Error loading r package within conda environment: libproj.so.15: cannot open shared object file

Question

I am creating the following conda environment:

 $ mamba create -n mexico -c conda-forge -c bioconda -c R r-base=4.2.3 r-data.table=1.14.8 r-terra=1.5_21

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        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.3.1) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['r-base=4.2.3', 'r-data.table=1.14.8', 'r-terra=1.5_21']

warning  libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/47929eba.json" was modified by another program
warning  libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/3e39a7aa.json" was modified by another program
warning  libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/2ce54b42.json" was modified by another program
warning  libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/4ea078d6.json" was modified by another program
conda-forge/linux-64                                          No change
conda-forge/noarch                                            No change
R/linux-64                                                    No change
R/noarch                                                      No change
pkgs/main/noarch                                   821.1kB @ 748.6kB/s  0.8s
pkgs/r/linux-64                                      1.4MB @ 845.8kB/s  1.4s
pkgs/r/noarch                                        1.3MB @ 599.8kB/s  1.0s
bioconda/noarch                                      4.2MB @   1.7MB/s  3.2s
bioconda/linux-64                                    4.6MB @   1.4MB/s  3.9s
pkgs/main/linux-64                                   5.5MB @   1.4MB/s  4.2s
warning  libmamba Invalid package cache, file '/home/grizzo/miniconda3/pkgs/r-base-4.2.3-h4a03800_2/lib/R/doc/html/packages.html' has incorrect size
Transaction

  Prefix: /home/grizzo/miniconda3/envs/mexico

  Updating specs:

