Closed swryan closed 6 years ago
swryan
commented
8 years ago Am able to work around this on my local machine by pre-loading the system level libgfortran, bypassing the anaconda provided one:
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.3
Seems like the the anaconda libgfortran just needs rebuilt with the "proper" compiler?
Please advise...
rowanc1
commented
8 years ago I just came across this as well. The "fix" that I worked up for now was to revert to scipy to 0.16.0.
I also found that bypassing the libgfortran.so.3 in the conda/lib folder also works. I would love to test my packages against the most recent versions of scipy however. A better solution would be ideal!
Broken: https://travis-ci.org/rowanc1/pymatsolver/builds/107373331 'Fixed': https://travis-ci.org/rowanc1/pymatsolver/builds/114681631
jakirkham
commented
8 years ago @basnijholt, you may be interested in following this issue.
basnijholt
commented
8 years ago @jakirkham thank you! :+1:
I build a package that also depends on libgfortan, however after the update of libgfortran it didn't work anymore.
Then I tried to force the package to depend on libgfortran v1, however in conda < 4 this specification is not respected.
This is a problem on Binder for example, where a Docker image is generated from an environment.yml file. Here I could specify conda v4, however it will then install conda with the old version and simultaneously install incorrect versions of other packages.
jakirkham
commented
8 years ago So, maybe you could suggest to the Binder maintainers that they update to a newer version of conda. Though I don't know how many bug fix releases we are going to go through with 4.x.
In the interim, you could add some hacky steps in your notebook in the beginning to fix conda by running conda update and such.
Alternatively, Binder let's you use Docker. So, you could write a Dockerfile that provides you with a working conda environment of your choosing.
Of the two options, adding hacky steps with conda is probably the easiest, but also the most error prone. Using Docker requires a bit more work (depending on your familiarity), but is probably the most reliable solution.
basnijholt
commented
8 years ago I already asked the Binder guys to update conda, and they will do it :)
tritemio
commented
8 years ago Cross-posting from https://github.com/conda/conda/issues/2177
This (or a similar) issue is causing ReadTheDocs and Binder to fail in importing scipy when using conda envs: https://github.com/rtfd/readthedocs.org/issues/2074
The error is triggered when importing scipy.stats:
ImportError: libgfortran.so.1: cannot open shared object file: No such file or directoryFor the full RTD logs see http://readthedocs.org/projects/fretbursts/builds/3813468/
Binder images containing scipy are created correctly but then importing scipy.stats fails with the above message. An example image with the issue is here:
insertinterestingnamehere
commented
8 years ago @tritemio You're fixing the bugfix releases and even the build numbers for the packages. You can either specify libgfortran=1.0 as well, or you can use the latest builds. Either one will work.
basnijholt
commented
8 years ago Rebuilding with libgfortran 3 doesn't work. The linking with other packages that I depend on gcc , libgcc, and openblas, fails.
EDIT: there also is a dependency on zlib.
jakirkham
commented
8 years ago I wonder if the libgfortran dependency can be done away with and libgcc used instead. There are enough other things that use libgcc that this might just be the right way to go.
basnijholt
commented
8 years ago I don't know if it is of help for anyone, but the build of kwant that works fine with libgfortran 1, but not with 3 (the package MUMPS is not correctly linked), appears to work fine when I give gcc as a runtime lib and having libgfortran v3.
Maybe this gives a clue to someone with more knowledge in this area.
tritemio
commented
8 years ago @insertinterestingnamehere, thanks. Yes the problem was that I generated the environment file on os x and used it on linux. A given combination of anaconda packages may have different bugs on different platforms and the build number are increased independently in order to fix build issued such as the one here. Note to self: it is a good idea to remove the build number from the environment files in order to avoid this kind of issues.
msarahan
commented
8 years ago 
MoritzImendoerffer
commented
8 years ago I have a similar issue with the asssimulo package and scipy 0.17 on python 3.4.
anaconda3/envs/scipy0.17/lib/python3.4/site-packages/scipy/linalg/../../../../libgfortran.so.3: versionGFORTRAN_1.4' not found (required by /home/moritz/anaconda3/envs/scipy0.17/lib/python3.4/site-packages/assimulo/lib/radau5.cpython-34m.so`
The tip from swryan helped.
