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cffi 1.13 breaks rpy2 3.1.0 on R 3.6 and Python 3.7 #35

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hermidalc opened this issue Oct 15, 2019 · 1 comment
Closed

cffi 1.13 breaks rpy2 3.1.0 on R 3.6 and Python 3.7 #35

hermidalc opened this issue Oct 15, 2019 · 1 comment

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@hermidalc
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Issue: Latest cffi on conda-forge is now 1.13.0 and if you upgrade to this then rpy2 3.1.0 will not work anymore. You get the following error when you try to import anything from rpy2:

Traceback (most recent call last):
  File "test_rpy2.py", line 4, in <module>
    import rpy2.robjects as robjects
  File "/home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 14, in <module>
    import rpy2.rinterface as rinterface
  File "/home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn/lib/python3.7/site-packages/rpy2/rinterface.py", line 6, in <module>
    from rpy2.rinterface_lib import openrlib
  File "/home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn/lib/python3.7/site-packages/rpy2/rinterface_lib/openrlib.py", line 45, in <module>
    _get_dataptr_fallback)
  File "/home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn/lib/python3.7/site-packages/rpy2/rinterface_lib/openrlib.py", line 30, in _get_symbol_or_fallback
    res = getattr(rlib, symbol)
RuntimeError: found a situation in which we try to build a type recursively.  This is known to occur e.g. in ``struct s { void(*callable)(struct s); }''.  Please report if you get this error and really need support for your case.

rpy2 3.1.0 should update dependency to cffi <1.13.0a0


Environment (conda list): 
$ conda list
# packages in environment at /home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_r-mutex                  1.0.1               anacondar_1    conda-forge
astroid                   2.3.1                    py37_0    conda-forge
attrs                     19.3.0                     py_0    conda-forge
autopep8                  1.4.4                      py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
binutils_impl_linux-64    2.31.1               h7fc9f1b_2    conda-forge
binutils_linux-64         2.31.1              h6176602_12    conda-forge
bioconductor-affy         1.62.0            r36h516909a_1    bioconda
bioconductor-affyio       1.54.0            r36h516909a_1    bioconda
bioconductor-affyplm      1.60.0            r36h516909a_1    bioconda
bioconductor-aldex2       1.16.0                    r36_1    bioconda
bioconductor-annotate     1.62.0                    r36_1    bioconda
bioconductor-annotationdbi 1.46.0                    r36_1    bioconda
bioconductor-apeglm       1.6.0             r36he1b5a44_1    bioconda
bioconductor-biobase      2.44.0            r36h516909a_1    bioconda
bioconductor-biocgenerics 0.30.0                    r36_1    bioconda
bioconductor-biocparallel 1.18.0            r36he1b5a44_1    bioconda
bioconductor-biocversion  3.9.0                     r36_1    bioconda
bioconductor-biostrings   2.52.0            r36h516909a_1    bioconda
bioconductor-delayedarray 0.10.0            r36h516909a_1    bioconda
bioconductor-deseq2       1.24.0            r36he1b5a44_1    bioconda
bioconductor-edger        3.26.5            r36he1b5a44_0    bioconda
bioconductor-gcrma        2.56.0            r36h516909a_1    bioconda
bioconductor-genefilter   1.66.0            r36hc99cbb1_1    bioconda
bioconductor-geneplotter  1.62.0                    r36_1    bioconda
bioconductor-genomeinfodb 1.20.0                    r36_1    bioconda
bioconductor-genomeinfodbdata 1.2.1                     r36_1    bioconda
bioconductor-genomicranges 1.36.0            r36h516909a_1    bioconda
bioconductor-geoquery     2.52.0                    r36_1    bioconda
bioconductor-go.db        3.8.2                     r36_1    bioconda
bioconductor-graph        1.62.0            r36h516909a_1    bioconda
bioconductor-gseabase     1.46.0                    r36_1    bioconda
bioconductor-gsva         1.32.0            r36h516909a_1    bioconda
bioconductor-ihw          1.12.0                    r36_1    bioconda
bioconductor-impute       1.58.0            r36h6e990d7_1    bioconda