   - r-base=4.2.3
   - r-data.table=1.14.8
   - r-terra=1.5_21


  Package                           Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                       0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                       4.5  2_gnu                conda-forge/linux-64     Cached
  + _r-mutex                          1.0.1  anacondar_1          conda-forge/noarch       Cached
  + binutils_impl_linux-64             2.40  hf600244_0           conda-forge/linux-64     Cached
  + bwidget                          1.9.14  ha770c72_1           conda-forge/linux-64     Cached
  + bzip2                             1.0.8  h7f98852_4           conda-forge/linux-64     Cached
  + c-ares                           1.18.1  h7f98852_0           conda-forge/linux-64     Cached
  + ca-certificates               2022.12.7  ha878542_0           conda-forge/linux-64     Cached
  + cairo                            1.16.0  h35add3b_1015        conda-forge/linux-64     Cached
  + curl                             7.88.1  hdc1c0ab_1           conda-forge/linux-64     Cached
  + expat                             2.5.0  hcb278e6_1           conda-forge/linux-64     Cached
  + font-ttf-dejavu-sans-mono          2.37  hab24e00_0           conda-forge/noarch       Cached
  + font-ttf-inconsolata              3.000  h77eed37_0           conda-forge/noarch       Cached
  + font-ttf-source-code-pro          2.038  h77eed37_0           conda-forge/noarch       Cached
  + font-ttf-ubuntu                    0.83  hab24e00_0           conda-forge/noarch       Cached
  + fontconfig                       2.14.2  h14ed4e7_0           conda-forge/linux-64     Cached
  + fonts-conda-ecosystem                 1  0                    conda-forge/noarch       Cached
  + fonts-conda-forge                     1  0                    conda-forge/noarch       Cached
  + freetype                         2.12.1  hca18f0e_1           conda-forge/linux-64     Cached
  + fribidi                          1.0.10  h36c2ea0_0           conda-forge/linux-64     Cached
  + gcc_impl_linux-64                12.2.0  hcc96c02_19          conda-forge/linux-64     Cached
  + gdal                              1.9.2  0                    bioconda/linux-64          41MB
  + gettext                          0.21.1  h27087fc_0           conda-forge/linux-64     Cached
  + gfortran_impl_linux-64           12.2.0  h55be85b_19          conda-forge/linux-64     Cached
  + graphite2                        1.3.13  h58526e2_1001        conda-forge/linux-64     Cached
  + gsl                                 2.7  he838d99_0           conda-forge/linux-64     Cached
  + gxx_impl_linux-64                12.2.0  hcc96c02_19          conda-forge/linux-64     Cached
  + harfbuzz                          6.0.0  h3ff4399_1           conda-forge/linux-64     Cached
  + icu                                72.1  hcb278e6_0           conda-forge/linux-64     Cached
  + kernel-headers_linux-64          2.6.32  he073ed8_15          conda-forge/noarch       Cached
  + keyutils                          1.6.1  h166bdaf_0           conda-forge/linux-64     Cached
  + krb5                             1.20.1  h81ceb04_0           conda-forge/linux-64     Cached
  + ld_impl_linux-64                   2.40  h41732ed_0           conda-forge/linux-64     Cached
  + lerc                              4.0.0  h27087fc_0           conda-forge/linux-64     Cached
  + libblas                           3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas                          3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libcurl                          7.88.1  hdc1c0ab_1           conda-forge/linux-64     Cached
  + libdeflate                         1.18  h0b41bf4_0           conda-forge/linux-64     Cached
  + libedit                    3.1.20191231  he28a2e2_2           conda-forge/linux-64     Cached
  + libev                              4.33  h516909a_1           conda-forge/linux-64     Cached
  + libexpat                          2.5.0  hcb278e6_1           conda-forge/linux-64     Cached
  + libffi                            3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc                            7.2.0  h69d50b8_2           conda-forge/linux-64      312kB
  + libgcc-devel_linux-64            12.2.0  h3b97bd3_19          conda-forge/linux-64     Cached
  + libgcc-ng                        12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libgfortran-ng                   12.2.0  h69a702a_19          conda-forge/linux-64     Cached
  + libgfortran5                     12.2.0  h337968e_19          conda-forge/linux-64     Cached
  + libglib                          2.74.1  h606061b_1           conda-forge/linux-64     Cached
  + libgomp                          12.2.0  h65d4601_19          conda-forge/linux-64     Cached
  + libiconv                           1.17  h166bdaf_0           conda-forge/linux-64     Cached
  + libjpeg-turbo                   2.1.5.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + liblapack                         3.9.0  16_linux64_openblas  conda-forge/linux-64     Cached
  + libnghttp2                       1.52.0  h61bc06f_0           conda-forge/linux-64     Cached
  + libopenblas                      0.3.21  pthreads_h78a6416_3  conda-forge/linux-64     Cached
  + libpng                           1.6.39  h753d276_0           conda-forge/linux-64     Cached
  + libsanitizer                     12.2.0  h46fd767_19          conda-forge/linux-64     Cached
  + libssh2                          1.10.0  hf14f497_3           conda-forge/linux-64     Cached
  + libstdcxx-devel_linux-64         12.2.0  h3b97bd3_19          conda-forge/linux-64     Cached
  + libstdcxx-ng                     12.2.0  h46fd767_19          conda-forge/linux-64     Cached
  + libtiff                           4.5.0  ha587672_6           conda-forge/linux-64     Cached
  + libuuid                          2.38.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + libwebp-base                      1.3.0  h0b41bf4_0           conda-forge/linux-64     Cached
  + libxcb                             1.13  h7f98852_1004        conda-forge/linux-64     Cached
  + libxml2                          2.10.3  hfdac1af_6           conda-forge/linux-64     Cached
  + libzlib                          1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + make                                4.3  hd18ef5c_1           conda-forge/linux-64     Cached
  + ncurses                             6.3  h27087fc_1           conda-forge/linux-64     Cached
  + openssl                           3.1.0  h0b41bf4_0           conda-forge/linux-64     Cached
  + pango                           1.50.14  hd33c08f_0           conda-forge/linux-64     Cached
  + pcre2                             10.40  hc3806b6_0           conda-forge/linux-64     Cached
  + pixman                           0.40.0  h36c2ea0_0           conda-forge/linux-64     Cached
  + pthread-stubs                       0.4  h36c2ea0_1001        conda-forge/linux-64     Cached
  + r-base                            4.2.3  h4a03800_2           conda-forge/linux-64     Cached
  + r-data.table                     1.14.8  r42h133d619_0        conda-forge/linux-64     Cached
  + r-rcpp                           1.0.10  r42h38f115c_0        conda-forge/linux-64     Cached
  + r-terra                          1.5_21  r42h884c59f_0        R/linux-64               Cached
  + readline                            8.2  h8228510_1           conda-forge/linux-64     Cached
  + sed                                 4.8  he412f7d_0           conda-forge/linux-64     Cached
  + sysroot_linux-64                   2.12  he073ed8_15          conda-forge/noarch       Cached
  + tk                               8.6.12  h27826a3_0           conda-forge/linux-64     Cached
  + tktable                            2.10  hb7b940f_3           conda-forge/linux-64     Cached
  + xorg-kbproto                      1.0.7  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-libice                      1.0.10  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libsm                        1.2.3  hd9c2040_1000        conda-forge/linux-64     Cached
  + xorg-libx11                       1.8.4  h0b41bf4_0           conda-forge/linux-64     Cached
  + xorg-libxau                       1.0.9  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxdmcp                     1.1.3  h7f98852_0           conda-forge/linux-64     Cached
  + xorg-libxext                      1.3.4  h0b41bf4_2           conda-forge/linux-64     Cached
  + xorg-libxrender                  0.9.10  h7f98852_1003        conda-forge/linux-64     Cached
  + xorg-libxt                        1.2.1  h7f98852_2           conda-forge/linux-64     Cached
  + xorg-renderproto                 0.11.1  h7f98852_1002        conda-forge/linux-64     Cached
  + xorg-xextproto                    7.3.0  h0b41bf4_1003        conda-forge/linux-64     Cached
  + xorg-xproto                      7.0.31  h7f98852_1007        conda-forge/linux-64     Cached
  + xz                                5.2.6  h166bdaf_0           conda-forge/linux-64     Cached
  + zlib                             1.2.13  h166bdaf_4           conda-forge/linux-64     Cached
  + zstd                              1.5.2  h3eb15da_6           conda-forge/linux-64     Cached