dprada
commented
8 years ago I had a similar problem. And also the annoying message saying that the license of mkl was about to expire. In my case this was solved updating conda to 4.0. After that numpy and scypi were also updated to:
numexpr: 2.4.4-np110py27_p0 [mkl] --> 2.5-np110py27_0
numpy: 1.10.2-py27_p0 [mkl] --> 1.10.4-py27_1
pytables: 3.2.2-np110py27_0 --> 3.2.2-np110py27_1
scikit-learn: 0.17-np110py27_p1 [mkl] --> 0.17.1-np110py27_0
scipy: 0.16.1-np110py27_p0 [mkl] --> 0.17.0-np110py27_2
Zaharid
commented
8 years ago It so happens that the conda libgcc package contains a good libgfortran.so.3 file, with the 1.4 symbols defined:
So if I only have libgcc,
(_test) $ conda list
# packages in environment at /home/zah/anaconda3/envs/_test:
#
apfel 2.7.1.102 3 file:///home/zah/anaconda3/conda-bld/linux-64/apfel-2.7.1.102-3.tar.bz2
boost 1.60.0 py35_0 defaults
icu 54.1 0 defaults
lhapdf 6.1.6 6 https://zigzah.com/static/conda-pkgs/linux-64/lhapdf-6.1.6-6.tar.bz2
libgcc 4.8.5 1 defaults
openssl 1.0.2g 0 defaults
pip 8.1.1 py35_0 defaults
python 3.5.1 0 defaults
readline 6.2 2 <unknown>
setuptools 20.3 py35_0 defaults
sqlite 3.9.2 0 defaults
tabulate 0.7.5 <pip>
tk 8.5.18 0 defaults
wheel 0.29.0 py35_0 defaults
xz 5.0.5 1 defaults
zlib 1.2.8 0 http://repo.continuum.io/pkgs/free/linux-64/zlib-1.2.8-0.tar.bz2I can
(_test)$ readelf -Ws /home/zah/anaconda3/envs/_test/bin/../lib/libgfortran.so.3 | grep GFORTRAN_1.4
9: 00000000000e91f0 53 FUNC GLOBAL DEFAULT 11 _gfortran_cshift0_16_char4@@GFORTRAN_1.4
48: 0000000000088a40 973 FUNC GLOBAL DEFAULT 11 _gfortran_miall_i2@@GFORTRAN_1.4
72: 00000000000df120 5 FUNC GLOBAL DEFAULT 11 _gfortran_transfer_complex128_write@@GFORTRAN_1.4
93: 000000000008ec10 893 FUNC GLOBAL DEFAULT 11 _gfortran_iparity_i1@@GFORTRAN_1.4However after installing lingfortran, I get an older version without those symbols:
$ conda install libgfortran --yes
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ..........
Solving package specifications: .........
Package plan for installation in environment /home/zah/anaconda3/envs/_test:
The following NEW packages will be INSTALLED:
libgfortran: 3.0-0
Linking packages ...
[ COMPLETE ]|########################################################################################| 100%
(_test) $ readelf -Ws /home/zah/anaconda3/envs/_test/bin/../lib/libgfortran.so.3 | grep GFORTRAN_1.4This is behaviour breaks packages that build well with libgcc, because the libffortran overwrites the more modern version of the .so, such as this:
https://github.com/Zaharid/conda-recipes/tree/master/apfel
Would be grateful if this could be fixed soon.
