1. * Package: sci-chemistry/freeon-1.0.8-r1
2. * Repository: gentoo
3. * Maintainer: nicolasbock@gentoo.org sci-chemistry@gentoo.org
4. * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. Installed LAPACK for library directory lib64
7. [1] reference *
8. Installed BLAS for library directory lib64
9. [1] reference *
10. Installed CBLAS for library directory lib64
11. [1] gsl
12. [2] reference *
13. >>> Unpacking source...
14. >>> Unpacking freeon-1.0.8.tar.bz2 to /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work
15. >>> Source unpacked in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work
16. >>> Preparing source in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8 ...
17. * Running eautoreconf in '/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8' ...
18. * Running libtoolize --install --copy --force --automake ...
19. [ ok ]
20. * Running aclocal -I m4 ...
21. [ ok ]
22. * Running autoconf ...
23. [ ok ]
24. * Running autoheader ...
25. [ ok ]
26. * Running automake --add-missing --copy --force-missing ...
27. [ ok ]
28. * Running elibtoolize in: freeon-1.0.8/
29. * Applying portage/1.2.0 patch ...
30. * Applying sed/1.5.6 patch ...
31. * Applying as-needed/2.4.2 patch ...
32. * Applying target-nm/2.4.2 patch ...
33. >>> Source prepared.
34. >>> Configuring source in /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8 ...
35. >>> Working in BUILD_DIR: "/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build"
36. * econf: updating freeon-1.0.8/config.sub with /usr/share/gnuconfig/config.sub
37. * econf: updating freeon-1.0.8/config.guess with /usr/share/gnuconfig/config.guess
38. /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/freeon-1.0.8-r1
39. configure: loading site script /usr/share/config.site
40. /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 40: /usr/share/config.site: [[: Permission denied
41. checking build system type... x86_64-pc-linux-gnu
42. checking host system type... x86_64-pc-linux-gnu
43. checking target system type... x86_64-pc-linux-gnu
44. checking for a BSD-compatible install... /usr/bin/install -c
45. checking whether build environment is sane... yes
46. checking for a thread-safe mkdir -p... /bin/mkdir -p
47. checking for gawk... gawk
48. checking whether make sets $(MAKE)... yes
49. checking whether make supports nested variables... yes
50. checking whether make supports nested variables... (cached) yes
51. configure: configuring local version master:release
52. checking whether to build fully parallel MPI version... no
53. checking whether to build MPI version, parallelized across clones only... no
54. checking for style of include used by make... GNU
55. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
56. checking whether the C compiler works... yes
57. checking for C compiler default output file name... a.out
58. checking for suffix of executables...
59. checking whether we are cross compiling... no
60. checking for suffix of object files... o
61. checking whether we are using the GNU C compiler... yes
62. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
63. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
64. checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
65. checking dependency style of x86_64-pc-linux-gnu-gcc... none
66. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... -std=gnu99
67. checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
68. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
69. checking whether we are using the GNU C++ compiler... yes
70. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
71. checking dependency style of x86_64-pc-linux-gnu-g++... none
72. checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran
73. checking whether we are using the GNU Fortran compiler... yes
74. checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes
75. checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran
76. checking whether we are using the GNU Fortran 77 compiler... yes
77. checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes
78. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -std=gnu99 -E
79. checking for grep that handles long lines and -e... /bin/grep
80. checking for egrep... /bin/grep -E
81. checking for ANSI C header files... yes
82. checking for sys/types.h... yes
83. checking for sys/stat.h... yes
84. checking for stdlib.h... yes
85. checking for string.h... yes
86. checking for memory.h... yes
87. checking for strings.h... yes
88. checking for inttypes.h... yes
89. checking for stdint.h... yes
90. checking for unistd.h... yes
91. checking minix/config.h usability... no
92. checking minix/config.h presence... no
93. checking for minix/config.h... no
94. checking whether it is safe to define __EXTENSIONS__... yes
95. configure: CC: identified GNU gcc compiler
96. configure: CXX: identified GNU gcc compiler
97. configure: F77: identified GNU gcc compiler
98. configure: FC: identified GNU gcc compiler
99. configure: C compiler version: x86_64-pc-linux-gnu-gcc (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1
100. configure: CXX compiler version: x86_64-pc-linux-gnu-g++ (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1
101. configure: F77 compiler version: GNU Fortran (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1
102. configure: FC compiler version: GNU Fortran (Gentoo 4.9.1 p1.0, pie-0.6.0) 4.9.1
103. checking how to get verbose linking output from x86_64-pc-linux-gnu-gfortran... -v
104. checking for Fortran 77 libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../.. -lgfortran -lm -lquadmath
105. checking for dummy main to link with Fortran 77 libraries... none
106. checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
107. checking how to get verbose linking output from x86_64-pc-linux-gnu-gfortran... -v
108. checking for Fortran libraries of x86_64-pc-linux-gnu-gfortran... -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.1/../../.. -lgfortran -lm -lquadmath
109. checking for dummy main to link with Fortran libraries... none
110. checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
111. checking for python version... 2.7
112. checking for python platform... linux2
113. checking for python script directory... ${prefix}/lib64/python2.7/site-packages
114. checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages
115. checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to support OpenMP... -fopenmp
116. checking for x86_64-pc-linux-gnu-gfortran option to support OpenMP... -fopenmp
117. checking for Fortran flag to compile .F90 files... none
118. checking for Fortran flag needed to accept free-form source... none
119. checking how to print strings... printf
120. checking for a sed that does not truncate output... /bin/sed
121. checking for fgrep... /bin/grep -F
122. checking for ld used by x86_64-pc-linux-gnu-gcc -std=gnu99... /usr/x86_64-pc-linux-gnu/bin/ld
123. checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
124. checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
125. checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
126. checking whether ln -s works... yes
127. checking the maximum length of command line arguments... 1572864
