Open pcm32 opened 4 years ago
On conda list of the env, libopenblas shows to be installed:
libopenblas 0.3.9 h3d69b6c_0 conda-forge
ha! it is pointing to an older than expected lib....
Installing libopenblas 0.3.7 in the environment through conda fixes this, however I wonder if pinning libopenblas to 0.3.7 on bioconda will be the long term solution. I could imagine that as versions of R change, this will become incompatible.
If this is a proper R package, shouldn't this be an r-
sort of package in bioconda? @nh3 ?
Last time this happened, it was due to r-matrix
specifically asked for v0.3.7. https://github.com/conda-forge/r-matrix-feedstock/pull/14 fixed the error.
If this is a proper R package, shouldn't this be an
r-
sort of package in bioconda? @nh3 ?
Err, not quite sure. Does r-
require the package in CRAN?
I might be wrong, but my impression is that r-
packages in bioconda get re-built with every new version of R available in conda, but it is irrespective of them being on CRAN or not. Might be worth asking in the conda gitter channel.
How do we trigger something like the conda-forge fix that you mention @nh3 ?
Last time @dpryan79 fixed r-matrix
, of which the issue is highly visible as it caused many r packages to fail. r-leidenbase
is much less used, so worth poking him directly, I think.
@pcm32 Can you post the output of conda list
?
After a clean install (macOS) of monocle3-cli:
# packages in environment at /Users/pmoreno/miniconda3/envs/monocle3-cli-test:
#
# Name Version Build Channel
_r-mutex 1.0.1 anacondar_1 conda-forge
bioconductor-batchelor 1.2.1 r36h6de7cb9_0 bioconda
bioconductor-beachmat 2.2.0 r36h6de7cb9_0 bioconda
bioconductor-biobase 2.46.0 r36h01d97ff_0 bioconda
bioconductor-biocgenerics 0.32.0 r36_0 bioconda
bioconductor-biocneighbors 1.4.0 r36h6de7cb9_0 bioconda
bioconductor-biocparallel 1.20.0 r36h6de7cb9_0 bioconda
bioconductor-biocsingular 1.2.0 r36h6de7cb9_0 bioconda
bioconductor-delayedarray 0.12.0 r36h01d97ff_0 bioconda
bioconductor-delayedmatrixstats 1.8.0 r36_0 bioconda
bioconductor-genomeinfodb 1.22.0 r36_0 bioconda
bioconductor-genomeinfodbdata 1.2.2 r36_0 bioconda
bioconductor-genomicranges 1.38.0 r36h01d97ff_0 bioconda
bioconductor-hdf5array 1.14.0 r36h01d97ff_0 bioconda
bioconductor-iranges 2.20.0 r36h01d97ff_0 bioconda
bioconductor-limma 3.42.0 r36h01d97ff_0 bioconda
bioconductor-rhdf5 2.30.0 r36h6de7cb9_0 bioconda
bioconductor-rhdf5lib 1.8.0 r36h01d97ff_0 bioconda
bioconductor-s4vectors 0.24.0 r36h01d97ff_0 bioconda
bioconductor-scater 1.14.0 r36h6de7cb9_0 bioconda
bioconductor-singlecellexperiment 1.8.0 r36_0 bioconda
bioconductor-summarizedexperiment 1.16.0 r36_0 bioconda
bioconductor-xvector 0.26.0 r36h01d97ff_0 bioconda
bioconductor-zlibbioc 1.32.0 r36h01d97ff_0 bioconda
boost-cpp 1.72.0 hdf9ef73_0 conda-forge
bwidget 1.9.14 0 conda-forge
bzip2 1.0.8 h0b31af3_2 conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
