jonashaag
commented
1 year ago Closed gonzarizzo closed 1 year ago
jonashaag
commented
1 year ago 
gonzarizzo
commented
1 year ago Hi @jonashaag! I have read that. I have both conda and mamba installed in base and no other package is installed there. I create independent environments to my different projects. I did not find a solution going through that link.
jonashaag
commented
1 year ago Did you see the
Mixing the defaults and conda-forge channels
section that I linked to?
jonashaag
commented
1 year ago Please let me know if there is anything we can do to improve this piece of documentation.
gonzarizzo
commented
1 year ago Yes, I have seen that section. Sorry, but I did not get the point. I mean, I don't see the connection between that part of the documentation and my problem. Could you explain that? I don't think I am mixing defaults with conda-forge channels here. Sorry for not understanding your point.
jonashaag
commented
1 year ago gonzarizzo
commented
1 year ago I have removed the -c R and still I have the same error.
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/test/lib/R/library/terra/libs/terra.so':
libproj.so.15: cannot open shared object file: No such file or directoryIt still does not install libproj.so.15.
(base) envs $ find . -iname 'libproj*'
./test/lib/libproj.so
./test/lib/libproj.so.25
./test/lib/libproj.so.25.9.2.0Can you please show the entire output of the new command? Does it still contain the R channel?
jonashaag
commented
1 year ago + r-terra 1.5_21 r42h884c59f_0 R/linux-64 Cached
Here is the entire command:
(base) ~ $ mamba create -n test -c conda-forge r-base=4.2.3 r-data.table=1.14.8 r-terra=1.5_21 gdal=3.6.3
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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', 'gdal=3.6.3']
warning libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/497deca9.json" was modified by another program
warning libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/09cdf8bf.json" was modified by another program
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
pkgs/main/noarch 821.1kB @ 1.5MB/s 0.7s
pkgs/r/linux-64 1.4MB @ 1.7MB/s 1.1s
pkgs/r/noarch 1.3MB @ 1.0MB/s 0.8s
pkgs/main/linux-64 5.5MB @ 3.0MB/s 2.5s
conda-forge/noarch 11.8MB @ 2.2MB/s 6.6s
conda-forge/linux-64 30.7MB @ 3.5MB/s 12.9s
warning libmamba Invalid package cache, file '/home/grizzo/miniconda3/pkgs/r-base-4.2.3-h062c8ea_1/lib/R/doc/html/packages.html' has incorrect size
Transaction
Prefix: /home/grizzo/miniconda3/envs/test
Updating specs:
- r-base=4.2.3
- r-data.table=1.14.8
- r-terra=1.5_21
- gdal=3.6.3
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
+ blosc 1.21.3 hafa529b_0 conda-forge/linux-64 Cached
+ boost-cpp 1.78.0 h5adbc97_2 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 ha61ee94_1014 conda-forge/linux-64 Cached
+ cfitsio 4.2.0 hd9d235c_0 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
+ freexl 1.0.6 h166bdaf_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 3.6.3 py311h51841c2_7 conda-forge/linux-64 Cached
+ geos 3.11.2 hcb278e6_0 conda-forge/linux-64 Cached
+ geotiff 1.7.1 h480ec47_8 conda-forge/linux-64 Cached
+ 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
+ giflib 5.2.1 h0b41bf4_3 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 h8e241bc_0 conda-forge/linux-64 Cached
+ hdf4 4.2.15 h501b40f_6 conda-forge/linux-64 Cached
+ hdf5 1.14.0 nompi_hb72d44e_103 conda-forge/linux-64 Cached
+ icu 70.1 h27087fc_0 conda-forge/linux-64 Cached
+ json-c 0.16 hc379101_0 conda-forge/linux-64 Cached
+ kealib 1.5.0 he7a6254_1 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
+ lcms2 2.15 haa2dc70_1 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
+ libaec 1.0.6 hcb278e6_1 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-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
+ libgdal 3.6.3 h9c5bede_7 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
+ libkml 1.3.0 h37653c0_1015 conda-forge/linux-64 Cached
+ liblapack 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
+ libnetcdf 4.9.2 nompi_hf3f8848_103 conda-forge/linux-64 Cached
+ libnghttp2 1.52.0 h61bc06f_0 conda-forge/linux-64 Cached
+ libnsl 2.0.0 h7f98852_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
+ libpq 15.2 hb675445_0 conda-forge/linux-64 Cached
+ librttopo 1.1.0 h0d5128d_13 conda-forge/linux-64 Cached
+ libsanitizer 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
+ libspatialite 5.0.1 h7d1ca68_25 conda-forge/linux-64 Cached
+ libsqlite 3.40.0 h753d276_0 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 hca2bb57_4 conda-forge/linux-64 Cached
+ libzip 1.9.2 hc929e4a_1 conda-forge/linux-64 Cached
+ libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
+ lz4-c 1.9.4 hcb278e6_0 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
+ nspr 4.35 h27087fc_0 conda-forge/linux-64 Cached
+ nss 3.89 he45b914_0 conda-forge/linux-64 Cached