128. checking whether the shell understands some XSI constructs... yes
129. checking whether the shell understands "+="... no
130. checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
131. checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
132. checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
133. checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
134. checking how to recognize dependent libraries... pass_all
135. checking for x86_64-pc-linux-gnu-dlltool... no
136. checking for dlltool... no
137. checking how to associate runtime and link libraries... printf %s\n
138. checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
139. checking for archiver @FILE support... @
140. checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
141. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
142. checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc -std=gnu99 object... ok
143. checking for sysroot... no
144. checking for x86_64-pc-linux-gnu-mt... no
145. checking for mt... mt
146. checking if mt is a manifest tool... no
147. checking for dlfcn.h... yes
148. checking for objdir... .libs
149. checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
150. checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
151. checking if x86_64-pc-linux-gnu-gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
152. checking if x86_64-pc-linux-gnu-gcc -std=gnu99 static flag -static works... yes
153. checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... yes
154. checking if x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o file.o... (cached) yes
155. checking whether the x86_64-pc-linux-gnu-gcc -std=gnu99 linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
156. checking whether -lc should be explicitly linked in... no
157. checking dynamic linker characteristics... GNU/Linux ld.so
158. checking how to hardcode library paths into programs... immediate
159. checking whether stripping libraries is possible... yes
160. checking if libtool supports shared libraries... yes
161. checking whether to build shared libraries... yes
162. checking whether to build static libraries... yes
163. checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
164. checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
165. checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
166. checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
167. checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
168. checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
169. checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
170. checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
171. checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
172. checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
173. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
174. checking how to hardcode library paths into programs... immediate
175. checking if libtool supports shared libraries... yes
176. checking whether to build shared libraries... yes
177. checking whether to build static libraries... yes
178. checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC
179. checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes
180. checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes
181. checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes
182. checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes
183. checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
184. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
185. checking how to hardcode library paths into programs... immediate
186. checking if libtool supports shared libraries... yes
187. checking whether to build shared libraries... yes
188. checking whether to build static libraries... yes
189. checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC
190. checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes
191. checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes
192. checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes
193. checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes
194. checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
195. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
196. checking how to hardcode library paths into programs... immediate
197. checking whether make sets $(MAKE)... (cached) yes
198. checking whether to add compiler optimizations... no
199. checking whether to check for case differences in names... no
200. checking how to set line length limits of f90 compiler... gfortran detected, setting unlimited line-length limit (-ffree-line-length-none)
201. checking for ANSI C header files... (cached) yes
202. checking sys/resource.h usability... yes
203. checking sys/resource.h presence... yes
204. checking for sys/resource.h... yes
205. checking sys/time.h usability... yes
206. checking sys/time.h presence... yes
207. checking for sys/time.h... yes
208. checking for unistd.h... (cached) yes
209. checking sys/ioctl.h usability... yes
210. checking sys/ioctl.h presence... yes
211. checking for sys/ioctl.h... yes
212. checking for sys/types.h... (cached) yes
213. checking math.h usability... yes
214. checking math.h presence... yes
215. checking for math.h... yes
216. checking sys/wait.h usability... yes
217. checking sys/wait.h presence... yes
218. checking for sys/wait.h... yes
219. checking for random number generator seed... use random seed
220. checking whether to use PHiPAC... no
221. /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 25266: /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: declare: Permission denied
222. checking whether to debug MD... no
223. checking for round in -lm... yes
224. checking for library containing clock_gettime... none required
225. checking for possible compiler problems... good, none found
226. checking for library containing dgemm... -lblas
227. checking for library containing dsyev... -llapack
228. checking for hdf5 version... /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8/configure: 1: eval: h5cc: Permission denied
230. configure: error: in `/tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build':
231. configure: error: unsupported hdf5 library version:
232. See `config.log' for more details
234. !!! Please attach the following file when seeking support:
235. !!! /tmp/portage/sci-chemistry/freeon-1.0.8-r1/work/freeon-1.0.8_build/config.log
236. * ERROR: sci-chemistry/freeon-1.0.8-r1::gentoo failed (configure phase):
237. * econf failed
238. *
239. * Call stack:
240. * ebuild.sh, line 93: Called src_configure
241. * environment, line 3963: Called autotools-utils_src_configure
242. * environment, line 974: Called econf '--docdir=/usr/share/doc/freeon-1.0.8-r1'
243. * phase-helpers.sh, line 584: Called die
244. * The specific snippet of code:
245. * die "econf failed"
246. *
247. * If you need support, post the output of `emerge --info '=sci-chemistry/freeon-1.0.8-r1::gentoo'`,
248. * the complete build log and the output of `emerge -pqv '=sci-chemistry/freeon-1.0.8-r1::gentoo'`.
249. sed: couldn't open temporary file /etc/portage/package.mask/sedAos7tV: Permission denied