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ebi-gene-expression-group / monocle-scripts

Command line scripts wrapping functions in monocle3
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Dynamic library missing on macOS Mojave #11

Open pcm32 opened 4 years ago

pcm32 commented 4 years ago

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:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Users/pmoreno/miniconda3/envs/monocle3-scripts/lib/R/library/leidenbase/libs/leidenbase.dylib':
  dlopen(/Users/pmoreno/miniconda3/envs/monocle3-scripts/lib/R/library/leidenbase/libs/leidenbase.dylib, 6): Library not loaded: @rpath/libopenblasp-r0.3.7.dylib
  Referenced from: /Users/pmoreno/miniconda3/envs/monocle3-scripts/lib/R/library/leidenbase/libs/leidenbase.dylib
  Reason: image not found

Maybe we need to add openblas? I remember others having issues with this. Maybe @a-solovyev12 recently? How did you sort it?

pcm32 commented 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....

pcm32 commented 4 years ago

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.

pcm32 commented 4 years ago

If this is a proper R package, shouldn't this be an r- sort of package in bioconda? @nh3 ?

nh3 commented 4 years ago

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.

nh3 commented 4 years ago

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?

pcm32 commented 4 years ago

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 ?

nh3 commented 4 years ago

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.

dpryan79 commented 4 years ago

@pcm32 Can you post the output of conda list?

pcm32 commented 4 years ago

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.

dpryan79 commented 4 years ago

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).

pcm32 commented 4 years ago

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.

pcm32 commented 4 years ago

or could this break the linux package somehow?

pcm32 commented 4 years ago

do you expect the originally written container to work fine? I could try to move our setup to singularity.

dpryan79 commented 4 years ago

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.