valerievandervorst
commented
8 months ago Hi, I fixed the configurations of the channels in install.sh, could you try it again with the updated script?
Closed ocstringham closed 8 months ago
valerievandervorst
commented
8 months ago Hi, I fixed the configurations of the channels in install.sh, could you try it again with the updated script?
ocstringham
commented
8 months ago Now it finishes the install. Thanks. I will try to test it with data. A suggestion would be to put test data make sure the install works correctly.
valerievandervorst
commented
8 months ago Thanks for the suggestion, I have added a test dataset to the repository
I'm trying to install on linux using
bash install.shand I get the following error:Do you have a docker image/Dockerfile to run PIMENTA in a container?
Full output here
> (base) [olivers@annotate2 PIMENTA]$ bash install.sh > Retrieving notices: ...working... done > Channels: > - conda-forge > - defaults > Platform: linux-64 > Collecting package metadata (repodata.json): done > Solving environment: done > > ## Package Plan ## > > environment location: /local/home/olivers/miniconda3 > > added / updated specs: > - mamba > > > The following packages will be downloaded: > > package | build > ---------------------------|----------------- > ca-certificates-2024.2.2 | hbcca054_0 152 KB conda-forge > certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge > conda-23.11.0 | py311h38be061_1 1.2 MB conda-forge > fmt-10.2.1 | h00ab1b0_0 189 KB conda-forge > icu-73.2 | h59595ed_0 11.5 MB conda-forge > libarchive-3.7.2 | h2aa1ff5_1 846 KB conda-forge > libcurl-8.5.0 | h251f7ec_0 416 KB > libmamba-1.5.6 | had39da4_0 1.6 MB conda-forge > libmambapy-1.5.6 | py311hf2555c7_0 297 KB conda-forge > libxml2-2.12.5 | h232c23b_0 688 KB conda-forge > lzo-2.10 | h516909a_1000 314 KB conda-forge > mamba-1.5.6 | py311h3072747_0 65 KB conda-forge > openssl-3.2.1 | hd590300_0 2.7 MB conda-forge > python_abi-3.11 | 2_cp311 5 KB conda-forge > ------------------------------------------------------------ > Total: 20.1 MB > > The following NEW packages will be INSTALLED: > > libiconv conda-forge/linux-64::libiconv-1.17-hd590300_2 > libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5 > lzo conda-forge/linux-64::lzo-2.10-h516909a_1000 > mamba conda-forge/linux-64::mamba-1.5.6-py311h3072747_0 > python_abi conda-forge/linux-64::python_abi-3.11-2_cp311 > > The following packages will be UPDATED: > > ca-certificates pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hbcca054_0 > certifi pkgs/main/linux-64::certifi-2023.11.1~ --> conda-forge/noarch::certifi-2024.2.2-pyhd8ed1ab_0 > conda pkgs/main::conda-23.11.0-py311h06a430~ --> conda-forge::conda-23.11.0-py311h38be061_1 > fmt pkgs/main::fmt-9.1.0-hdb19cb5_0 --> conda-forge::fmt-10.2.1-h00ab1b0_0 > icu pkgs/main::icu-73.1-h6a678d5_0 --> conda-forge::icu-73.2-h59595ed_0 > libarchive pkgs/main::libarchive-3.6.2-h6ac8c49_2 --> conda-forge::libarchive-3.7.2-h2aa1ff5_1 > libcurl 8.4.0-h251f7ec_1 --> 8.5.0-h251f7ec_0 > libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 > libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 > libmamba