Zaharid
commented
8 years ago A workaround seems to be simply:
conda remove libgfortran
conda install libgcc --force
nickvandewiele
commented
8 years ago +1
mikaem
commented
8 years ago This may be related. I just downloaded and installed Anaconda 4.0.0. Then did conda install gcc. The gcc and g++ versions are as expected the conda version 4.8.5. However, gfortran is now using version 4.9.2, which is my native gfortran compiler on my ubuntu 15.04. If I'm doing which gfortran, the answer is still ~/anaconda2/bin/gfortran though. With Anaconda 2.5.0 the conda install gcc gives me as expected gfortran version 4.8.5. Removing libgfortran as @Zaharid says fixes my problem.
bjodah
commented
8 years ago I just encountered this and @Zaharid's work-around solved my problem.
basnijholt
commented
8 years ago Any updates on this?
msarahan
commented
8 years ago Thanks for the ping. I have rebuilt the libgfortran package against our docker image with GCC 5.2. I bumped the build number (current is build 1). I hope this works, but please post here if it does not address the issue. I'm going to leave this issue open for now until we flesh out what else might need to be done.
basnijholt
commented
8 years ago Great! But, where can I find it, I don't see it on the anaconda channel, nor on your channel.
msarahan
commented
8 years ago Also, I should add that my update is a short-term band-aid. We are trying to figure out how to capture build requirements better at build time - so things like the GFORTRAN_1.x as well as package version numbers. That will be necessary to fix these kinds of issues long-term.
msarahan
commented
8 years ago Should be in the default channel, let me make sure...
I see it as:
libgfortran 1.0 0 defaults
3.0 0 defaults
3.0.0 1 defaultsThe last one is the "good" one
fivejjs
commented
8 years ago export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgfortran.so.3
works for me.
MoritzImendoerffer
commented
8 years ago Just did a fresh install. Unfortunately conda update libgfortran (conda update --all did not update libgfortran) results in a downgrade of scipy to version 0.16 and scipy.optimize.least_squares is not longer available. I did conda update scipy --force afterwards and it works now. Easier: conda update libgfortran --force
kayhan-batmanghelich
commented
8 years ago Any update on this? I tried removing and installing libgfortran as suggested by @MoritzImendoerffer and @Zaharid . None of those worked for me. This is the error message I get:
In [1]: import numpy as np
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-4ee716103900> in <module>()
----> 1 import numpy as np
/home/batmanghelich/anaconda/lib/python2.7/site-packages/numpy/__init__.py in <module>()
178 return loader(*packages, **options)
179
--> 180 from . import add_newdocs
181 __all__ = ['add_newdocs',
182 'ModuleDeprecationWarning',
/home/batmanghelich/anaconda/lib/python2.7/site-packages/numpy/add_newdocs.py in <module>()