  Summary:

  Install: 96 packages

  Total download: 42MB

───────────────────────────────────────────────────────────────────────────────────────────────────


Confirm changes: [Y/n] Y
libgcc                                             311.7kB @ 749.4kB/s  0.4s
gdal                                                41.5MB @  30.2MB/s  1.4s

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: \ 
SafetyError: The package for r-base located at /home/grizzo/miniconda3/pkgs/r-base-4.2.3-h4a03800_2
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
  reported size: 3423 bytes
  actual size: 3826 bytes


done
Executing transaction: done

To activate this environment, use

     $ mamba activate mexico

To deactivate an active environment, use

     $ mamba deactivate

Installation resulted successful, but when trying to load terra package I have the following error:

 $ conda activate mexico
 $ R

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("terra")
Error: package or namespace load failed for ‘terra’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/grizzo/miniconda3/envs/mexico/lib/R/library/terra/libs/terra.so':
  libproj.so.15: cannot open shared object file: No such file or directory

It seems to me that there is some conflicts between dependencies, because if I do not install data.table package, the terra package loads (with some warning).

Any idea about how to fix it? Thank you

While I cannot help you with the conda / mamba aspect, I can point you to a plausible alternative: using [r2u](https://eddelbuettel.github.io/r2u/), an Ubuntu 22.04 (and 20.04) repository for system-level `apt` installation _with full dependency resolution at the OS level_ which provides _all of CRAN_. I just ran a quick demo: one command, from R, taking sixteen seconds to get you `terra` with all its dependencies as well as `data.table`. But I cannot post the full 3.6mb gif here, sadly, as there is a 2mb limit. — Dirk Eddelbuettel, Apr 09 '23 at 00:34
From what I see, you are using "GDAL 1.9.2". That is *much* too old and terra won't compile with that. "terra" specifies a minimum requirement of `GDAL >= 2.2.3`; but even that is very old -- I would expect version 3.4 or higher. — Robert Hijmans, Apr 09 '23 at 23:39
Other system requirements such as GEOS seem to be missing. Is there a way to show and inspect the output of the terra install process as you would see when you do a standard install? — Robert Hijmans, Apr 09 '23 at 23:43
Thank you for your quick respond! I have added `gdal` `version 3.6.3` to the code to create a new environment with no success. There is not a way to look to the process of installation of the `terra` package as in the standard install. But looking further in the installed libraries, I saw that libproj.so.15 is not installed, instead, I found libproj.so.25 to be installed. Could it be the problem? If yes, how could I get libproj.so.15 instead fo libproj.so.25? — Gonzalo Rizzo, Apr 10 '23 at 02:20
@DirkEddelbuettel, thank you for your suggestion! Would it work on Debian 11? Also, would it get the packages installed within a `conda` environment or they would be installed system-wise? — Gonzalo Rizzo, Apr 10 '23 at 13:56
@GonzaloRizzo Generally speaking, "no" and "no". Ubuntu binaries are really aimed for use on Ubuntu. Not Debian, not Conda running on Ubuntu. — Dirk Eddelbuettel, Apr 10 '23 at 14:37
(Conda R Team Member) Could you please try again without the `-c R` channel? That looks like the root issue here. And possibly force `conda-forge`, i.e., `conda-forge::r-terra=1.5_21`. — merv, Apr 10 '23 at 15:37
Yes, the issue was that `r-terra` was being installed from a default channel - [which is not supported in mamba](https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#mixing-the-defaults-and-conda-forge-channels). This problem was successfully solved here: https://github.com/mamba-org/mamba/issues/2450#issuecomment-1502043758 — Gonzalo Rizzo, Apr 10 '23 at 16:50

Error loading r package within conda environment: libproj.so.15: cannot open shared object file

0 Answers0