pkgs/main::libmamba-1.5.3-haf1ee3a_0 --> conda-forge::libmamba-1.5.6-had39da4_0 > libmambapy pkgs/main::libmambapy-1.5.3-py311h2da~ --> conda-forge::libmambapy-1.5.6-py311hf2555c7_0 > libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 > libxml2 pkgs/main::libxml2-2.10.4-hf1b16e4_1 --> conda-forge::libxml2-2.12.5-h232c23b_0 > openssl pkgs/main::openssl-3.0.12-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_0 > zlib pkgs/main::zlib-1.2.13-h5eee18b_0 --> conda-forge::zlib-1.2.13-hd590300_5 > > The following packages will be SUPERSEDED by a higher-priority channel: > > _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge > _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu > > > > Downloading and Extracting Packages: > > Preparing transaction: done > Verifying transaction: done > Executing transaction: done > Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba. > Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba. > Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba. > Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba. > Currently, only install, create, list, search, run, info, clean, remove, update, repoquery, activate and deactivate are supported through mamba. > > Looking for: [] > > Preparing transaction: done > Verifying transaction: done > Executing transaction: done > > To activate this environment, use > > $ mamba activate pimenta > > To deactivate an active environment, use > > $ mamba deactivate > > > Looking for: ['cd-hit'] > > warning libmamba Could not parse mod/etag header > bioconda/linux-64 (check zst) Checked 0.1s > warning libmamba Could not parse mod/etag header > bioconda/noarch (check zst) Checked 0.1s > warning libmamba Could not parse mod/etag header > pkgs/main/linux-64 (check zst) Checked 0.0s > warning libmamba Could not parse mod/etag header > pkgs/main/noarch (check zst) Checked 0.0s > warning libmamba Could not parse mod/etag header > pkgs/r/linux-64 (check zst) Checked 0.0s > warning libmamba Could not parse mod/etag header > pkgs/r/noarch (check zst) Checked 0.0s > pkgs/r/linux-64 1.6MB @ 32.4MB/s 0.1s > pkgs/main/linux-64 5.8MB @ 82.6MB/s 0.1s > pkgs/main/noarch 702.8kB @ 9.7MB/s 0.1s > pkgs/r/noarch 2.1MB @ 21.3MB/s 0.0s > bioconda/linux-64 5.3MB @ 4.9MB/s 1.1s > bioconda/noarch 5.1MB @ 4.3MB/s 1.2s > Transaction > > Prefix: /local/home/olivers/miniconda3/envs/pimenta > > Updating specs: > > - cd-hit > > > Package Version Build Channel Size > ────────────────────────────────────────────────────────────── > Install: > ────────────────────────────────────────────────────────────── > > + _libgcc_mutex 0.1 main pkgs/main Cached > + libstdcxx-ng 11.2.0 h1234567_1 pkgs/main Cached > + libgomp 11.2.0 h1234567_1 pkgs/main Cached > + _openmp_mutex 5.1 1_gnu pkgs/main Cached > + libgcc-ng 11.2.0 h1234567_1 pkgs/main Cached > + zlib 1.2.13 h5eee18b_0 pkgs/main Cached > + cd-hit 4.8.1 h2e03b76_5 bioconda 257kB > > Summary: > > Install: 7 packages > > Total download: 257kB > > ────────────────────────────────────────────────────────────── > > > cd-hit 257.1kB @ 1.5MB/s 0.2s > > Downloading and Extracting Packages: > > Preparing transaction: done > Verifying