:info:configure checking sched.h usability... yes
367:info:configure checking sched.h presence... yes
368:info:configure checking for sched.h... yes
369:info:configure checking for strings.h... (cached) yes
370:info:configure checking sys/param.h usability... yes
371:info:configure checking sys/param.h presence... yes
372:info:configure checking for sys/param.h... yes
373:info:configure checking sys/resource.h usability... yes
374:info:configure checking sys/resource.h presence... yes
375:info:configure checking for sys/resource.h... yes
376:info:configure checking sys/select.h usability... yes
377:info:configure checking sys/select.h presence... yes
378:info:configure checking for sys/select.h... yes
379:info:configure checking sys/socket.h usability... yes
380:info:configure checking sys/socket.h presence... yes
381:info:configure checking for sys/socket.h... yes
382:info:configure checking for sys/stat.h... (cached) yes
383:info:configure checking sys/time.h usability... yes
384:info:configure checking sys/time.h presence... yes
385:info:configure checking for sys/time.h... yes
386:info:configure checking sys/times.h usability... yes
387:info:configure checking sys/times.h presence... yes
388:info:configure checking for sys/times.h... yes
389:info:configure checking sys/utsname.h usability... yes
390:info:configure checking sys/utsname.h presence... yes
391:info:configure checking for sys/utsname.h... yes
392:info:configure checking for unistd.h... (cached) yes
393:info:configure checking utime.h usability... yes
394:info:configure checking utime.h presence... yes
395:info:configure checking for utime.h... yes
396:info:configure checking stdalign.h usability... yes
397:info:configure checking stdalign.h presence... yes
398:info:configure checking for stdalign.h... yes
399:info:configure checking errno.h usability... yes
400:info:configure checking errno.h presence... yes
401:info:configure checking for errno.h... yes
402:info:configure checking for inttypes.h... (cached) yes
403:info:configure checking limits.h usability... yes
404:info:configure checking limits.h presence... yes
405:info:configure checking for limits.h... yes
406:info:configure checking locale.h usability... yes
407:info:configure checking locale.h presence... yes
408:info:configure checking for locale.h... yes
409:info:configure checking stdarg.h usability... yes
410:info:configure checking stdarg.h presence... yes
411:info:configure checking for stdarg.h... yes
412:info:configure checking stdbool.h usability... yes
413:info:configure checking stdbool.h presence... yes
414:info:configure checking for stdbool.h... yes
415:info:configure checking for stdint.h... (cached) yes
416:info:configure checking for string.h... (cached) yes
417:info:configure checking whether setjmp.h is POSIX.1 compatible... yes
418:info:configure checking whether sigsetjmp is declared... yes
419:info:configure checking whether siglongjmp is declared... yes
420:info:configure checking for GNU C library with version >= 2... no
421:info:configure checking return type of signal handlers... void
422:info:configure checking for uint64_t... yes
423:info:configure checking for int64_t... yes
424:info:configure checking for int_fast64_t... yes
425:info:configure checking for pid_t... yes
426:info:configure checking for size_t... yes
427:info:configure checking whether SIZE_MAX is declared... yes
428:info:configure checking for blkcnt_t... yes
429:info:configure checking for type of socket length... socklen_t *
430:info:configure checking for stack_t... yes
431:info:configure checking for intptr_t... yes
432:info:configure checking for uintptr_t... yes
433:info:configure checking whether byte ordering is bigendian... no
434:info:configure checking for an ANSI C-conforming const... yes
435:info:configure checking for /usr/bin/clang option to accept ISO C99... none needed
436:info:configure checking for /usr/bin/clang option to accept ISO Standard C... (cached) none needed
437:info:configure checking for inline... inline
438:info:configure checking size of int... 4
439:info:configure checking size of long... 8
440:info:configure checking size of long long... 8
441:info:configure checking size of double... 8
442:info:configure checking size of size_t... 8
443:info:configure checking size of long double... 16
444:info:configure checking whether we can compute C Make dependencies... yes, using $(CC) -MM
445:info:configure checking whether /usr/bin/clang supports -c -o FILE.lo... yes
446:info:configure checking for /usr/bin/clang option to support OpenMP... unsupported
447:info:configure checking how to get verbose linking output from /opt/local/bin/gfortran-mp-5... -v
448:info:configure checking for Fortran 77 libraries of /opt/local/bin/gfortran-mp-5...  -L/opt/local/lib -L/opt/local/lib/gcc5/gcc/x86_64-apple-darwin16/5.4.0 -L/opt/local/lib/gcc5/gcc/x86_64-apple-darwin16/5.4.0/../../.. -lgfortran -lquadmath -lm
449:info:configure checking how to get verbose linking output from /usr/bin/clang... configure: WARNING: cannot determine how to obtain linking information from /usr/bin/clang
450:info:configure
451:info:configure checking for C libraries of /usr/bin/clang...