+ numpy 1.24.2 py311h8e6699e_0 conda-forge/linux-64 Cached
+ openjpeg 2.5.0 hfec8fc6_2 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
+ pip 23.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pixman 0.40.0 h36c2ea0_0 conda-forge/linux-64 Cached
+ poppler 23.04.0 hf052cbe_1 conda-forge/linux-64 Cached
+ poppler-data 0.4.12 hd8ed1ab_0 conda-forge/noarch Cached
+ postgresql 15.2 h3248436_0 conda-forge/linux-64 Cached
+ proj 9.2.0 h8ffa02c_0 conda-forge/linux-64 Cached
+ pthread-stubs 0.4 h36c2ea0_1001 conda-forge/linux-64 Cached
+ python 3.11.3 h2755cc3_0_cpython conda-forge/linux-64 Cached
+ python_abi 3.11 3_cp311 conda-forge/linux-64 Cached
+ r-base 4.2.3 h062c8ea_1 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 pkgs/r/linux-64 Cached
+ readline 8.2 h8228510_1 conda-forge/linux-64 Cached
+ sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
+ setuptools 67.6.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ snappy 1.1.10 h9fff704_0 conda-forge/linux-64 Cached
+ sqlite 3.40.0 h4ff8645_0 conda-forge/linux-64 Cached
+ sysroot_linux-64 2.12 he073ed8_15 conda-forge/noarch Cached
+ tiledb 2.13.2 hd532e3d_0 conda-forge/linux-64 Cached
+ tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
+ tktable 2.10 hb7b940f_3 conda-forge/linux-64 Cached
+ tzcode 2023c h0b41bf4_0 conda-forge/linux-64 Cached
+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xerces-c 3.2.4 h55805fa_1 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: 137 packages
Total download: 0 B
───────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
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-h062c8ea_1
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 3423 bytes
actual size: 4015 bytes
done
Executing transaction: done
To activate this environment, use
$ mamba activate test
To deactivate an active environment, use
$ mamba deactivate
(base) ~ $ conda activate test
(test) ~ $ 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/test/lib/R/library/terra/libs/terra.so':
libproj.so.15: cannot open shared object file: No such file or directoryAs you can see it is still installing from defaults. You can add -c nodefaults to the channel list. I recommend to add
channels:
- nodefaultsto your ~/.condarc.
gonzarizzo
commented
1 year ago Thank you very much for your help! It was successfully solved! Below an updated report:
(base) ~ $ mamba create -n test -c conda-forge -c nodefaults r-base=4.2.3 r-data.table=1.14.8 r-terra=1.7_23 gdal=3.6 r-codetools=0.2_19Which produce the following output:
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
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=1.7_23', 'gdal=3.6', 'r-codetools=0.2_19']
warning libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/497deca9.json" was modified by another program
warning libmamba Cache file "/home/grizzo/miniconda3/pkgs/cache/09cdf8bf.json" was modified by another program
nodefaults/linux-64 144.0 B @ 453.0 B/s 0.3s
nodefaults/noarch 130.0 B @ 390.0 B/s 0.3s
conda-forge/noarch 11.8MB @ 4.0MB/s 4.3s
conda-forge/linux-64 30.8MB @ 3.4MB/s 13.0s
warning libmamba Invalid package cache, file '/home/grizzo/miniconda3/pkgs/r-base-4.2.3-ha7d60f8_0/lib/R/doc/html/packages.html' has incorrect size
Transaction
Prefix: /home/grizzo/miniconda3/envs/test
Updating specs:
- r-base=4.2.3
- r-data.table=1.14.8
- r-terra=1.7_23
- gdal=3.6
- r-codetools=0.2_19
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
+ blosc 1.21.3 hafa529b_0 conda-forge/linux-64 Cached
+ boost-cpp 1.78.0 h5adbc97_2 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 ha61ee94_1014 conda-forge/linux-64 Cached
+ cfitsio 4.2.0 hd9d235c_0 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
+ freexl 1.0.6 h166bdaf_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 3.6.2 py311hadb6153_3 conda-forge/linux-64 Cached
+ geos 3.11.1 h27087fc_0 conda-forge/linux-64 Cached
+ geotiff 1.7.1 h7157cca_5 conda-forge/linux-64 Cached
+ 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
+ giflib 5.2.1 h0b41bf4_3 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 h8e241bc_0 conda-forge/linux-64 Cached
+ hdf4 4.2.15 h9772cbc_5 conda-forge/linux-64 Cached
+ hdf5 1.12.2 nompi_h4df4325_101 conda-forge/linux-64 Cached
+ icu 70.1 h27087fc_0 conda-forge/linux-64 Cached
+ jpeg 9e h0b41bf4_3 conda-forge/linux-64 Cached
+ json-c 0.16 hc379101_0 conda-forge/linux-64 Cached
+ kealib 1.5.0 ha7026e8_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
+ lcms2 2.15 hfd0df8a_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
+ libaec 1.0.6 hcb278e6_1 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 1.17 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-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
+ libgdal 3.6.2 h10cbb15_3 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
+ libkml 1.3.0 h37653c0_1015 conda-forge/linux-64 Cached