transaction: done > Executing transaction: done > > Looking for: ['r-base'] > > warning libmamba Could not parse mod/etag header > warning libmamba Could not parse mod/etag header > pkgs/main/linux-64 Using cache > pkgs/main/noarch Using cache > pkgs/r/linux-64 Using cache > pkgs/r/noarch Using cache > conda-forge/noarch 13.6MB @ 67.2MB/s 0.2s > conda-forge/linux-64 32.6MB @ 121.6MB/s 0.3s > Transaction > > Prefix: /local/home/olivers/miniconda3/envs/pimenta > > Updating specs: > > - r-base > > > Package Version Build Channel Size > ────────────────────────────────────────────────────────────────────────────────────────── > Install: > ────────────────────────────────────────────────────────────────────────────────────────── > > + ld_impl_linux-64 2.40 h41732ed_0 conda-forge 705kB > + ca-certificates 2024.2.2 hbcca054_0 conda-forge Cached > + graphite2 1.3.13 h58526e2_1001 conda-forge 105kB > + xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge 19kB > + pthread-stubs 0.4 h36c2ea0_1001 conda-forge 6kB > + fribidi 1.0.10 h36c2ea0_0 conda-forge 114kB > + sed 4.8 he412f7d_0 conda-forge 271kB > + xorg-renderproto 0.11.1 h7f98852_1002 conda-forge 10kB > + xorg-xproto 7.0.31 h7f98852_1007 conda-forge 75kB > + xorg-kbproto 1.0.7 h7f98852_1002 conda-forge 27kB > + c-ares 1.26.0 hd590300_0 conda-forge 163kB > + libev 4.33 hd590300_2 conda-forge 113kB > + ncurses 6.4 h59595ed_2 conda-forge 884kB > + pixman 0.43.2 h59595ed_0 conda-forge 387kB > + libexpat 2.5.0 hcb278e6_1 conda-forge 78kB > + libffi 3.4.2 h7f98852_5 conda-forge 58kB > + openssl 3.2.1 hd590300_0 conda-forge Cached > + libwebp-base 1.3.2 hd590300_0 conda-forge 402kB > + xorg-libxau 1.0.11 hd590300_0 conda-forge 14kB > + libdeflate 1.19 hd590300_0 conda-forge 67kB > + lerc 4.0.0 h27087fc_0 conda-forge 282kB > + libjpeg-turbo 3.0.0 hd590300_1 conda-forge 619kB > + gettext 0.21.1 h27087fc_0 conda-forge 4MB > + xz 5.2.6 h166bdaf_0 conda-forge 418kB > + make 4.3 hd18ef5c_1 conda-forge 519kB > + libiconv 1.17 hd590300_2 conda-forge Cached > + libgfortran5 13.2.0 ha4646dd_5 conda-forge 1MB > + libsanitizer 13.2.0 h7e041cc_5 conda-forge 4MB > + keyutils 1.6.1 h166bdaf_0 conda-forge 118kB > + bzip2 1.0.8 hd590300_5 conda-forge 254kB > + xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge 30kB > + libzlib 1.2.13 hd590300_5 conda-forge Cached > + libuuid 2.38.1 h0b41bf4_0 conda-forge 34kB > + xorg-libice 1.1.1 hd590300_0 conda-forge 58kB > + icu 73.2 h59595ed_0 conda-forge Cached > + libedit 3.1.20191231 he28a2e2_2 conda-forge 124kB > + readline 8.2 h8228510_1 conda-forge 281kB > + expat 2.5.0 hcb278e6_1 conda-forge 137kB > + libxcb 1.15 h0b41bf4_0 conda-forge 384kB > + libgfortran-ng 13.2.0 h69a702a_5 conda-forge 24kB > + libnghttp2 1.58.0 h47da74e_1 conda-forge 632kB > + tk 8.6.13 noxft_h4845f30_101 conda-forge 3MB > + pcre2 10.42 hcad00b1_0 conda-forge 1MB > + libpng 1.6.42 h2797004_0 conda-forge 289kB > + zstd 1.5.5 hfc55251_0 conda-forge 545kB > + libssh2 1.11.0 h0841786_0 conda-forge 271kB > + xorg-libsm 1.2.4 h7391055_0 conda-forge 27kB > + krb5 1.21.2 h659d440_0 conda-forge 1MB > + xorg-libx11 1.8.7 h8ee46fc_0 conda-forge 829kB > + libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge 6MB > + tktable 2.10 h0c5db8f_5 conda-forge 90kB > + bwidget 1.9.14 ha770c72_1 conda-forge 122kB > + libglib 2.78.4 h783c2da_0 conda-forge 3MB > + freetype 2.12.1 h267a509_2 conda-forge 635kB > + libtiff 4.6.0 ha9c0a0a_2 conda-forge 283kB > + libcurl 8.5.0 hca28451_0 conda-forge 389kB > + xorg-libxext 1.3.4 h0b41bf4_2 conda-forge 50kB > + xorg-libxt 1.3.0 hd590300_1 conda-forge 379kB > + xorg-libxrender 0.9.11 hd590300_0 conda-forge 38kB > + libblas 3.9.0 21_linux64_openblas conda-forge 15kB > + fontconfig 2.14.2 h14ed4e7_0 conda-forge 272kB > + curl 8.5.0 hca28451_0 conda-forge 95kB > + liblapack 3.9.0 21_linux64_openblas conda-forge 15kB > + _r-mutex 1.0.1 anacondar_1 conda-forge 4kB > + libgcc-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge 3MB > + libstdcxx-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge 13MB > + kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge 711kB > + font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge 397kB > + font-ttf-inconsolata 3.000 h77eed37_0 conda-forge 97kB > + font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge 701kB > + font-ttf-ubuntu 0.83 h77eed37_1 conda-forge 2MB > + sysroot_linux-64 2.12 he073ed8_17 conda-forge 15MB > + fonts-conda-forge 1 0 conda-forge 4kB > + fonts-conda-ecosystem 1 0 conda-forge 4kB > + binutils_impl_linux-64 2.40 hf600244_0 conda-forge 5MB > + cairo 1.18.0 h3faef2a_0 conda-forge 982kB > + gcc_impl_linux-64 13.2.0 h338b0a0_5 conda-forge 53MB > + harfbuzz 8.3.0 h3d44ed6_0 conda-forge 2MB > + gfortran_impl_linux-64 13.2.0 h76e1118_5 conda-forge 16MB > + gxx_impl_linux-64 13.2.0 h338b0a0_5 conda-forge 14MB > + pango 1.50.14 ha41ecd1_2 conda-forge 444kB > + r-base 4.3.2 hb8ee39d_2 conda-forge 26MB > > Change: > ────────────────────────────────────────────────────────────────────────────────────────── > > - _libgcc_mutex 0.1 main pkgs/main Cached > + _libgcc_mutex 0.1 conda_forge conda-forge Cached > - zlib 1.2.13 h5eee18b_0 pkgs/main Cached > + zlib 1.2.13 hd590300_5 conda-forge Cached > > Upgrade: > ────────────────────────────────────────────────────────────────────────────────────────── > > - libstdcxx-ng 11.2.0 h1234567_1 pkgs/main Cached > + libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge Cached > - libgomp 11.2.0 h1234567_1 pkgs/main Cached > + libgomp 13.2.0 h807b86a_5 conda-forge Cached > - libgcc-ng 11.2.0 h1234567_1 pkgs/main Cached > + libgcc-ng 13.2.0 h807b86a_5 conda-forge Cached > > Downgrade: > ────────────────────────────────────────────────────────────────────────────────────────── > > - _openmp_mutex 5.1 1_gnu pkgs/main Cached > + _openmp_mutex 4.5 2_gnu conda-forge Cached > > Summary: > > Install: 82 packages > Change: 2 packages > Upgrade: 3 packages > Downgrade: 1 packages > > Total download: 187MB > > ────────────────────────────────────────────────────────────────────────────────────────── > > > graphite2 104.7kB @ 2.1MB/s 0.1s > fribidi 114.4kB @ 2.0MB/s 0.1s > ld_impl_linux-64 704.7kB @ 11.2MB/s 0.1s > pthread-stubs 5.6kB @ 89.1kB/s 0.1s > xorg-libxdmcp 19.1kB @ 301.4kB/s 0.1s > libexpat 78.0kB @ 845.6kB/s 0.0s > xorg-libxau 