bioconductor-iranges      2.18.2            r36h516909a_0    bioconda
bioconductor-limma        3.40.2            r36h516909a_0    bioconda
bioconductor-lpsymphony   1.12.0            r36he1b5a44_1    bioconda
bioconductor-metagenomeseq 1.26.2                    r36_0    bioconda
bioconductor-multtest     2.40.0            r36h516909a_1    bioconda
bioconductor-preprocesscore 1.46.0            r36h516909a_1    bioconda
bioconductor-pvca         1.24.0                    r36_1    bioconda
bioconductor-s4vectors    0.22.0            r36h516909a_1    bioconda
bioconductor-singscore    1.4.0                     r36_1    bioconda
bioconductor-summarizedexperiment 1.14.0                    r36_1    bioconda
bioconductor-sva          3.32.1            r36h516909a_0    bioconda
bioconductor-variancepartition 1.14.0                    r36_1    bioconda
bioconductor-vsn          3.52.0            r36h516909a_1    bioconda
bioconductor-wrench       1.2.0                     r36_1    bioconda
bioconductor-xvector      0.24.0            r36h516909a_1    bioconda
bioconductor-zlibbioc     1.30.0            r36h516909a_1    bioconda
bleach                    3.1.0                      py_0    conda-forge
bwidget                   1.9.13                        0    conda-forge
bzip2                     1.0.8                h516909a_1    conda-forge
ca-certificates           2019.9.11            hecc5488_0    conda-forge
cairo                     1.16.0            hfb77d84_1002    conda-forge
certifi                   2019.9.11                py37_0    conda-forge
cffi                      1.12.3           py37h8022711_0    conda-forge
curl                      7.65.3               hf8cf82a_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.13          py37he1b5a44_0    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
decorator                 4.4.0                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3                   py37_1000    conda-forge
expat                     2.2.5             he1b5a44_1003    conda-forge
flake8                    3.7.8                    py37_1    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.0               he983fc9_1    conda-forge
fribidi                   1.0.5             h516909a_1002    conda-forge
future                    0.18.0                   py37_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_2    conda-forge
gcc_linux-64              7.3.0               h553295d_12    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_2    conda-forge
gfortran_linux-64         7.3.0               h553295d_12    conda-forge
glib                      2.58.3            h6f030ca_1002    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
gst-plugins-base          1.14.5               h0935bb2_0    conda-forge
gstreamer                 1.14.5               h36ae1b5_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_2    conda-forge
gxx_linux-64              7.3.0               h553295d_12    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
importlib_metadata        0.23                     py37_0    conda-forge
intel-openmp              2019.4                      243  
ipykernel                 5.1.2            py37h5ca1d4c_0    conda-forge
ipython                   7.8.0            py37h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isort                     4.3.21                   py37_0    conda-forge
jedi                      0.15.1                   py37_0    conda-forge
jinja2                    2.10.3                     py_0    conda-forge
joblib                    0.14.0                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.1.1                    py37_0    conda-forge
jupyter_client            5.3.3                    py37_1    conda-forge
jupyter_core              4.5.0                      py_0    conda-forge
kiwisolver                1.1.0            py37hc9558a2_0    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
lazy-object-proxy         1.4.2            py37h516909a_0    conda-forge
libblas                   3.8.0                    14_mkl    conda-forge
libcblas                  3.8.0                    14_mkl    conda-forge
libclang                  9.0.0                hc9558a2_1    conda-forge
libcurl                   7.65.3               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_2    conda-forge