cairo 1.16.0 hec6a9b0_1003 conda-forge
cctools 927.0.2 h5ba7a2e_4 conda-forge
certifi 2020.4.5.1 py38h32f6830_0 conda-forge
cfitsio 3.470 h84d2f63_2 conda-forge
clang 9.0.1 default_hf57f61e_0 conda-forge
clang_osx-64 9.0.1 h05bbb7f_0 conda-forge
clangxx 9.0.1 default_hf57f61e_0 conda-forge
clangxx_osx-64 9.0.1 h05bbb7f_0 conda-forge
colormath 3.0.0 py_2 conda-forge
compiler-rt 9.0.1 h6a512c6_3 conda-forge
compiler-rt_osx-64 9.0.1 h99342c6_3 conda-forge
curl 7.68.0 h8754def_0 conda-forge
decorator 4.4.2 py_0 conda-forge
expat 2.2.9 h4a8c4bd_2 conda-forge
fontconfig 2.13.1 h6b1039f_1001 conda-forge
freetype 2.10.1 h8da9a1a_0 conda-forge
freexl 1.0.5 h1de35cc_1002 conda-forge
fribidi 1.0.9 h0b31af3_0 conda-forge
geos 3.8.1 h4a8c4bd_0 conda-forge
geotiff 1.5.1 h4bdff65_9 conda-forge
gettext 0.19.8.1 h46ab8bc_1002 conda-forge
gfortran_impl_osx-64 7.3.0 hf4212f2_2 conda-forge
gfortran_osx-64 7.3.0 h22b1bf0_9 conda-forge
giflib 5.2.1 h0b31af3_2 conda-forge
glib 2.58.3 py38h338c551_1004 conda-forge
gmp 6.2.0 h4a8c4bd_2 conda-forge
graphite2 1.3.13 h12caacf_1001 conda-forge
gsl 2.6 ha2d443c_0 conda-forge
harfbuzz 2.4.0 hd8d2a14_3 conda-forge
hdf4 4.2.13 h84186c3_1003 conda-forge
hdf5 1.10.5 nompi_h3e39495_1104 conda-forge
icu 64.2 h6de7cb9_1 conda-forge
isl 0.19 0 conda-forge
jpeg 9c h1de35cc_1001 conda-forge
json-c 0.13.1 h1de35cc_1001 conda-forge
kealib 1.4.13 h2324030_0 conda-forge
krb5 1.16.4 h1752a42_0 conda-forge
ld64 450.3 h3c32e8a_4 conda-forge
libblas 3.8.0 16_openblas conda-forge
libcblas 3.8.0 16_openblas conda-forge
libcurl 7.68.0 h709d2b2_0 conda-forge
libcxx 10.0.0 0 conda-forge
libdap4 3.20.4 habf5908_0 conda-forge
libedit 3.1.20170329 hcfe32e1_1001 conda-forge
libffi 3.2.1 h4a8c4bd_1007 conda-forge
libgdal 3.0.4 hec54991_3 conda-forge
libgfortran 4.0.0 2 conda-forge
libiconv 1.15 h0b31af3_1006 conda-forge
libkml 1.3.0 h169b8f9_1011 conda-forge
liblapack 3.8.0 16_openblas conda-forge
libllvm9 9.0.1 ha1b3eb9_0 conda-forge
libnetcdf 4.7.4 nompi_he461dc0_101 conda-forge
libopenblas 0.3.9 h3d69b6c_0 conda-forge
libpng 1.6.37 hbbe82c9_1 conda-forge
libpq 12.2 h554dc5a_0 conda-forge
libspatialite 4.3.0a hbcd37d4_1037 conda-forge
libssh2 1.8.2 hcdc9a53_2 conda-forge
libtiff 4.1.0 ha78913b_3 conda-forge
libwebp 1.0.2 hd3bf737_5 conda-forge
libxml2 2.9.10 h53d96d6_0 conda-forge
llvm-openmp 10.0.0 h28b9765_0 conda-forge
lz4-c 1.8.3 h6de7cb9_1001 conda-forge
make 4.3 h0b31af3_0 conda-forge
monocle3-cli 0.0.7 r36_1 bioconda
mpc 1.1.0 h4160ff4_1007 conda-forge
mpfr 4.0.2 h65ac59c_1 conda-forge
ncurses 6.1 h0a44026_1002 conda-forge
networkx 2.4 py_1 conda-forge
numpy 1.18.1 py38h1f821a2_1 conda-forge
openjpeg 2.3.1 h254dc36_3 conda-forge
openssl 1.1.1f h0b31af3_0 conda-forge
pandoc 2.9.2.1 0 conda-forge
pango 1.42.4 haa940fe_4 conda-forge
pcre 8.44 h4a8c4bd_0 conda-forge
pip 20.0.2 py_2 conda-forge
pixman 0.38.0 h01d97ff_1003 conda-forge