14.5kB @ 153.4kB/s 0.0s > libev 112.8kB @ 1.2MB/s 0.0s > libdeflate 67.1kB @ 664.3kB/s 0.0s > keyutils 117.8kB @ 960.8kB/s 0.0s > xorg-libice 58.5kB @ 455.7kB/s 0.0s > gettext 4.3MB @ 32.8MB/s 0.1s > libgfortran-ng 23.8kB @ 177.7kB/s 0.0s > libuuid 33.6kB @ 231.1kB/s 0.1s > bwidget 122.5kB @ 727.7kB/s 0.0s > libssh2 271.1kB @ 1.5MB/s 0.0s > xorg-libx11 828.7kB @ 4.6MB/s 0.0s > libtiff 283.2kB @ 1.5MB/s 0.0s > pcre2 1.0MB @ 5.2MB/s 0.1s > xorg-libxt 379.3kB @ 1.9MB/s 0.0s > fontconfig 272.0kB @ 1.3MB/s 0.0s > _r-mutex 3.6kB @ 16.8kB/s 0.0s > kernel-headers_linux-64 710.6kB @ 3.1MB/s 0.0s > fonts-conda-forge 4.1kB @ 17.5kB/s 0.0s > cairo 982.4kB @ 4.0MB/s 0.0s > font-ttf-source-code-pro 700.8kB @ 2.8MB/s 0.1s > xorg-xproto 74.9kB @ 283.9kB/s 0.0s > ncurses 884.4kB @ 3.0MB/s 0.0s > libwebp-base 401.8kB @ 1.3MB/s 0.0s > xz 418.4kB @ 1.4MB/s 0.0s > gfortran_impl_linux-64 15.8MB @ 49.2MB/s 0.1s > libxcb 384.2kB @ 1.2MB/s 0.0s > libedit 123.9kB @ 369.5kB/s 0.0s > libpng 289.1kB @ 816.1kB/s 0.0s > libsanitizer 4.1MB @ 11.4MB/s 0.1s > krb5 1.4MB @ 3.8MB/s 0.0s > libglib 2.7MB @ 7.4MB/s 0.0s > r-base 25.7MB @ 68.8MB/s 0.1s > xorg-libxext 50.1kB @ 131.7kB/s 0.0s > curl 94.9kB @ 241.0kB/s 0.0s > font-ttf-ubuntu 1.6MB @ 4.1MB/s 0.0s > xorg-renderproto 9.6kB @ 22.7kB/s 0.0s > binutils_impl_linux-64 5.4MB @ 12.7MB/s 0.1s > pixman 386.8kB @ 891.2kB/s 0.0s > libjpeg-turbo 618.6kB @ 1.3MB/s 0.0s > bzip2 254.2kB @ 548.4kB/s 0.0s > expat 136.8kB @ 293.2kB/s 0.0s > gxx_impl_linux-64 13.6MB @ 28.4MB/s 0.1s > zstd 545.2kB @ 1.1MB/s 0.0s > tktable 89.8kB @ 181.2kB/s 0.0s > xorg-libxrender 37.8kB @ 75.5kB/s 0.0s > libstdcxx-devel_linux-64 13.0MB @ 25.6MB/s 0.1s > libgcc-devel_linux-64 2.6MB @ 4.9MB/s 0.0s > fonts-conda-ecosystem 3.7kB @ 6.9kB/s 0.0s > sed 270.8kB @ 504.2kB/s 0.0s > lerc 281.8kB @ 519.8kB/s 0.0s > xorg-xextproto 30.3kB @ 54.5kB/s 0.0s > sysroot_linux-64 15.1MB @ 27.0MB/s 0.1s > freetype 635.0kB @ 1.1MB/s 0.0s > tk 3.3MB @ 5.8MB/s 0.0s > liblapack 14.6kB @ 25.6kB/s 0.0s > make 518.9kB @ 872.8kB/s 0.0s > xorg-kbproto 27.3kB @ 45.6kB/s 0.0s > xorg-libsm 27.4kB @ 45.4kB/s 0.0s > libnghttp2 631.9kB @ 1.0MB/s 0.0s > font-ttf-inconsolata 96.5kB @ 155.7kB/s 0.0s > c-ares 162.7kB @ 256.0kB/s 0.0s > readline 281.5kB @ 442.8kB/s 0.0s > libblas 14.7kB @ 22.8kB/s 0.0s > pango 443.6kB @ 682.1kB/s 0.0s > libcurl 389.2kB @ 581.1kB/s 0.0s > font-ttf-dejavu-sans-mono 397.4kB @ 589.9kB/s 0.0s > libgfortran5 1.4MB @ 2.1MB/s 0.0s > libopenblas 5.6MB @ 8.0MB/s 0.1s > libffi 58.3kB @ 82.6kB/s 0.0s > harfbuzz 1.5MB @ 2.2MB/s 0.0s > gcc_impl_linux-64 53.3MB @ 69.3MB/s 0.2s > > Downloading and Extracting Packages: > > Preparing transaction: done > Verifying transaction: done > Executing transaction: done > > Looking for: ['perl-cgi', 'perl-bioperl', 'perl-cairo', 'perl-statistics-basic', 'perl-json'] > > bioconda/linux-64 Using cache > bioconda/noarch Using cache > pkgs/main/linux-64 Using cache > pkgs/main/noarch Using cache > pkgs/r/linux-64 Using cache > pkgs/r/noarch Using cache > Could not solve for environment specs > The following packages are incompatible > ├─ libblas is installable and it requires > │ └─ libopenblas >=0.3.26,<0.3.27.0a0 , which requires > │ └─ libgfortran5 >=12.3.0 , which requires > │ └─ libgfortran-ng 13.2.0 , which can be installed; > ├─ libexpat is installable and it requires > │ └─ libgcc-ng >=12 , which can be installed; > ├─ libjpeg-turbo is installable and it requires > │ └─ jpeg <0.0.0a , which can be installed; > ├─ perl-bioperl is installable with the potential options > │ ├─ perl-bioperl 1.7.8 would require > │ │ └─ perl-bioperl-core 1.7.8.