452:info:configure checking for dummy main to link with Fortran 77 libraries... none
453:info:configure checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
454:info:configure checking whether /opt/local/bin/gfortran-mp-5 appends underscores to external names... yes
455:info:configure checking whether /opt/local/bin/gfortran-mp-5 appends extra underscores to external names... no
456:info:configure checking whether mixed C/Fortran code can be run... yes
457:info:configure checking whether /opt/local/bin/gfortran-mp-5 and /usr/bin/clang agree on int and double... yes
458:info:configure checking whether /opt/local/bin/gfortran-mp-5 and /usr/bin/clang agree on double complex... yes
459:info:configure checking for /opt/local/bin/gfortran-mp-5 option to support OpenMP... -fopenmp
460:info:configure checking whether /usr/bin/clang++ accepts -M for generating dependencies... yes
461:info:configure checking for /usr/bin/clang++ option to support OpenMP... unsupported
462:info:configure checking whether we can compute ObjC Make dependencies... yes, using /usr/bin/clang -MM
463:info:configure checking for ObjC runtime library... -lobjc
464:info:configure checking for ObjC runtime style... next
465:info:configure checking whether /usr/bin/clang accepts -fobjc-exceptions... yes
466:info:configure checking for cached Foundation settings... no
467:info:configure checking whether default Foundation framework works... no
468:info:configure checking whether -framework Foundation works... yes
469:info:configure checking for working Foundation implementation... yes
470:info:configure checking whether C runtime needs -D__NO_MATH_INLINES... no
471:info:configure checking for xmkmf... no
472:info:configure checking whether linker supports dynamic lookup... yes
473:info:configure checking whether /usr/bin/clang++  supports C++11 features by default... no
474:info:configure checking whether /usr/bin/clang++  supports C++11 features with -std=c++11... yes
475:info:configure checking for off_t... yes
476:info:configure checking for working alloca.h... yes
477:info:configure checking for alloca... yes
478:info:configure checking whether alloca is declared... yes
479:info:configure checking whether expm1 exists and is declared... yes
480:info:configure checking whether hypot exists and is declared... yes
481:info:configure checking whether log1p exists and is declared... yes
482:info:configure checking whether log1pl exists and is declared... yes
483:info:configure checking whether log2 exists and is declared... yes
484:info:configure checking whether log10 exists and is declared... yes
485:info:configure checking whether nearbyint exists and is declared... yes
486:info:configure checking whether nearbyintl exists and is declared... yes
487:info:configure checking whether powl exists and is declared... yes
488:info:configure checking whether rint exists and is declared... yes
489:info:configure checking whether rintl exists and is declared... yes
490:info:configure checking whether va_copy exists and is declared... yes
491:info:configure checking for isblank... yes
492:info:configure checking sunmath.h usability... no
493:info:configure checking sunmath.h presence... no
494:info:configure checking for sunmath.h... no
495:info:configure checking for cospi in -lsunmath... no
496:info:configure checking for atanpi... no
497:info:configure checking for atan2pi... no
498:info:configure checking for cospi... no
499:info:configure checking for exp10... no
500:info:configure checking for pown... no
501:info:configure checking for sinpi... no
502:info:configure checking for tanpi... no
503:info:configure checking for __cospi... yes
504:info:configure checking for __sinpi... yes
505:info:configure checking for __tanpi... yes
506:info:configure checking for fseeko... yes
507:info:configure checking for ftello... yes
508:info:configure checking for matherr... yes
509:info:configure checking whether fcntl exists and is declared... yes
510:info:configure checking whether getgrgid exists and is declared... yes
511:info:configure checking whether getpwuid exists and is declared... yes
512:info:configure checking whether kill exists and is declared... yes
513:info:configure checking whether sigaction exists and is declared... yes
514:info:configure checking whether sigaltstack exists and is declared... yes
515:info:configure checking whether sigemptyset exists and is declared... yes
516:info:configure checking whether fdopen exists and is declared... yes
517:info:configure checking whether popen exists and is declared... yes
518:info:configure checking whether getline exists and is declared... yes
519:info:configure checking whether setenv exists and is declared... yes
520:info:configure checking whether unsetenv exists and is declared... yes
521:info:configure checking whether getrlimit exists and is declared... yes
522:info:configure checking whether getrusage exists and is declared... yes
523:info:configure checking whether getpriority exists and is declared... yes