+ liblapack 3.9.0 16_linux64_openblas conda-forge/linux-64 Cached
+ libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge/linux-64 Cached
+ libnghttp2 1.52.0 h61bc06f_0 conda-forge/linux-64 Cached
+ libnsl 2.0.0 h7f98852_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
+ libpq 15.2 hb675445_0 conda-forge/linux-64 Cached
+ librttopo 1.1.0 ha49c73b_12 conda-forge/linux-64 Cached
+ libsanitizer 12.2.0 h46fd767_19 conda-forge/linux-64 Cached
+ libspatialite 5.0.1 h7c8129e_22 conda-forge/linux-64 Cached
+ libsqlite 3.40.0 h753d276_0 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 h6adf6a1_2 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 hca2bb57_4 conda-forge/linux-64 Cached
+ libzip 1.9.2 hc929e4a_1 conda-forge/linux-64 Cached
+ libzlib 1.2.13 h166bdaf_4 conda-forge/linux-64 Cached
+ lz4-c 1.9.4 hcb278e6_0 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
+ nspr 4.35 h27087fc_0 conda-forge/linux-64 Cached
+ nss 3.89 he45b914_0 conda-forge/linux-64 Cached
+ numpy 1.24.2 py311h8e6699e_0 conda-forge/linux-64 Cached
+ openjpeg 2.5.0 hfec8fc6_2 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
+ pip 23.0.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pixman 0.40.0 h36c2ea0_0 conda-forge/linux-64 Cached
+ poppler 22.12.0 h091648b_1 conda-forge/linux-64 Cached
+ poppler-data 0.4.12 hd8ed1ab_0 conda-forge/noarch Cached
+ postgresql 15.2 h3248436_0 conda-forge/linux-64 Cached
+ proj 9.1.0 h8ffa02c_1 conda-forge/linux-64 Cached
+ pthread-stubs 0.4 h36c2ea0_1001 conda-forge/linux-64 Cached
+ python 3.11.3 h2755cc3_0_cpython conda-forge/linux-64 Cached
+ python_abi 3.11 3_cp311 conda-forge/linux-64 Cached
+ r-base 4.2.3 ha7d60f8_0 conda-forge/linux-64 Cached
+ r-codetools 0.2_19 r42hc72bb7e_0 conda-forge/noarch 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 1.7_23 r42h0f53b7d_0 conda-forge/linux-64 Cached
+ readline 8.2 h8228510_1 conda-forge/linux-64 Cached
+ sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
+ setuptools 67.6.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ snappy 1.1.10 h9fff704_0 conda-forge/linux-64 Cached
+ sqlite 3.40.0 h4ff8645_0 conda-forge/linux-64 Cached
+ sysroot_linux-64 2.12 he073ed8_15 conda-forge/noarch Cached
+ tiledb 2.13.2 hd532e3d_0 conda-forge/linux-64 Cached
+ tk 8.6.12 h27826a3_0 conda-forge/linux-64 Cached
+ tktable 2.10 hb7b940f_3 conda-forge/linux-64 Cached
+ tzcode 2023c h0b41bf4_0 conda-forge/linux-64 Cached
+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xerces-c 3.2.4 h55805fa_1 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: 138 packages
Total download: 0 B
───────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
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-ha7d60f8_0
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 3423 bytes
actual size: 6749 bytes
done
Executing transaction: done
To activate this environment, use
$ mamba activate test
To deactivate an active environment, use
$ mamba deactivate
(base) ~ $ conda activate test
(test) ~ $ 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)
terra 1.7.23Good to hear!
Would you be so kind and make some suggestions how to improve that piece of documentation for people who have your amount of experience with Conda?
gonzarizzo
commented
1 year ago Sure! I think that for someone like me, very new on conda/mamba it is very difficult to know what is a default channel. So, it would be nice to see a list of those default channels to avoid, and how they look in the command line (i.e., like the one I was running at the beginning).
I also think that there should be a clear statement suggesting the inclusion of -c nodefaults in the command line to prevent installing from a package from defaults, plus including
channels:
- nodefaultsto the ~/.condarc as you suggested.
I think that would be help full.
jonashaag
commented
1 year ago See PR #2451
Troubleshooting docs
Search tried in issue tracker
libproj.so.15
Latest version of Mamba
Tried in Conda?
Reproducible with Conda
Describe your issue
I am trying to build a the following conda environment in a Debian 11 - (WLS):
mamba create -n test -c conda-forge -c bioconda -c R r-base=4.2.3 r-data.table=1.14.8 r-terra=1.5_21 gdal=3.6.3Which results in the following output:
However when I activate the environment and try to load
terrapackage inRI get the following message:Looking at the files being installed in the
/miniconda3/envs/test/I can see that libproj.so.15 is not being installed when installingprojpackage.I suspect that
terrapackage is looking for libproj.so.15 but it can't find it in the environment's packages. I also think that the conda-forge for proj does not contain that libproj.so.15 file. How could I get that libproj.so.15 to be installed in by mamba?Any guidance would be very much appreciated!
mamba info / micromamba info
No response
Logs
No response
environment.yml
No response
~/.condarc
No response