* with the potential options > │ │ ├─ perl-bioperl-core 1.7.8 would require > │ │ │ └─ perl >=5.32.1,<5.33.0a0 *_perl5, which can be installed; > │ │ └─ perl-bioperl-core 1.7.8 would require > │ │ └─ perl-db_file, which does not exist (perhaps a missing channel); > │ ├─ perl-bioperl 1.6.924 would require > │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ ├─ perl-bioperl 1.6.924 would require > │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ ├─ perl-bioperl 1.7.2 would require > │ │ └─ perl-bioperl-core [1.007002 |1.7.2 ], which requires > │ │ └─ perl-gd but there are no viable options > │ │ ├─ perl-gd [2.56|2.68|2.69|2.70|2.71] would require > │ │ │ └─ libgd [ |>=2.2.4 |>=2.2.5,<2.3.0a0 ] but there are no viable options > │ │ │ ├─ libgd [2.2.5|2.3.2] would require > │ │ │ │ └─ jpeg >=9b,<10a , which conflicts with any installable versions previously reported; > │ │ │ ├─ libgd 2.3.3 would require > │ │ │ │ └─ jpeg >=9d,<10a , which conflicts with any installable versions previously reported; > │ │ │ └─ libgd 2.3.3 would require > │ │ │ └─ jpeg >=9e,<10a , which conflicts with any installable versions previously reported; > │ │ ├─ perl-gd 2.56 would require > │ │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ │ ├─ perl-gd 2.56 would require > │ │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ │ ├─ perl-gd 2.56 would require > │ │ │ └─ perl >=5.22.0,<5.22.1.0a0 , which does not exist (perhaps a missing channel); > │ │ └─ perl-gd [2.74|2.76] would require > │ │ └─ libgd >=2.3.3,<2.4.0a0 , which cannot be installed (as previously explained); > │ └─ perl-bioperl 1.7.8 would require > │ └─ perl-bio-searchio-hmmer, which requires > │ └─ perl-db_file, which does not exist (perhaps a missing channel); > ├─ perl-cairo is installable with the potential options > │ ├─ perl-cairo 1.109 would require > │ │ └─ perl >=5.32.1,<5.33.0a0 *_perl5, which can be installed; > │ ├─ perl-cairo 1.106 would require > │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ ├─ perl-cairo 1.106 would require > │ │ └─ cairo >=1.14.12,<1.15.0a0 , which can be installed; > │ └─ perl-cairo [1.106|1.109] would require > │ └─ cairo >=1.16.0,<1.17.0a0 , which can be installed; > ├─ perl-cgi is not installable because there are no viable options > │ ├─ perl-cgi 4.22 would require > │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ ├─ perl-cgi 4.22 would require > │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ ├─ perl-cgi [4.22|4.40|4.43|4.44] would require > │ │ └─ perl [>=5.26.2,<5.26.3.0a0 |>=5.26.2,<5.27.0a0 ], which conflicts with any installable versions previously reported; > │ └─ perl-cgi [4.44|4.54|4.55|4.56] would require > │ └─ perl-file-temp