libglu                    9.0.0             hf484d3e_1000    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                    14_mkl    conda-forge
libllvm9                  9.0.0                hc9558a2_2    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.0.10            h57b8799_1003    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxkbcommon              0.8.4                h516909a_0    conda-forge
libxml2                   2.9.9                hee79883_5    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
lxml                      4.4.1            py37h7ec2d77_0    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
markupsafe                1.1.1            py37h14c3975_0    conda-forge
matplotlib                3.1.1                    py37_1    conda-forge
matplotlib-base           3.1.1            py37he7580a8_1    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
mistune                   0.8.4           py37h14c3975_1000    conda-forge
mkl                       2019.4                      243  
mlxtend                   0.17.0                     py_0    conda-forge
more-itertools            7.2.0                      py_0    conda-forge
natsort                   6.0.0                      py_0    conda-forge
nbconvert                 5.6.0                    py37_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
notebook                  6.0.1                    py37_0    conda-forge
nspr                      4.20              hf484d3e_1000    conda-forge
nss                       3.46                 he751ad9_0    conda-forge
numpy                     1.17.2           py37h95a1406_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openjdk                   8.0.192           h14c3975_1003    conda-forge
openssl                   1.1.1c               h516909a_0    conda-forge
pandas                    0.25.1           py37hb3f55d8_0    conda-forge
pandoc                    2.7.3                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.42.4               ha030887_1    conda-forge
parso                     0.5.1                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41              he1b5a44_1004    conda-forge
pexpect                   4.7.0                    py37_0    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pillow                    6.2.0            py37h6b7be26_0    conda-forge
pip                       19.2.3                   py37_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pluggy                    0.13.0                   py37_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            2.0.10                     py_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pycodestyle               2.5.0                      py_0    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pydocstyle                4.0.1                      py_0    conda-forge
pyflakes                  2.1.1                      py_0    conda-forge
pygments                  2.4.2                      py_0    conda-forge
pylint                    2.4.2                    py37_0    conda-forge
pyparsing                 2.4.2                      py_0    conda-forge
pyqt                      5.12.3           py37hcca6a23_0    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.15.4           py37h516909a_0    conda-forge
python                    3.7.3                h33d41f4_1    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python-jsonrpc-server     0.2.0                      py_0    conda-forge
python-language-server    0.29.1                   py37_0    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyzmq                     18.1.0           py37h1768529_0    conda-forge
qt                        5.12.5               h0c104cb_0    conda-forge
r-acepack                 1.4.1           r36h9bbef5b_1004    conda-forge
r-argparse                2.0.1             r36h6115d3f_1    conda-forge
r-arules                  1.6_4             r36hcdcec82_0    conda-forge
r-askpass                 1.1               r36hcdcec82_1    conda-forge
r-assertthat              0.2.1             r36h6115d3f_1    conda-forge
r-backports               1.1.5             r36hcdcec82_0    conda-forge
