Ticket #24575: rpy2-2.8.2.p0.log

File rpy2-2.8.2.p0.log, 19.5 KB (added by vdelecroix, 3 years ago)
Line 
1Found local metadata for rpy2-2.8.2.p0
2Using cached file /opt/sage/upstream/rpy2-2.8.2.tar.gz
3rpy2-2.8.2.p0
4====================================================
5Setting up build directory for rpy2-2.8.2.p0
6Finished extraction
7Applying patches from ../patches...
8Applying ../patches/cygwin.patch
9patching file rpy/rinterface/na_values.c
10patching file rpy/rinterface/_rinterface.c
11Hunk #1 succeeded at 1156 (offset -6 lines).
12Hunk #2 succeeded at 3750 (offset 1 line).
13Hunk #3 succeeded at 3760 (offset 1 line).
14Hunk #4 succeeded at 3770 (offset 1 line).
15Hunk #5 succeeded at 3780 (offset 1 line).
16patching file setup.py
17Hunk #1 succeeded at 200 (offset 40 lines).
18****************************************************
19Host system:
20Linux mangouste 4.14.15-1-ARCH #1 SMP PREEMPT Tue Jan 23 21:49:25 UTC 2018 x86_64 GNU/Linux
21****************************************************
22C compiler: gcc
23C compiler version:
24Using built-in specs.
25COLLECT_GCC=/usr/bin/gcc
26COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/lto-wrapper
27Target: x86_64-pc-linux-gnu
28Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp
29Thread model: posix
30gcc version 7.3.0 (GCC)
31****************************************************
32Installing rpy2-2.8.2.p0
33make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
34make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
35make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
36make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
37make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
38R was not built as a library
39make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
40make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
41make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
42make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
43make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
44R was not built as a library
45setup.py:251: UserWarning: No include specified
46  warnings.warn('No include specified')
47setup.py:262: UserWarning: No libraries as -l arguments to the compiler.
48  warnings.warn('No libraries as -l arguments to the compiler.')
49Warning: This package has a badly-behaved setup.py which outputs
50more than the package name for 'setup.py --name'; using the last
51line as the package name: rpy2
52Installing package rpy2 using pip2
53Ignoring indexes: https://pypi.python.org/simple
54Processing /opt/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src
55  Running setup.py (path:/tmp/pip-5ANz7l-build/setup.py) egg_info for package from file:///opt/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src
56    Running command python setup.py egg_info
57    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
58    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
59    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
60    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
61    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
62    R was not built as a library
63    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
64    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
65    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
66    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
67    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
68    R was not built as a library
69    /tmp/pip-5ANz7l-build/setup.py:251: UserWarning: No include specified
70      warnings.warn('No include specified')
71    /tmp/pip-5ANz7l-build/setup.py:262: UserWarning: No libraries as -l arguments to the compiler.
72      warnings.warn('No libraries as -l arguments to the compiler.')
73    R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
74    /opt/sage/local/lib/R/bin/R CMD config --ldflags
75    /opt/sage/local/lib/R/bin/R CMD config --cppflags
76
77        Compilation parameters for rpy2's C components:
78            include_dirs    = []
79            library_dirs    = []
80            libraries       = ['readline']
81            extra_link_args = []
82
83    running egg_info
84    creating pip-egg-info/rpy2.egg-info
85    writing requirements to pip-egg-info/rpy2.egg-info/requires.txt
86    writing pip-egg-info/rpy2.egg-info/PKG-INFO
87    writing top-level names to pip-egg-info/rpy2.egg-info/top_level.txt
88    writing dependency_links to pip-egg-info/rpy2.egg-info/dependency_links.txt
89    writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
90    R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
91    reading manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
92    reading manifest template 'MANIFEST.in'
93    warning: no previously-included files matching '*patch*' found anywhere in distribution
94    warning: no previously-included files matching '*diff*' found anywhere in distribution
95    warning: no previously-included files matching '.hg' found anywhere in distribution
96    warning: no files found matching 'MANIFEST'
97    warning: no files found matching 'README'
98    warning: no files found matching 'MPL_LICENSE'
99    warning: no files found matching 'GPL_LICENSE'
100    warning: no files found matching 'LGPL_LICENSE'
101    no previously-included directories found matching 'dist'
102    warning: no files found matching 'doc/source/rpy2_logo.png'
103    writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
104  Source in /tmp/pip-5ANz7l-build has version 2.8.2, which satisfies requirement rpy2==2.8.2 from file:///opt/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0/src
105Installing collected packages: rpy2
106  Running setup.py install for rpy2: started
107    Running command /opt/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-5ANz7l-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-sBZOee-record/install-record.txt --single-version-externally-managed --compile
108    R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
109    /opt/sage/local/lib/R/bin/R CMD config --ldflags
110    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
111    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
112    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
113    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
114    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
115    R was not built as a library
116    /opt/sage/local/lib/R/bin/R CMD config --cppflags
117    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
118    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
119    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
120    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
121    make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol: GC_move_disappearing_link
122    R was not built as a library
123    /tmp/pip-5ANz7l-build/setup.py:251: UserWarning: No include specified
124      warnings.warn('No include specified')
125    /tmp/pip-5ANz7l-build/setup.py:262: UserWarning: No libraries as -l arguments to the compiler.