11 from __future__ import division, absolute_import, print_function
12
---> 13 from numpy.lib import add_newdoc
14
15 ###############################################################################
/home/batmanghelich/anaconda/lib/python2.7/site-packages/numpy/lib/__init__.py in <module>()
6 from numpy.version import version as __version__
7
----> 8 from .type_check import *
9 from .index_tricks import *
10 from .function_base import *
/home/batmanghelich/anaconda/lib/python2.7/site-packages/numpy/lib/type_check.py in <module>()
9 'common_type']
10
---> 11 import numpy.core.numeric as _nx
12 from numpy.core.numeric import asarray, asanyarray, array, isnan, \
13 obj2sctype, zeros
/home/batmanghelich/anaconda/lib/python2.7/site-packages/numpy/core/__init__.py in <module>()
12 os.environ[envkey] = '1'
13 env_added.append(envkey)
---> 14 from . import multiarray
15 for envkey in env_added:
16 del os.environ[envkey]
ImportError: libgfortran.so.1: cannot open shared object file: No such file or directoryThis is my package info:
[batmanghelich@login001 ~]$ conda list
# packages in environment at /home/batmanghelich/anaconda:
#
_license 1.1 py27_0 <unknown>
abstract-rendering 0.5.1 np19py27_0 <unknown>
accelerate 1.10.0 np19py27_p0 http://repo.continuum.io/pkgs/pro/linux-64/accelerate-1.10.0-np19py27_p0.tar.bz2
alabaster 0.7.3 py27_0 defaults
anaconda 2.3.0 np19py27_0 defaults
anaconda-client 1.2.1 py27_0 defaults
apache-maven 3.2.1 0 mutirri
argcomplete 0.8.9 py27_0 defaults
astropy 1.0.3 np19py27_0 defaults
atom 0.3.9 py27_0 <unknown>
autograd 1.1.4 <pip>
babel 1.3 py27_0 defaults
backports-abc 0.4 <pip>
backports.ssl-match-hostname 3.4.0.2 <pip>
backports_abc 0.4 py27_0 defaults
bcolz 0.9.0 np19py27_0 defaults
beautiful-soup 4.3.2 py27_0 <unknown>
beautifulsoup4 4.4.1 py27_0 defaults
binstar 0.11.0 py27_0 defaults
bitarray 0.8.1 py27_0 <unknown>
blaze 0.7.0.post112.g28557e4 np19py27_98 https://conda.binstar.org/blaze/linux-64/blaze-0.7.0.post112.g28557e4-np19py27_98.tar.bz2
blaze-core 0.8.0 np19py27_0 defaults
blz 0.6.2 np19py27_1 defaults
bokeh 0.9.0 np19py27_0 defaults
boto 2.38.0 py27_0 defaults
bottleneck 1.0.0 np19py27_0 defaults
brewer2mpl 1.4 py27_0 salford_systems
cairo 1.12.18 4 defaults
casuarius 1.1 py27_0 <unknown>
cdecimal 2.3 py27_0 <unknown>
certifi 14.05.14 py27_0 defaults
cffi 1.1.0 py27_0 defaults
chaco 4.4.1 np19py27_0 <unknown>
chest 0.2.3 py27_0 defaults
click 6.2 <pip>
cloudpickle 0.1.1 <pip>
clyent 0.3.4 py27_0 defaults
cmake 3.3.1 0 defaults
colorama 0.3.3 py27_0 defaults
conda 4.0.7 py27_0 defaults
conda-build 1.8.2 py27_0 <unknown>
conda-env 2.4.5 py27_0 defaults
configobj 5.0.6 py27_0 <unknown>
cryptography 0.9.1 py27_0 defaults
cudamat 0.3 <pip>
cudatoolkit 6.0 p0 http://repo.continuum.io/pkgs/pro/linux-64/cudatoolkit-6.0-p0.tar.bz2
curl 7.43.0 0 defaults
cycler 0.9.0 py27_0 defaults
cyflann 0.1.23 np19py27_2 dougal
cython 0.22.1 py27_0 defaults
cytoolz 0.7.3 py27_0 defaults
dask 0.7.5 py27_0 defaults