r-base                    3.6.1                hba50c9b_4    conda-forge
r-base64enc               0.1_3           r36hcdcec82_1003    conda-forge
r-bbmle                   1.0.20            r36h6115d3f_1    conda-forge
r-bh                      1.69.0_1          r36h6115d3f_1    conda-forge
r-biocmanager             1.30.7            r36h6115d3f_0    conda-forge
r-bit                     1.1_14            r36hcdcec82_1    conda-forge
r-bit64                   0.9_7           r36hcdcec82_1001    conda-forge
r-bitops                  1.0_6           r36hcdcec82_1003    conda-forge
r-blob                    1.2.0                     r36_1    conda-forge
r-boot                    1.3_23            r36h6115d3f_2    conda-forge
r-brew                    1.0_6           r36h6115d3f_1002    conda-forge
r-broom                   0.5.2             r36h6115d3f_1    conda-forge
r-callr                   3.3.2             r36h6115d3f_0    conda-forge
r-caret                   6.0_84            r36hcdcec82_1    conda-forge
r-catools                 1.17.1.2          r36h0357c0b_1    conda-forge
r-cellranger              1.1.0           r36h6115d3f_1002    conda-forge
r-checkmate               1.9.4             r36hcdcec82_1    conda-forge
r-class                   7.3_15          r36hcdcec82_1001    conda-forge
r-cli                     1.1.0             r36h6115d3f_2    conda-forge
r-clipr                   0.7.0             r36h6115d3f_0    conda-forge
r-clisymbols              1.2.0           r36h6115d3f_1002    conda-forge
r-clue                    0.3_57            r36h516909a_1    conda-forge
r-cluster                 2.1.0             r36h9bbef5b_2    conda-forge
r-coda                    0.19_3            r36h6115d3f_1    conda-forge
r-codetools               0.2_16          r36h6115d3f_1001    conda-forge
r-collections             0.2.1             r36hcdcec82_0    conda-forge
r-colorramps              2.3                    r36_1002    conda-forge
r-colorspace              1.4_1             r36hcdcec82_1    conda-forge
r-commonmark              1.7             r36hcdcec82_1001    conda-forge
r-corpcor                 1.6.9           r36h6115d3f_1002    conda-forge
r-covr                    3.3.1             r36h0357c0b_0    conda-forge
r-crayon                  1.3.4           r36h6115d3f_1002    conda-forge
r-crosstalk               1.0.0           r36h6115d3f_1002    conda-forge
r-curl                    4.2               r36hcdcec82_0    conda-forge
r-cyclocomp               1.1.0           r36h6115d3f_1003    conda-forge
r-data.table              1.12.4            r36hcdcec82_0    conda-forge
r-dbi                     1.0.0           r36h6115d3f_1002    conda-forge
r-dbplyr                  1.4.2             r36h6115d3f_1    conda-forge
r-deoptimr                1.0_8           r36h6115d3f_1002    conda-forge
r-desc                    1.2.0           r36h6115d3f_1002    conda-forge
r-devtools                2.2.1             r36h6115d3f_0    conda-forge
r-digest                  0.6.21            r36h0357c0b_0    conda-forge
r-doparallel              1.0.15            r36h6115d3f_0    conda-forge
r-dplyr                   0.8.3             r36h0357c0b_3    conda-forge
r-dt                      0.9               r36h6115d3f_0    conda-forge
r-dynamictreecut          1.63_1          r36h6115d3f_1002    conda-forge
r-e1071                   1.7_2             r36h0357c0b_1    conda-forge
r-ellipsis                0.3.0             r36hcdcec82_0    conda-forge
r-emdbook                 1.3.11                    r36_1    conda-forge
r-entropy                 1.2.1           r36h6115d3f_1002    conda-forge
r-essentials              3.6                    r36_2001    conda-forge
r-evaluate                0.14              r36h6115d3f_1    conda-forge
r-fansi                   0.4.0           r36hcdcec82_1001    conda-forge
r-fastcluster             1.1.25          r36hc99cbb1_1002    conda-forge
r-fastmap                 1.0.1             r36h0357c0b_0    conda-forge
r-fdrtool                 1.2.15          r36hcdcec82_1002    conda-forge
r-findpython              1.0.5             r36h6115d3f_1    conda-forge
r-fit.models              0.5_14          r36h6115d3f_1002    conda-forge
r-fnn                     1.1.3             r36h0357c0b_1    conda-forge