poppler 0.67.0 h16886b5_8 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 12.2 h16d8c28_0 conda-forge
proj 6.3.1 h773a61f_1 conda-forge
python 3.8.2 hd5f0129_5_cpython conda-forge
python_abi 3.8 1_cp38 conda-forge
r-askpass 1.1 r36h159158b_1 conda-forge
r-assertthat 0.2.1 r36h6115d3f_1 conda-forge
r-backports 1.1.6 r36h17f1fa6_0 conda-forge
r-base 3.6.3 h0f68305_1 conda-forge
r-base64enc 0.1_3 r36h159158b_1003 conda-forge
r-beeswarm 0.2.3 r36h6115d3f_1002 conda-forge
r-bh 1.72.0_3 r36h6115d3f_0 conda-forge
r-bitops 1.0_6 r36h159158b_1003 conda-forge
r-boot 1.3_24 r36h6115d3f_0 conda-forge
r-callr 3.4.3 r36h6115d3f_0 conda-forge
r-class 7.3_16 r36h17f1fa6_0 conda-forge
r-classint 0.4_3 r36h384270c_0 conda-forge
r-cli 2.0.2 r36h6115d3f_0 conda-forge
r-coda 0.19_3 r36h6115d3f_1 conda-forge
r-codetools 0.2_16 r36h6115d3f_1001 conda-forge
r-colorspace 1.4_1 r36h159158b_1 conda-forge
r-commonmark 1.7 r36h159158b_1001 conda-forge
r-crayon 1.3.4 r36h6115d3f_1002 conda-forge
r-crosstalk 1.1.0.1 r36h6115d3f_0 conda-forge
r-curl 4.3 r36h17f1fa6_0 conda-forge
r-data.table 1.12.8 r36h17f1fa6_0 conda-forge
r-dbi 1.1.0 r36h6115d3f_0 conda-forge
r-deldir 0.1_25 r36h384270c_0 conda-forge
r-desc 1.2.0 r36h6115d3f_1002 conda-forge
r-digest 0.6.25 r36hc5da6b9_0 conda-forge
r-dplyr 0.8.5 r36hc5da6b9_0 conda-forge
r-dqrng 0.2.1 r36hf99fc2c_1 conda-forge
r-e1071 1.7_3 r36hc5da6b9_0 conda-forge
r-ellipsis 0.3.0 r36h17f1fa6_0 conda-forge
r-evaluate 0.14 r36h6115d3f_1 conda-forge
r-expm 0.999_4 r36hb1cbdc7_3 conda-forge
r-fansi 0.4.1 r36h17f1fa6_0 conda-forge
r-farver 2.0.3 r36hc5da6b9_0 conda-forge
r-fastmap 1.0.1 r36hc5da6b9_0 conda-forge
r-fnn 1.1.3 r36hf99fc2c_1 conda-forge
r-formatr 1.7 r36h6115d3f_1 conda-forge
r-furrr 0.1.0 r36h6115d3f_1001 conda-forge
r-futile.logger 1.4.3 r36h6115d3f_1002 conda-forge
r-futile.options 1.0.1 r36h6115d3f_1001 conda-forge
r-future 1.16.0 r36h6115d3f_0 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-ggbeeswarm 0.6.0 r36_1002 conda-forge
r-ggplot2 3.3.0 r36h6115d3f_0 conda-forge
r-ggrepel 0.8.2 r36hc5da6b9_0 conda-forge
r-globals 0.12.5 r36h6115d3f_0 conda-forge
r-glue 1.4.0 r36h17f1fa6_0 conda-forge
r-gmodels 2.18.1 r36_1002 conda-forge
r-gridextra 2.3 r36h6115d3f_1002 conda-forge
r-grr 0.9.5 r36hf99fc2c_1003 conda-forge
r-gtable 0.3.0 r36h6115d3f_2 conda-forge
r-gtools 3.8.2 r36h17f1fa6_0 conda-forge
r-hexbin 1.28.1 r36h384270c_0 conda-forge
r-highr 0.8 r36h6115d3f_1 conda-forge
r-htmltools 0.4.0 r36hc5da6b9_0 conda-forge
r-htmlwidgets 1.5.1 r36h6115d3f_0 conda-forge
r-httpuv 1.5.2 r36hf99fc2c_1 conda-forge
r-httr 1.4.1 r36h6115d3f_1 conda-forge
r-hunspell 3.0 r36hf99fc2c_1001 conda-forge
r-igraph 1.2.5 r36h28033da_0 conda-forge
r-irlba 2.3.3 r36h26f5615_2 conda-forge
r-isoband 0.2.1 r36hc5da6b9_0 conda-forge
r-jsonlite 1.6.1 r36h17f1fa6_0 conda-forge
r-kernsmooth 2.23_16 r36h3830744_1 conda-forge
r-knitr 1.28 r36h6115d3f_0 conda-forge
r-labeling 0.3 r36h6115d3f_1002 conda-forge
