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conda-forge / rpy2-feedstock

A conda-smithy repository for rpy2.
BSD 3-Clause "New" or "Revised" License
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cffi 1.13 breaks rpy2 3.1.0 on R 3.6 and Python 3.7 #35

Closed hermidalc closed 4 years ago

hermidalc commented 4 years ago

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 commented 4 years ago

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.