r-forcats                 0.4.0             r36h6115d3f_1    conda-forge
r-foreach                 1.4.7             r36h6115d3f_0    conda-forge
r-foreign                 0.8_72            r36hcdcec82_0    conda-forge
r-formatr                 1.7               r36h6115d3f_1    conda-forge
r-formula                 1.2_3           r36h6115d3f_1002    conda-forge
r-fs                      1.3.1             r36h0357c0b_1    conda-forge
r-fselector               0.31              r36h6115d3f_1    conda-forge
r-futile.logger           1.4.3           r36h6115d3f_1002    conda-forge
r-futile.options          1.0.1           r36h6115d3f_1001    conda-forge
r-gdata                   2.18.0          r36h6115d3f_1002    conda-forge
r-generics                0.0.2           r36h6115d3f_1002    conda-forge
r-getopt                  1.20.3                    r36_1    conda-forge
r-ggplot2                 3.2.1             r36h6115d3f_0    conda-forge
r-ggrepel                 0.8.1             r36h0357c0b_1    conda-forge
r-gh                      1.0.1           r36h6115d3f_1002    conda-forge
r-gistr                   0.4.2           r36h6115d3f_1002    conda-forge
r-git2r                   0.26.1            r36h5ca76e2_1    conda-forge
r-glmnet                  2.0_18            r36h9bbef5b_2    conda-forge
r-glue                    1.3.1             r36hcdcec82_1    conda-forge
r-gower                   0.2.1             r36hcdcec82_1    conda-forge
r-gplots                  3.0.1.1           r36h6115d3f_1    conda-forge
r-gridextra               2.3             r36h6115d3f_1002    conda-forge
r-gtable                  0.3.0             r36h6115d3f_2    conda-forge
r-gtools                  3.8.1           r36hcdcec82_1003    conda-forge
r-haven                   2.1.1             r36hde08347_3    conda-forge
r-hexbin                  1.27.3            r36h9bbef5b_2    conda-forge
r-highr                   0.8               r36h6115d3f_1    conda-forge
r-hmisc                   4.2_0             r36h9bbef5b_2    conda-forge
r-hms                     0.5.1             r36h6115d3f_0    conda-forge
r-htmltable               1.13.2            r36h6115d3f_0    conda-forge
r-htmltools               0.4.0             r36h0357c0b_0    conda-forge
r-htmlwidgets             1.5.1             r36h6115d3f_0    conda-forge
r-httpuv                  1.5.2             r36h0357c0b_1    conda-forge
r-httr                    1.4.1             r36h6115d3f_1    conda-forge
r-ini                     0.3.1           r36h6115d3f_1002    conda-forge
r-ipred                   0.9_9             r36hcdcec82_1    conda-forge
r-irdisplay               0.7                    r36_1001    conda-forge
r-irkernel                1.0.2             r36h6115d3f_2    conda-forge
r-iterators               1.0.12            r36h6115d3f_0    conda-forge
r-jade                    2.0_2             r36h0357c0b_0    conda-forge
r-jsonlite                1.6             r36hcdcec82_1001    conda-forge
r-kernsmooth              2.23_15         r36h9bbef5b_1004    conda-forge
r-knitr                   1.25              r36h6115d3f_0    conda-forge
r-labeling                0.3             r36h6115d3f_1002    conda-forge
r-lambda.r                1.2.4             r36h6115d3f_0    conda-forge
r-languageserver          0.3.1             r36hcdcec82_0    conda-forge
r-later                   1.0.0             r36h0357c0b_0    conda-forge
r-lattice                 0.20_38         r36hcdcec82_1002    conda-forge
r-latticeextra            0.6_28          r36h6115d3f_1002    conda-forge
r-lava                    1.6.6             r36h6115d3f_0    conda-forge
r-lazyeval                0.2.2             r36hcdcec82_1    conda-forge
r-lifecycle               0.1.0             r36h6115d3f_0    conda-forge
r-lintr                   2.0.0             r36h6115d3f_0    conda-forge
r-lme4                    1.1_21            r36h0357c0b_1    conda-forge
r-lmertest                3.1_0             r36h6115d3f_1    conda-forge
r-locfit                  1.5_9.1         r36h516909a_1004    conda-forge
r-lubridate               1.7.4           r36h0357c0b_1002    conda-forge
r-magrittr                1.5             r36h6115d3f_1002    conda-forge
r-manipulatewidget        0.10.0          r36h6115d3f_1001    conda-forge