r-lambda.r 1.2.4 r36h6115d3f_0 conda-forge
r-later 1.0.0 r36hc5da6b9_0 conda-forge
r-lattice 0.20_41 r36h17f1fa6_0 conda-forge
r-lazyeval 0.2.2 r36h159158b_1 conda-forge
r-learnbayes 2.15.1 r36h6115d3f_1001 conda-forge
r-leidenbase 0.1.0 r36hfcebdee_0 bioconda
r-lifecycle 0.2.0 r36h6115d3f_0 conda-forge
r-listenv 0.8.0 r36h6115d3f_0 conda-forge
r-lmtest 0.9_37 r36h85e41a7_2 conda-forge
r-magrittr 1.5 r36h6115d3f_1002 conda-forge
r-markdown 1.1 r36h159158b_0 conda-forge
r-mass 7.3_51.5 r36h17f1fa6_0 conda-forge
r-matrix 1.2_18 r36h26f5615_2 conda-forge
r-matrix.utils 0.9.8 r36h6115d3f_0 conda-forge
r-matrixstats 0.56.0 r36h17f1fa6_0 conda-forge
r-mgcv 1.8_31 r36h26f5615_0 conda-forge
r-mime 0.9 r36h17f1fa6_0 conda-forge
r-monocle3 0.2.0 r36h770b8ee_1 bioconda
r-munsell 0.5.0 r36h6115d3f_1002 conda-forge
r-nlme 3.1_147 r36h384270c_0 conda-forge
r-openssl 1.4.1 r36hdb18a49_0 conda-forge
r-optparse 1.6.4 r36h6115d3f_0 conda-forge
r-pbapply 1.4_2 r36h6115d3f_0 conda-forge
r-pbmcapply 1.5.0 r36h159158b_0 conda-forge
r-pheatmap 1.0.12 r36h6115d3f_1 conda-forge
r-pillar 1.4.3 r36h6115d3f_0 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 r36hc5da6b9_1001 conda-forge
r-plogr 0.2.0 r36h6115d3f_1002 conda-forge
r-plotly 4.9.2.1 r36h6115d3f_0 conda-forge
r-plyr 1.8.6 r36hc5da6b9_0 conda-forge
r-praise 1.0.0 r36h6115d3f_1003 conda-forge
r-prettyunits 1.1.1 r36h6115d3f_0 conda-forge
r-processx 3.4.2 r36h17f1fa6_0 conda-forge
r-promises 1.1.0 r36hc5da6b9_0 conda-forge
r-proxy 0.4_23 r36h159158b_1 conda-forge
r-pryr 0.1.4 r36hf99fc2c_1003 conda-forge
r-ps 1.3.2 r36h17f1fa6_0 conda-forge
r-pscl 1.5.5 r36h0b31af3_0 conda-forge
r-purrr 0.3.3 r36h17f1fa6_0 conda-forge
r-r6 2.4.1 r36h6115d3f_0 conda-forge
r-rann 2.6.1 r36hf99fc2c_1 conda-forge
r-rappdirs 0.3.1 r36h159158b_1003 conda-forge
r-raster 3.0_12 r36hc5da6b9_0 conda-forge
r-rcolorbrewer 1.1_2 r36h6115d3f_1002 conda-forge
r-rcpp 1.0.4.6 r36hc5da6b9_0 conda-forge
r-rcppannoy 0.0.16 r36hc5da6b9_0 conda-forge
r-rcppeigen 0.3.3.7.0 r36hc5da6b9_0 conda-forge
r-rcpphnsw 0.2.0 r36hf99fc2c_0 conda-forge
r-rcppparallel 5.0.0 r36hc5da6b9_0 conda-forge
r-rcppprogress 0.4.2 r36h6115d3f_0 conda-forge
r-rcurl 1.98_1.1 r36h17f1fa6_0 conda-forge
r-reshape2 1.4.4 r36hc5da6b9_0 conda-forge
r-reticulate 1.15 r36hc5da6b9_0 conda-forge
r-rhpcblasctl 0.20_17 r36h17f1fa6_0 conda-forge
r-rlang 0.4.5 r36h17f1fa6_0 conda-forge
r-rmarkdown 2.1 r36h6115d3f_0 conda-forge
r-rprojroot 1.3_2 r36h6115d3f_1002 conda-forge
r-rsample 0.0.5 r36h6115d3f_0 conda-forge
r-rspectra 0.16_0 r36hc5da6b9_0 conda-forge
r-rstudioapi 0.11 r36h6115d3f_0 conda-forge
r-rsvd 1.0.3 r36h6115d3f_0 conda-forge
r-rtsne 0.15 r36ha4e0109_2 conda-forge
r-scales 1.1.0 r36h6115d3f_0 conda-forge
r-sf 0.9_2 r36h7817547_0 conda-forge
r-shiny 1.4.0.2 r36h6115d3f_0 conda-forge
r-sitmo 2.0.1 r36hf99fc2c_1 conda-forge
r-slam 0.1_47 r36h17f1fa6_0 conda-forge
r-snow 0.4_3 r36h6115d3f_1001 conda-forge