126      warnings.warn('No libraries as -l arguments to the compiler.')
127
128        Compilation parameters for rpy2's C components:
129            include_dirs    = []
130            library_dirs    = []
131            libraries       = ['readline']
132            extra_link_args = []
133
134    running install
135    running build
136    running build_py
137    creating build
138    creating build/lib.linux-x86_64-2.7
139    creating build/lib.linux-x86_64-2.7/rpy2
140    copying ./rpy/rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
141    copying ./rpy/__init__.py -> build/lib.linux-x86_64-2.7/rpy2
142    copying ./rpy/tests_rpy_classic.py -> build/lib.linux-x86_64-2.7/rpy2
143    copying ./rpy/tests.py -> build/lib.linux-x86_64-2.7/rpy2
144    creating build/lib.linux-x86_64-2.7/rpy2/rlike
145    copying ./rpy/rlike/container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
146    copying ./rpy/rlike/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
147    copying ./rpy/rlike/functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
148    copying ./rpy/rlike/indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike
149    creating build/lib.linux-x86_64-2.7/rpy2/rlike/tests
150    copying ./rpy/rlike/tests/test_functional.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
151    copying ./rpy/rlike/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
152    copying ./rpy/rlike/tests/test_indexing.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
153    copying ./rpy/rlike/tests/test_container.py -> build/lib.linux-x86_64-2.7/rpy2/rlike/tests
154    creating build/lib.linux-x86_64-2.7/rpy2/rinterface
155    copying ./rpy/rinterface/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface
156    creating build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
157    copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
158    copying ./rpy/rinterface/tests/test_Device.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
159    copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
160    copying ./rpy/rinterface/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
161    copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
162    copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
163    copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
164    copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
165    copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
166    copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.linux-x86_64-2.7/rpy2/rinterface/tests
167    creating build/lib.linux-x86_64-2.7/rpy2/robjects
168    copying ./rpy/robjects/pandas2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
169    copying ./rpy/robjects/functions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
170    copying ./rpy/robjects/environments.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
171    copying ./rpy/robjects/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
172    copying ./rpy/robjects/numpy2ri.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
173    copying ./rpy/robjects/packages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
174    copying ./rpy/robjects/conversion.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
175    copying ./rpy/robjects/methods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
176    copying ./rpy/robjects/robject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
177    copying ./rpy/robjects/vectors.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
178    copying ./rpy/robjects/help.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
179    copying ./rpy/robjects/language.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
180    copying ./rpy/robjects/constants.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
181    copying ./rpy/robjects/packages_utils.py -> build/lib.linux-x86_64-2.7/rpy2/robjects
182    creating build/lib.linux-x86_64-2.7/rpy2/robjects/tests
183    copying ./rpy/robjects/tests/testHelp.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
184    copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
185    copying ./rpy/robjects/tests/testVector.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
186    copying ./rpy/robjects/tests/testRobjects.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
187    copying ./rpy/robjects/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
188    copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
189    copying ./rpy/robjects/tests/testFormula.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
190    copying ./rpy/robjects/tests/testRObject.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
191    copying ./rpy/robjects/tests/testMethods.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
192    copying ./rpy/robjects/tests/testFunction.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
193    copying ./rpy/robjects/tests/testPackages.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
194    copying ./rpy/robjects/tests/testLanguage.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
195    copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
196    copying ./rpy/robjects/tests/testArray.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
197    copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/tests