r-maps                    3.3.0           r36hcdcec82_1003    conda-forge
r-markdown                1.1               r36hcdcec82_0    conda-forge
r-mass                    7.3_51.4          r36hcdcec82_1    conda-forge
r-matrix                  1.2_17            r36hcdcec82_1    conda-forge
r-matrixstats             0.55.0            r36hcdcec82_0    conda-forge
r-memoise                 1.1.0           r36h6115d3f_1003    conda-forge
r-mgcv                    1.8_29            r36hcdcec82_0    conda-forge
r-mime                    0.7               r36hcdcec82_1    conda-forge
r-miniui                  0.1.1.1         r36h6115d3f_1001    conda-forge
r-minqa                   1.2.4           r36h6786f55_1004    conda-forge
r-mnormt                  1.5_5           r36h9bbef5b_1003    conda-forge
r-modelmetrics            1.2.2             r36h0357c0b_1    conda-forge
r-modelr                  0.1.5             r36h6115d3f_0    conda-forge
r-munsell                 0.5.0           r36h6115d3f_1002    conda-forge
r-mvtnorm                 1.0_11            r36h9bbef5b_2    conda-forge
r-nlme                    3.1_141           r36h9bbef5b_1    conda-forge
r-nloptr                  1.2.1             r36h0357c0b_1    conda-forge
r-nnet                    7.3_12          r36hcdcec82_1003    conda-forge
r-numderiv                2016.8_1.1        r36h6115d3f_1    conda-forge
r-openssl                 1.4.1             r36h9c8475f_0    conda-forge
r-pamr                    1.56.1            r36h9bbef5b_2    conda-forge
r-pbdzmq                  0.3_3           r36h559a7a4_1002    conda-forge
r-pbkrtest                0.4_7           r36h6115d3f_1002    conda-forge
r-pcapp                   1.9_73          r36h0357c0b_1001    conda-forge
r-pillar                  1.4.2             r36h6115d3f_2    conda-forge
r-pkgbuild                1.0.6             r36h6115d3f_0    conda-forge
r-pkgconfig               2.0.3             r36h6115d3f_0    conda-forge
r-pkgload                 1.0.2           r36h0357c0b_1001    conda-forge
r-plogr                   0.2.0           r36h6115d3f_1002    conda-forge
r-plotly                  4.9.0             r36h6115d3f_1    conda-forge
r-plyr                    1.8.4           r36h0357c0b_1003    conda-forge
r-praise                  1.0.0           r36h6115d3f_1003    conda-forge
r-prettyunits             1.0.2           r36h6115d3f_1002    conda-forge
r-proc                    1.15.3            r36h0357c0b_0    conda-forge
r-processx                3.4.1             r36hcdcec82_0    conda-forge
r-prodlim                 2018.04.18      r36h0357c0b_1003    conda-forge
r-progress                1.2.2             r36h6115d3f_1    conda-forge
r-promises                1.1.0             r36h0357c0b_0    conda-forge
r-pryr                    0.1.4           r36h0357c0b_1003    conda-forge
r-ps                      1.3.0           r36hcdcec82_1001    conda-forge
r-purrr                   0.3.2             r36hcdcec82_1    conda-forge
r-quantmod                0.4_15            r36h6115d3f_1    conda-forge
r-r6                      2.4.0             r36h6115d3f_2    conda-forge
r-randomforest            4.6_14          r36h9bbef5b_1002    conda-forge
r-rbokeh                  0.5.0           r36h6115d3f_1002    conda-forge
r-rcmdcheck               1.3.3             r36h6115d3f_2    conda-forge
r-rcolorbrewer            1.1_2           r36h6115d3f_1002    conda-forge
r-rcpp                    1.0.2             r36h0357c0b_0    conda-forge
r-rcpparmadillo           0.9.700.2.0       r36h0357c0b_0    conda-forge
r-rcppeigen               0.3.3.5.0         r36h0357c0b_1    conda-forge
r-rcppnumerical           0.3_3             r36h0357c0b_1    conda-forge
r-rcurl                   1.95_4.12         r36hcdcec82_1    conda-forge
r-readr                   1.3.1           r36h0357c0b_1002    conda-forge
r-readxl                  1.3.1             r36h0357c0b_2    conda-forge
r-recipes                 0.1.7             r36h6115d3f_0    conda-forge
r-recommended             3.6                    r36_1003    conda-forge
r-rematch                 1.0.1           r36h6115d3f_1002    conda-forge
r-rematch2                2.1.0             r36h6115d3f_0    conda-forge
r-remotes                 2.1.0             r36h6115d3f_1    conda-forge