524:info:configure checking whether chmod exists and is declared... yes
525:info:configure checking whether mkfifo exists and is declared... yes
526:info:configure checking whether stat exists and is declared... yes
527:info:configure checking whether umask exists and is declared... yes
528:info:configure checking whether gettimeofday exists and is declared... yes
529:info:configure checking whether utimes exists and is declared... yes
530:info:configure checking whether times exists and is declared... yes
531:info:configure checking whether gmtime_r exists and is declared... yes
532:info:configure checking whether localtime_r exists and is declared... yes
533:info:configure checking whether nl_langinfo exists and is declared... yes
534:info:configure checking whether access exists and is declared... yes
535:info:configure checking whether chdir exists and is declared... yes
536:info:configure checking whether execv exists and is declared... yes
537:info:configure checking whether ftruncate exists and is declared... yes
538:info:configure checking whether getcwd exists and is declared... yes
539:info:configure checking whether geteuid exists and is declared... yes
540:info:configure checking whether getuid exists and is declared... yes
541:info:configure checking whether link exists and is declared... yes
542:info:configure checking whether readlink exists and is declared... yes
543:info:configure checking whether symlink exists and is declared... yes
544:info:configure checking whether sysconf exists and is declared... yes
545:info:configure checking whether sched_setaffinity exists and is declared... no
546:info:configure checking whether sched_getaffinity exists and is declared... no
547:info:configure checking whether utime exists and is declared... yes
548:info:configure checking for clock_gettime in -lrt... no
549:info:configure checking whether clock_gettime exists and is declared... yes
550:info:configure checking whether timespec_get exists and is declared... no
551:info:configure checking for putenv... yes
552:info:configure checking whether putenv is declared... yes
553:info:configure checking for vasprintf... yes
554:info:configure checking whether vasprintf is declared... yes
555:info:configure checking for mempcpy... no
556:info:configure checking for realpath... yes
557:info:configure checking whether realpath is declared... yes
558:info:configure checking whether glob exists and is declared... yes
559:info:configure checking for isnan... yes
560:info:configure checking whether isfinite is declared... yes
561:info:configure checking whether isnan is declared... yes
562:info:configure checking whether you have IEEE 754 floating-point arithmetic... yes
563:info:configure checking whether putenv("FOO") can unset an environment variable... no
564:info:configure checking whether putenv("FOO=") can unset an environment variable... no
565:info:configure checking for nl_langinfo and CODESET... yes
566:info:configure checking for mkdtemp... yes
567:info:configure checking for strdup... yes
568:info:configure checking for strncasecmp... yes
569:info:configure checking whether mkdtemp is declared... yes
570:info:configure checking whether strdup is declared... yes
571:info:configure checking whether strncasecmp is declared... yes
572:info:configure checking for library containing connect... none required
573:info:configure checking for library containing gethostbyname... none required
574:info:configure checking for library containing xdr_string... none required
575:info:configure checking for __setfpucw... no
576:info:configure checking for working calloc... yes
577:info:configure checking for working isfinite... yes
578:info:configure checking for working log1p... yes
579:info:configure checking whether ftell works correctly on files opened for append... yes
580:info:configure checking for working sigaction... yes
581:info:configure checking whether mktime sets errno... no
582:info:configure checking whether mktime works correctly outside 1902-2037... no
583:info:configure checking complex.h usability... yes
584:info:configure checking complex.h presence... yes
585:info:configure checking for complex.h... yes
586:info:configure checking for double complex... yes
587:info:configure checking whether C99 double complex is supported... yes
588:info:configure checking whether cabs exists and is declared... yes
589:info:configure checking whether carg exists and is declared... yes
590:info:configure checking whether cexp exists and is declared... yes
591:info:configure checking whether clog exists and is declared... yes
592:info:configure checking whether csqrt exists and is declared... yes
593:info:configure checking whether cpow exists and is declared... yes
594:info:configure checking whether ccos exists and is declared... yes
595:info:configure checking whether csin exists and is declared... yes
596:info:configure checking whether ctan exists and is declared... yes
597:info:configure checking whether cacos exists and is declared... yes