198    creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib
199    copying ./rpy/robjects/lib/dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
200    copying ./rpy/robjects/lib/tidyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
201    copying ./rpy/robjects/lib/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
202    copying ./rpy/robjects/lib/grdevices.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
203    copying ./rpy/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
204    copying ./rpy/robjects/lib/grid.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib
205    creating build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
206    copying ./rpy/robjects/lib/tests/test_grdevices.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
207    copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
208    copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
209    copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.linux-x86_64-2.7/rpy2/robjects/lib/tests
210    creating build/lib.linux-x86_64-2.7/rpy2/interactive
211    copying ./rpy/interactive/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/interactive
212    copying ./rpy/interactive/packages.py -> build/lib.linux-x86_64-2.7/rpy2/interactive
213    copying ./rpy/interactive/process_revents.py -> build/lib.linux-x86_64-2.7/rpy2/interactive
214    creating build/lib.linux-x86_64-2.7/rpy2/interactive/tests
215    copying ./rpy/interactive/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/interactive/tests
216    creating build/lib.linux-x86_64-2.7/rpy2/ipython
217    copying ./rpy/ipython/ggplot.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
218    copying ./rpy/ipython/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
219    copying ./rpy/ipython/rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
220    copying ./rpy/ipython/html.py -> build/lib.linux-x86_64-2.7/rpy2/ipython
221    creating build/lib.linux-x86_64-2.7/rpy2/ipython/tests
222    copying ./rpy/ipython/tests/__init__.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
223    copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.linux-x86_64-2.7/rpy2/ipython/tests
224    running build_clib
225    building 'r_utils' library
226    creating build/temp.linux-x86_64-2.7
227    creating build/temp.linux-x86_64-2.7/rpy
228    creating build/temp.linux-x86_64-2.7/rpy/rinterface
229    gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I./rpy/rinterface -c ./rpy/rinterface/r_utils.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/r_utils.o
230    ./rpy/rinterface/r_utils.c:23:10: fatal error: Rdefines.h: No such file or directory
231     #include <Rdefines.h>
232              ^~~~~~~~~~~~
233    compilation terminated.
234    error: command 'gcc' failed with exit status 1
235    Running setup.py install for rpy2: finished with status 'error'
236Cleaning up...
237  Removing source in /tmp/pip-5ANz7l-build
238Command "/opt/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-5ANz7l-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-sBZOee-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-5ANz7l-build/
239Exception information:
240Traceback (most recent call last):
241  File "/opt/sage/local/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
242    status = self.run(options, args)
243  File "/opt/sage/local/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run
244    prefix=options.prefix_path,
245  File "/opt/sage/local/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install
246    **kwargs
247  File "/opt/sage/local/lib/python2.7/site-packages/pip/req/req_install.py", line 878, in install
248    spinner=spinner,
249  File "/opt/sage/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
250    % (command_desc, proc.returncode, cwd))
251InstallationError: Command "/opt/sage/local/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip-5ANz7l-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" --no-user-cfg install --record /tmp/pip-sBZOee-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-5ANz7l-build/
252Error: installing with pip2 failed
253********************************************************************************
254Error installing rpy2-2.8.2.p0
255********************************************************************************
256
257real    0m1.614s
258user    0m1.432s
259sys     0m0.217s
260************************************************************************
261Error installing package rpy2-2.8.2.p0
262************************************************************************
263Please email sage-devel (http://groups.google.com/group/sage-devel)
264explaining the problem and including the log file
265  /opt/sage/logs/pkgs/rpy2-2.8.2.p0.log
266Describe your computer, operating system, etc.
267If you want to try to fix the problem yourself, *don't* just cd to
268/opt/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0 and type 'make' or whatever is appropriate.
269Instead, the following commands setup all environment variables
270correctly and load a subshell for you to debug the error:
271  (cd '/opt/sage/local/var/tmp/sage/build/rpy2-2.8.2.p0' && '/opt/sage/sage' --sh)
272When you are done debugging, you can type "exit" to leave the subshell.
273************************************************************************