r-repr                    1.0.1             r36h6115d3f_1    conda-forge
r-reprex                  0.3.0             r36h6115d3f_1    conda-forge
r-reshape                 0.8.8             r36hcdcec82_1    conda-forge
r-reshape2                1.4.3           r36h0357c0b_1004    conda-forge
r-rex                     1.1.2           r36h6115d3f_1001    conda-forge
r-rgl                     0.100.30          r36ha687ee4_0    conda-forge
r-rjava                   0.9_11            r36hcdcec82_1    conda-forge
r-rlang                   0.4.0             r36hcdcec82_1    conda-forge
r-rmarkdown               1.16              r36h6115d3f_0    conda-forge
r-robust                  0.4_18.1          r36h9bbef5b_2    conda-forge
r-robustbase              0.93_5            r36h9bbef5b_2    conda-forge
r-rocr                    1.0_7           r36h6115d3f_1002    conda-forge
r-roxygen2                6.1.1           r36h0357c0b_1001    conda-forge
r-rpart                   4.1_15            r36hcdcec82_1    conda-forge
r-rprojroot               1.3_2           r36h6115d3f_1002    conda-forge
r-rrcov                   1.4_7             r36h9bbef5b_2    conda-forge
r-rsqlite                 2.1.2             r36h0357c0b_1    conda-forge
r-rstudioapi              0.10              r36h6115d3f_2    conda-forge
r-rversions               2.0.0             r36h6115d3f_1    conda-forge
r-rvest                   0.3.4             r36h6115d3f_1    conda-forge
r-rweka                   0.4_40            r36h6115d3f_1    conda-forge
r-rwekajars               3.9.3_1           r36h6115d3f_1    conda-forge
r-scales                  1.0.0           r36h0357c0b_1002    conda-forge
r-selectr                 0.4_1           r36h6115d3f_1001    conda-forge
r-sessioninfo             1.1.1           r36h6115d3f_1001    conda-forge
r-shiny                   1.4.0             r36h6115d3f_0    conda-forge
r-shinythemes             1.1.2             r36h6115d3f_1    conda-forge
r-slam                    0.1_45            r36hcdcec82_1    conda-forge
r-snow                    0.4_3           r36h6115d3f_1001    conda-forge
r-sourcetools             0.1.7           r36he1b5a44_1001    conda-forge
r-spatial                 7.3_11          r36hcdcec82_1003    conda-forge
r-squarem                 2017.10_1       r36h6115d3f_1002    conda-forge
r-statmod                 1.4.32            r36h6e990d7_2    conda-forge
r-stringdist              0.9.5.3           r36hcdcec82_0    conda-forge
r-stringi                 1.4.3             r36h0e574ca_3    conda-forge
r-stringr                 1.4.0             r36h6115d3f_1    conda-forge
r-styler                  1.1.1             r36h6115d3f_1    conda-forge
r-survival                2.44_1.1          r36hcdcec82_1    conda-forge
r-sys                     3.3               r36hcdcec82_0    conda-forge
r-testthat                2.2.1             r36h0357c0b_0    conda-forge
r-tibble                  2.1.3             r36hcdcec82_1    conda-forge
r-tidyr                   1.0.0             r36h0357c0b_0    conda-forge
r-tidyselect              0.2.5           r36h0357c0b_1001    conda-forge
r-tidyverse               1.2.1           r36h6115d3f_1002    conda-forge
r-timedate                3043.102        r36h6115d3f_1001    conda-forge
r-tinytex                 0.16              r36h6115d3f_0    conda-forge
r-ttr                     0.23_5            r36hcdcec82_0    conda-forge
r-usethis                 1.5.1             r36h6115d3f_1    conda-forge
r-utf8                    1.1.4           r36hcdcec82_1001    conda-forge
r-uuid                    0.1_2           r36hcdcec82_1002    conda-forge
r-vctrs                   0.2.0             r36hcdcec82_1    conda-forge
r-viridis                 0.5.1           r36h6115d3f_1003    conda-forge
r-viridislite             0.3.0           r36h6115d3f_1002    conda-forge
r-webshot                 0.5.1           r36h6115d3f_1001    conda-forge
r-wgcna                   1.68              r36h0357c0b_1    bioconda
r-whisker                 0.4               r36h6115d3f_0    conda-forge
r-withr                   2.1.2           r36h6115d3f_1001    conda-forge
r-xfun                    0.10              r36h6115d3f_0    conda-forge
r-xml                     3.98_1.20         r36hcdcec82_1    conda-forge