datashape 0.4.5 np19py27_0 defaults
dateutil 2.1 py27_2 <unknown>
decorator 3.4.2 py27_0 defaults
dill 0.2.4 py27_0 defaults
distributed 1.6.1 <pip>
docutils 0.12 py27_0 <unknown>
dynd-python 0.6.5 np19py27_0 <unknown>
ecdsa 0.13 <pip>
enable 4.3.0 np19py27_2 <unknown>
enaml 0.9.8 py27_1 defaults
enum34 1.0.4 py27_0 http://repo.continuum.io/pkgs/free/linux-64/enum34-1.0.4-py27_0.tar.bz2
fastcache 1.0.2 py27_0 defaults
flann 1.8.5dev 8 dougal
flask 0.10.1 py27_1 <unknown>
fontconfig 2.11.1 4 defaults
freetype 2.5.2 2 defaults
funcsigs 0.4 py27_0 http://repo.continuum.io/pkgs/free/linux-64/funcsigs-0.4-py27_0.tar.bz2
future 0.13.1 py27_0 <unknown>
futures 2.1.6 py27_0 <unknown>
gevent 1.0.1 py27_0 <unknown>
gevent-websocket 0.9.3 py27_0 <unknown>
glib 2.43.0 2 r
gpy 1.0.9 <pip>
greenlet 0.4.7 py27_0 defaults
grin 1.2.1 py27_1 <unknown>
gslrandom 0.1.1 <pip>
h5py 2.5.0 np19py27_3 defaults
harfbuzz 0.9.39 0 defaults
hdf5 1.8.15.1 1 defaults
heapdict 1.0.0 py27_0 defaults
idna 2.0 py27_0 defaults
into 0.1.3 np19py27_0 http://repo.continuum.io/pkgs/free/linux-64/into-0.1.3-np19py27_0.tar.bz2
iopro 1.6.11 np19py27_p0 http://repo.continuum.io/pkgs/pro/linux-64/iopro-1.6.11-np19py27_p0.tar.bz2
ipaddress 1.0.7 py27_0 defaults
ipykernel 4.0.3 py27_0 defaults
ipyparallel 4.1.0 py27_0 defaults
ipython 3.2.0 py27_0 defaults
ipython-cluster-helper 0.5.0 py27_0 bioconda
ipython-genutils 0.1.0 <pip>
ipython-notebook 3.2.0 py27_0 defaults
ipython-qtconsole 3.2.0 py27_0 defaults
ipython_genutils 0.1.0 py27_0 defaults
ipywidgets 4.1.0 py27_0 defaults
itsdangerous 0.24 py27_0 <unknown>
jbig 2.1 0 defaults
jdcal 1.0 py27_0 <unknown>
jedi 0.8.1 py27_0 defaults
jinja2 2.7.3 py27_1 <unknown>
joblib 0.8.4 py27_0 defaults
jpeg 8d 0 <unknown>
jsonschema 2.4.0 py27_0 defaults
jupyter 1.0.0 py27_1 defaults
jupyter-client 4.1.1 <pip>
jupyter-console 4.0.3 <pip>
jupyter-core 4.0.6 <pip>
jupyter_client 4.1.1 py27_0 defaults
jupyter_console 4.0.3 py27_0 defaults
jupyter_core 4.0.6 py27_0 defaults
kiwisolver 0.1.3 py27_0 <unknown>
lcms 1.19 0 <unknown>
libdynd 0.6.5 0 <unknown>
libffi 3.0.13 0 <unknown>
libgcc 5.2.0 0 defaults
libpng 1.6.17 0 defaults
libsodium 0.4.5 0 <unknown>
libtiff 4.0.2 1 <unknown>
libxml2 2.9.2 0 defaults
libxslt 1.1.28 0 <unknown>
llvm 3.3 0 <unknown>
llvmlite 0.5.0 py27_0 defaults
llvmpy 0.12.7 py27_0 <unknown>
locket 0.2.0 py27_0 defaults
lxml 3.4.4 py27_0 defaults
markupsafe 0.23 py27_0 <unknown>
matlabengineforpython R2015a <pip>
matplotlib 1.4.3 np19py27_2 defaults
mistune 0.5.1 py27_1 defaults
mkl 11.3.1 0 defaults
mkl-rt 11.1 p0 http://repo.continuum.io/pkgs/pro/linux-64/mkl-rt-11.1-p0.tar.bz2
mkl-service 1.0.0 py27_p1 http://repo.continuum.io/pkgs/pro/linux-64/mkl-service-1.0.0-py27_p1.tar.bz2
mklfft 2.0 np19py27_p0 http://repo.continuum.io/pkgs/pro/linux-64/mklfft-2.0-np19py27_p0.tar.bz2
mock 1.0.1 py27_0 <unknown>
mpi4py 1.3 py27_0 <unknown>
mpich2 1.4.1p1 0 <unknown>
mpld3 0.2 <pip>
multipledispatch 0.4.7 py27_0 <unknown>