r-sourcetools 0.1.7 r36h6de7cb9_1001 conda-forge
r-sp 1.4_1 r36h17f1fa6_0 conda-forge
r-spdata 0.3.5 r36h6115d3f_0 conda-forge
r-spdep 1.1_3 r36h39f91c9_1 conda-forge
r-speedglm 0.3_2 r36_1002 conda-forge
r-spelling 2.1 r36h6115d3f_1 conda-forge
r-stringi 1.4.6 r36h3211bb2_0 conda-forge
r-stringr 1.4.0 r36h6115d3f_1 conda-forge
r-sys 3.3 r36h159158b_0 conda-forge
r-testthat 2.3.2 r36hc5da6b9_0 conda-forge
r-tibble 3.0.0 r36h17f1fa6_0 conda-forge
r-tidyr 1.0.2 r36hc5da6b9_0 conda-forge
r-tidyselect 1.0.0 r36h6115d3f_0 conda-forge
r-tinytex 0.21 r36h6115d3f_0 conda-forge
r-units 0.6_6 r36hc5da6b9_0 conda-forge
r-utf8 1.1.4 r36h17f1fa6_1002 conda-forge
r-uwot 0.1.8 r36hc5da6b9_0 conda-forge
r-vctrs 0.2.4 r36h17f1fa6_0 conda-forge
r-vipor 0.4.5 r36h6115d3f_1002 conda-forge
r-viridis 0.5.1 r36h6115d3f_1003 conda-forge
r-viridislite 0.3.0 r36h6115d3f_1002 conda-forge
r-withr 2.1.2 r36h6115d3f_1001 conda-forge
r-xfun 0.13 r36h6115d3f_0 conda-forge
r-xml2 1.3.1 r36hc5da6b9_0 conda-forge
r-xtable 1.8_4 r36h6115d3f_2 conda-forge
r-yaml 2.2.1 r36h17f1fa6_0 conda-forge
r-zeallot 0.1.0 r36h6115d3f_1001 conda-forge
r-zoo 1.8_7 r36h17f1fa6_0 conda-forge
readline 8.0 hcfe32e1_0 conda-forge
setuptools 46.1.3 py38h32f6830_0 conda-forge
spectra 0.0.11 py_1 conda-forge
sqlite 3.30.1 h93121df_0 conda-forge
tapi 1000.10.8 ha1b3eb9_4 conda-forge
tbb 2018.0.5 h2d50403_0 conda-forge
tiledb 1.7.0 hd5e958f_2 conda-forge
tk 8.6.10 hbbe82c9_0 conda-forge
tktable 2.10 h008db23_3 conda-forge
tzcode 2019a h01d97ff_1002 conda-forge
udunits2 2.2.27.6 h776b7f1_1001 conda-forge
wheel 0.34.2 py_1 conda-forge
xerces-c 3.2.2 h8f8adb3_1004 conda-forge
xz 5.2.5 h0b31af3_0 conda-forge
zlib 1.2.11 h0b31af3_1006 conda-forge
zstd 1.4.4 hed8d7c8_2 conda-forge
Thanks for looking into this @dpryan79.
FYI, the fix for this is going to take a while. I'd actually prefer to wait until we roll out R 4.0 in a couple weeks since I need to rebuild all R packages at that point (fixing this would require rebuilding an unknown number of them already).
Thanks @dpryan79 . Would it be advisable then to pin down openblas to the required version in the monocle-cli conda package? current package cannot be used as it is.
or could this break the linux package somehow?
do you expect the originally written container to work fine? I could try to move our setup to singularity.
The container should still work fine. You can try pinning openblas. The issue is mostly that since most R packages that need to pin to it don't that it won't have a big effect. Note that this is an OSX-specific issue, Linux is unaffected.
After installing the package in a clean environment on macOS Mojave, and trying the steps in https://cole-trapnell-lab.github.io/monocle3/docs/clustering/, you get this error when running the
cluster_cells
method:Maybe we need to add openblas? I remember others having issues with this. Maybe @a-solovyev12 recently? How did you sort it?