r-xml2                    1.2.2             r36h0357c0b_0    conda-forge
r-xmlparsedata            1.0.3             r36h6115d3f_0    conda-forge
r-xopen                   1.0.0           r36h6115d3f_1002    conda-forge
r-xptr                    1.1.1             r36hcdcec82_0    conda-forge
r-xtable                  1.8_4             r36h6115d3f_2    conda-forge
r-xts                     0.11_2            r36hcdcec82_1    conda-forge
r-yaml                    2.2.0           r36hcdcec82_1002    conda-forge
r-zeallot                 0.1.0           r36h6115d3f_1001    conda-forge
r-zoo                     1.8_6             r36hcdcec82_1    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
rope                      0.14.0                     py_0    conda-forge
rpy2                      3.1.0           py37r36hc1659b7_0    conda-forge
scikit-learn              0.21.3           py37hcdab131_0    conda-forge
scipy                     1.3.1            py37h921218d_2    conda-forge
seaborn                   0.9.0                      py_1    conda-forge
sed                       4.7               h1bed415_1000    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                41.4.0                   py37_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
six                       1.12.0                py37_1000    conda-forge
snowballstemmer           2.0.0                      py_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
statsmodels               0.10.1           py37hc1659b7_0    conda-forge
terminado                 0.8.2                    py37_0    conda-forge
testpath                  0.4.2                   py_1001    conda-forge
tk                        8.6.9             hed695b0_1003    conda-forge
tktable                   2.10                 h555a92e_3    conda-forge
tornado                   6.0.3            py37h516909a_0    conda-forge
traitlets                 4.3.3                    py37_0    conda-forge
tzlocal                   2.0.0                      py_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.33.6                   py37_0    conda-forge
wrapt                     1.11.2           py37h516909a_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yapf                      0.28.0                     py_0    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      0.6.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.0                h3b9ef0a_0    conda-forge

Details about conda and system ( conda info ): 
$ conda info
     active environment : ml-omics-sklearn
    active env location : /home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn
            shell level : 1
       user config file : /home/hermidalc/.condarc
 populated config files : /home/hermidalc/.condarc
                          /home/hermidalc/soft/miniconda3/envs/ml-omics-sklearn/.condarc
          conda version : 4.7.12
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /home/hermidalc/soft/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/hermidalc/soft/miniconda3/pkgs
                          /home/hermidalc/.conda/pkgs
       envs directories : /home/hermidalc/soft/miniconda3/envs
                          /home/hermidalc/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.3 Linux/5.2.18-200.fc30.x86_64 fedora/30 glibc/2.29
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
@ocefpaf
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ocefpaf commented Oct 15, 2019

rpy2 3.1.0 should update dependency to cffi <1.13.0a0

Do you want to send a PR updating that?

You would need to change the line

https://github.com/conda-forge/rpy2-feedstock/blob/master/recipe/meta.yaml#L30

and bump the build number.

@hermidalc hermidalc mentioned this issue Oct 15, 2019
Merged
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@hermidalc hermidalc changed the title cffi 1.13 breaks rpy2 3.1.0 cffi 1.13 breaks rpy2 3.1.0 on R 3.6 Oct 15, 2019
@hermidalc hermidalc changed the title cffi 1.13 breaks rpy2 3.1.0 on R 3.6 cffi 1.13 breaks rpy2 3.1.0 on R 3.6 and Python 3.7 Oct 15, 2019
@ejolly ejolly mentioned this issue Oct 16, 2019
Closed
@yannikschaelte yannikschaelte mentioned this issue Oct 20, 2019
Closed
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@hermidalc @ocefpaf