nbconvert 4.1.0 py27_0 defaults
nbformat 4.0.1 py27_0 defaults
ncurses 5.9 4 r
netifaces 0.10.4 py27_1 bioconda
networkx 1.9.1 py27_0 <unknown>
neurosynth 0.3.3 <pip>
nibabel 2.0.0 py27_0 arthurmensch
nlopt 2.4.2 1 r
nltk 3.0.3 np19py27_0 defaults
nose 1.3.7 py27_0 defaults
notebook 4.0.6 py27_0 defaults
numba 0.19.1 np19py27_0 defaults
numbapro 0.17.1 np19py27_p0 http://repo.continuum.io/pkgs/pro/linux-64/numbapro-0.17.1-np19py27_p0.tar.bz2
numbapro_cudalib 0.2 0 http://repo.continuum.io/pkgs/free/linux-64/numbapro_cudalib-0.2-0.tar.bz2
numexpr 2.4.3 np19py27_0 defaults
numpy 1.9.2 py27_0 defaults
odo 0.3.2 np19py27_0 defaults
openblas 0.2.14 0 defaults
openpyxl 1.8.5 py27_0 <unknown>
openssl 1.0.1k 1 http://repo.continuum.io/pkgs/free/linux-64/openssl-1.0.1k-1.tar.bz2
pandas 0.16.2 np19py27_0 defaults
pango 1.39.0 0 defaults
paramiko 1.16.0 <pip>
paramz 0.5.5 <pip>
partd 0.3.2 py27_1 defaults
patchelf 0.6 0 defaults
path.py 8.1.2 py27_1 defaults
patsy 0.3.0 np19py27_0 <unknown>
pbr 1.3.0 py27_0 defaults
pcre 8.31 0 defaults
pep8 1.6.2 py27_0 defaults
pexpect 3.3 py27_0 defaults
pgmult (/home/batmanghelich/gitSandbox/pgmult) 0.1 <pip>
pickleshare 0.5 py27_0 defaults
pil 1.1.7 py27_2 defaults
pillow 2.8.2 py27_0 defaults
pip 7.0.3 py27_0 defaults
pixman 0.26.2 0 <unknown>
plinkio 0.9.6 <pip>
ply 3.6 py27_0 defaults
prettyplotlib 0.1.7 py27_1 salford_systems
progressbar 0.2.3 py27_1 http://conda.binstar.org/dougal/linux-64/progressbar-0.2.3-py27_1.tar.bz2
protobuf 3.0.0b2 py27_1 jjhelmus
psutil 2.2.1 py27_0 defaults
psycopg2 2.6.1 py27_0 defaults
ptyprocess 0.4 py27_0 defaults
py 1.4.27 py27_0 defaults
py-sdm 0.1.0dev np19py27_15 http://conda.binstar.org/dougal/linux-64/py-sdm-0.1.0dev-np19py27_15.tar.bz2
py2cairo 1.10.0 py27_2 defaults
pyasn1 0.1.7 py27_0 defaults
pybasicbayes 0.2.1 <pip>
pycairo 1.10.0 py27_0 defaults
pycosat 0.6.1 py27_0 <unknown>
pycparser 2.14 py27_0 defaults
pycrypto 2.6.1 py27_0 <unknown>
pycurl 7.19.5.1 py27_2 defaults
pyface 4.4.0 py27_0 <unknown>
pyflakes 0.9.2 py27_0 defaults
pygments 2.0.2 py27_0 defaults
pylds 0.0.1 <pip>
pymongo 2.7.2 py27_0 http://repo.continuum.io/pkgs/free/linux-64/pymongo-2.7.2-py27_0.tar.bz2
pyopenssl 0.15.1 py27_1 defaults
pyparsing 2.0.3 py27_0 defaults
pypolyagamma 0.2 <pip>
pyprind 2.9.1 <pip>
pyqt 4.11.3 py27_1 defaults
pystan 2.8.0.0 py27_0 defaults
pytables 3.2.0 np19py27_0 defaults
pytest 2.7.1 py27_0 defaults
python 2.7.10 0 defaults
python-dateutil 2.4.2 py27_0 defaults
pytz 2015.4 py27_0 defaults
pyyaml 3.11 py27_1 defaults
pyzmq 14.7.0 py27_0 defaults
qt 4.8.6 3 defaults
qtconsole 4.0.1 py27_0 defaults
r 3.2.2 0 r
r-assertthat 0.1 r3.2.2_1a r
r-base 3.2.2 0 r
r-base64enc 0.1_3 r3.2.2_0a r
r-bh 1.58.0_1 r3.2.2_0a r
r-bitops 1.0_6 r3.2.2_1a r
r-boot 1.3_17 r3.2.2_0 r
r-brew 1.0_6 r3.2.2_1a r
r-car 2.1_0 r3.2.2_0a r
r-caret 6.0_62 r3.2.2_0a r
r-catools 1.17.1 r3.2.2_2a r
r-chron 2.3_47 r3.2.2_0a r
r-class 7.3_14 r3.2.2_0 r
r-cluster 2.0.3 r3.2.2_0 r
r-codetools 0.2_14 r3.2.2_0 r