598:info:configure checking whether casin exists and is declared... yes
599:info:configure checking whether catan exists and is declared... yes
600:info:configure checking whether ccosh exists and is declared... yes
601:info:configure checking whether csinh exists and is declared... yes
602:info:configure checking whether ctanh exists and is declared... yes
603:info:configure checking whether 'struct tm' includes tm_zone... yes
604:info:configure checking whether 'struct tm' includes tm_gmtoff... yes
605:info:configure checking for dgemm_ in -framework Accelerate... yes
606:info:configure checking whether double complex BLAS can be used... yes
607:info:configure checking whether the BLAS is complete... yes
608:info:configure checking whether external BLAS is visible through libRblas... no
609:info:configure checking can it be fixed by using -sub_umbrella... yes
610:info:configure checking for dpstrf_... no
611:info:configure checking for dpstrf_ in -llapack... no
612:info:configure checking iconv.h usability... yes
613:info:configure checking iconv.h presence... yes
614:info:configure checking for iconv.h... yes
615:info:configure checking for iconv... in libiconv
616:info:configure checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
617:info:configure checking for iconvlist... yes
618:info:configure checking for iconv... yes
619:info:configure checking for iconv declaration...
620:info:configure          extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
621:info:configure checking wchar.h usability... yes
622:info:configure checking wchar.h presence... yes
623:info:configure checking for wchar.h... yes
624:info:configure checking wctype.h usability... yes
625:info:configure checking wctype.h presence... yes
626:info:configure checking for wctype.h... yes
627:info:configure checking whether mbrtowc exists and is declared... yes
628:info:configure checking whether wcrtomb exists and is declared... yes
629:info:configure checking whether wcscoll exists and is declared... yes
630:info:configure checking whether wcsftime exists and is declared... yes
631:info:configure checking whether wcstod exists and is declared... yes
632:info:configure checking whether mbstowcs exists and is declared... yes
633:info:configure checking whether wcstombs exists and is declared... yes
634:info:configure checking whether wctrans exists and is declared... yes
635:info:configure checking whether iswblank exists and is declared... yes
636:info:configure checking whether wctype exists and is declared... yes
637:info:configure checking whether iswctype exists and is declared... yes
638:info:configure checking for wctrans_t... yes
639:info:configure checking for mbstate_t... yes
640:info:configure checking for ICU... yes
641:info:configure checking for X... disabled
642:info:configure using X11 ... no
643:info:configure checking whether pkg-config knows about cairo and pango... yes
644:info:configure checking whether cairo including pango is >= 1.2 and works... yes
645:info:configure checking for CFStringGetSystemEncoding in CoreFoundation framework... -framework CoreFoundation
646:info:configure checking for BSD networking... yes
647:info:configure checking rpc/types.h usability... yes
648:info:configure checking rpc/types.h presence... yes
649:info:configure checking for rpc/types.h... yes
650:info:configure checking for rpc/xdr.h... yes
651:info:configure checking for XDR support... yes
652:info:configure checking for inflateInit2_ in -lz... yes
653:info:configure checking zlib.h usability... yes
654:info:configure checking zlib.h presence... yes
655:info:configure checking for zlib.h... yes
656:info:configure checking if zlib version >= 1.2.5... no
657:info:configure checking whether zlib support suffices... configure: error: zlib library and headers are required
658:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2" && ./configure --prefix=/opt/local/Library/Frameworks --enable-R-framework --enable-memory-profiling --enable-R-shlib --enable-BLAS-shlib --without-tcltk --with-system-zlib --without-internal-tzcode --without-x --with-included-gettext --with-blas="-framework Accelerate" --with-lapack --with-cairo --with-recommended-packages
659:info:configure Exit code: 1
660:error:configure Failed to configure R, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/work/R-3.3.2/config.log
661:error:configure org.macports.configure for port R returned: configure failure: command execution failed
662:debug:configure Error code: NONE
663:debug:configure Backtrace: configure failure: command execution failed
664    while executing
665"portconfigure::configure_main org.macports.configure"
666    ("eval" body line 1)
667    invoked from within
668"eval $procedure $targetname"
669:info:configure Warning: targets not executed for R: org.macports.destroot org.macports.configure org.macports.build
670:notice:configure Please see the log file for port R for details:
671    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_R/R/main.log