r-colorspace 1.2_6 r3.2.2_0a r
r-curl 0.9.4 r3.2.2_0a r
r-data.table 1.9.6 r3.2.2_0a r
r-dbi 0.3.1 r3.2.2_2a r
r-devtools 1.9.1 r3.2.2_0a r
r-dichromat 2.0_0 r3.2.2_2a r
r-digest 0.6.8 r3.2.2_2a r
r-dplyr 0.4.3 r3.2.2_0a r
r-essentials 1.1 r3.2.2_1a r
r-evaluate 0.8 r3.2.2_0a r
r-foreach 1.4.3 r3.2.2_0a r
r-foreign 0.8_66 r3.2.2_0 r
r-formatr 1.2.1 r3.2.2_0a r
r-ggplot2 1.0.1 r3.2.2_0a r
r-git2r 0.11.0 r3.2.2_0a r
r-glmnet 2.0_2 r3.2.2_0a r
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r-htmlwidgets 0.5 r3.2.2_0a r
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r-jsonlite 0.9.17 r3.2.2_0a r
r-kernsmooth 2.23_15 r3.2.2_0 r
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r-magrittr 1.5 r3.2.2_1a r
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readline 6.2 2 <unknown>
redis 2.6.9 0 <unknown>
redis-py 2.10.3 py27_0 defaults
requests 2.7.0 py27_0 defaults
rope 0.9.4 py27_1 <unknown>
rpy2 2.7.0 py27r3.2.2_0 r
runipy 0.1.3 py27_0 defaults
scikit-image 0.11.3 np19py27_0 defaults
scikit-learn 0.16.1 np19py27_0 defaults
scikits.bootstrap 0.3.2 np18py27_0 rgrout
scipy 0.15.1 np19py27_0 defaults
seaborn 0.6.0 np110py27_0 defaults
setuptools 17.1.1 py27_0 defaults
simplegeneric 0.8.1 py27_0 defaults
simpleitk 0.8.0 <pip>
singledispatch 3.4.0.3 py27_1 r
sip 4.16.5 py27_0 defaults
six 1.9.0 py27_0 http://repo.continuum.io/pkgs/free/linux-64/six-1.9.0-py27_0.tar.bz2
skl-groups 0.1.5 np19py27_0 dougal
skl-groups-accel 0.1.5 <pip>
snowballstemmer 1.2.0 py27_0 defaults
sockjs-tornado 1.0.1 py27_0 <unknown>
sphinx 1.3.1 py27_0 defaults
sphinx-rtd-theme 0.1.7 <pip>
sphinx_rtd_theme 0.1.7 py27_0 defaults
spyder 2.3.5.2 py27_0 defaults
spyder-app 2.3.5.2 py27_0 defaults
sqlalchemy 1.0.5 py27_0 defaults
sqlite 3.8.4.1 1 http://repo.continuum.io/pkgs/free/linux-64/sqlite-3.8.4.1-1.tar.bz2
ssl_match_hostname 3.4.0.2 py27_0 <unknown>
statsmodels 0.6.1 np19py27_0 defaults
sympy 0.7.6 py27_0 defaults
system 5.8 2 defaults
tables 3.2.0 <pip>
tabulate 0.7.2 py27_0 https://conda.binstar.org/auto/linux-64/tabulate-0.7.2-py27_0.tar.bz2
tensorflow 0.7.1 py27_1 jjhelmus
terminado 0.5 py27_0 defaults
theano 0.7.0 np19py27_0 defaults
tk 8.5.18 0 http://repo.continuum.io/pkgs/free/linux-64/tk-8.5.18-0.tar.bz2
toolz 0.7.2 py27_0 defaults
tornado 4.2 py27_0 defaults
traitlets 4.0.0 py27_0 defaults
traits 4.4.0 py27_0 <unknown>
traitsui 4.4.0 py27_0 <unknown>
ujson 1.33 py27_0 <unknown>
unicodecsv 0.9.4 py27_0 <unknown>
unixodbc 2.3.1 1 http://repo.continuum.io/pkgs/free/linux-64/unixodbc-2.3.1-1.tar.bz2
util-linux 2.21 0 <unknown>
vlfeat-ctypes 0.1.4 py27_0 http://conda.binstar.org/dougal/linux-64/vlfeat-ctypes-0.1.4-py27_0.tar.bz2
werkzeug 0.10.4 py27_0 defaults
wheel 0.29.0 py27_0 defaults
xlrd 0.9.3 py27_0 <unknown>
xlsxwriter 0.7.3 py27_0 defaults
xlwt 1.0.0 py27_0 defaults
xz 5.0.5 1 defaults
yaml 0.1.6 0 defaults
zeromq 4.0.5 0 defaults
zlib 1.2.8 0 http://repo.continuuNumpy 1.9 was not correctly pinned to libgfortran version 1.
conda install -f libgfortran==1
should make things work again.
@ilanschnell, can you alter numpy 1.9's metadata to reflect this dependency/pinning?
kayhan-batmanghelich
commented
8 years ago @msarahan I ended up re-installing conda, I read this message after re-installation :( Thank you for your reply.
I have to say, I did try conda update libgfortran --force but that didn't help. The command didn't have -f libgfortran==1. I don't know it makes a difference.
Thanks again,
msarahan
commented
8 years ago The critically important part is not the --force, but the ==1 part. The latest libgfortran package is version 3, which is not compatible with numpy 1.9. Thus, you must manually tell it to install the older version.
ketch
commented
8 years ago I ran into this today too. Any idea when it will be fixed? The workaround is nice but users still get tripped up.
olaurino
commented
8 years ago I was about to release new binaries for our package (Sherpa, the modeling package of the Chandra X-Ray telescope software) when I realized the binaries I had been testing were broken by an update in libgcc at the build number level.
libgcc 4.8.5-1 contained libgfortran, while 4.8.5-2 does not. This is a big change for a build number increase, and I am not sure how to proceed. Should I pin libgcc 4.8.5 to build number 1 hoping this doesn't collide with other packages user may have? Or should I assume that libgfortran has been fixed (which doesn't seem to be the case as libgfortran hasn't been updated)?
insertinterestingnamehere
commented
7 years ago libgcc 5.2 is backwards compatible with binaries built with gcc 4.8. Using the newer version should work. That aside, pulling libgfortran out in a new build seems wrong to me. I'm not sure on what the rationale could have been for that.
olaurino
commented
7 years ago Thanks @insertinterestingnamehere.
Whatever the rationale, I was rather surprised by the fact that such a big change was introduced in a build number increase. Should I start pinning down dependencies at the build number level?
rmathar
commented
7 years ago A bug in the libgfortran package for at least a decade, see https://bugzilla.redhat.com/show_bug.cgi?id=191497 .I usually patch this by creating the symbolic link (as root) ` cd /usr/lib64
if [ -a libgfortran.so.3 ] ; then
if [ ! -a libgfortran.so ] ; then
ln -s libgfortran.so.3 libgfortran.so
fifi `
msarahan
commented
6 years ago With the Anaconda-5 series of packages, we're building with gcc 7.2, which finally bumps the gfortran version - it's .so.4 now. I think this issue is solved.
Note: the old gcc package (4.8.*) is incompatible with the new packages, and should not be mixed with them. Prefer the new compilers instead. We have docs on doing that at https://www.anaconda.com/blog/developer-blog/utilizing-the-new-compilers-in-anaconda-distribution-5/
Started getting this error a couple days ago:
ImportError: /home/travis/miniconda/lib/python2.7/site-packages/scipy/special/../../../../libgfortran.so.3: versionGFORTRAN_1.4' not found (required by /usr/lib/liblapack.so.3gf)`It seems coincident with the latest update to libgfortran: https://anaconda.org/anaconda/libgfortran/files
Would appreciate any insight into what the issue is and more importantly, what the fix is: https://travis-ci.org/OpenMDAO/OpenMDAO/jobs/114269055
Thanks!