but there are no viable options > │ ├─ perl-file-temp 0.2304 would require > │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ └─ perl-file-temp 0.2304 would require > │ └─ perl >=5.26.2,<5.27.0a0 , which conflicts with any installable versions previously reported; > ├─ perl-statistics-basic is not installable because there are no viable options > │ ├─ perl-statistics-basic 1.6611 would require > │ │ └─ perl-number-format but there are no viable options > │ │ ├─ perl-number-format 1.75 would require > │ │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ │ ├─ perl-number-format 1.75 would require > │ │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ │ ├─ perl-number-format 1.75 would require > │ │ │ └─ perl [>=5.26.2,<5.26.3.0a0 |>=5.26.2,<5.27.0a0 ], which conflicts with any installable versions previously reported; > │ │ └─ perl-number-format [1.75|1.76] would require > │ │ └─ perl-carp but there are no viable options > │ │ ├─ perl-carp 1.38 would require > │ │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ │ ├─ perl-carp 1.38 would require > │ │ │ └─ perl [>=5.26.2,<5.26.3.0a0 |>=5.26.2,<5.27.0a0 ], which conflicts with any installable versions previously reported; > │ │ └─ perl-carp 1.38 would require > │ │ └─ perl-extutils-makemaker but there are no viable options > │ │ ├─ perl-extutils-makemaker 6.66 would require > │ │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ │ ├─ perl-extutils-makemaker [6.66|7.24] would require > │ │ │ └─ perl 5.22.0* , which does not exist (perhaps a missing channel); > │ │ └─ perl-extutils-makemaker [7.24|7.34|7.36] would require > │ │ └─ perl [>=5.26.2,<5.26.3.0a0 |>=5.26.2,<5.27.0a0 ], which conflicts with any installable versions previously reported; > │ ├─ perl-statistics-basic 1.6611 would require > │ │ └─ perl >=5.22.0,<5.23.0 , which does not exist (perhaps a missing channel); > │ └─ perl-statistics-basic 1.6611 would require > │ └─ perl >=5.26.2,<5.27.0a0 , which conflicts with any installable versions previously reported; > ├─ r-base is installable with the potential options > │ ├─ r-base 4.3.2 would require > │ │ └─ cairo >=1.18.0,<2.0a0 , which conflicts with any installable versions previously reported; > │ ├─ r-base [3.3.1|3.3.2|3.4.1] would require > │ │ └─ icu 54.* , which does not exist (perhaps a missing channel); > │ ├─ r-base 3.4.2 would require > │ │ └─ libgcc-ng 7.2.0.* , which conflicts with any installable versions previously reported; > │ ├─ r-base 3.4.3 would require > │ │ └─ libgfortran-ng >=7,<8.0a0 , which conflicts with any installable versions previously reported; > │ ├─ r-base [3.4.3|3.5.0] would require > │ │ └─ libopenblas >=0.2.20,<0.2.21.0a0 , which conflicts with any installable versions previously reported; > │ ├─ r-base [3.5.0|3.5.1|3.5.3|3.6.0|3.6.1] would require > │ │ └─ libuuid >=1.0.3,<2.0a0 , which can be installed; > │ └─ r-base [4.2.0|4.3.1] would require > │ └─ gfortran_linux-64 11.2.0.* , which requires > │ └─ gfortran_impl_linux-64 11.2.0.* , which requires > │ └─ libgfortran5 >=11.2.0,<12.0a0 , which conflicts with any installable versions previously reported; > └─ xorg-libsm is not installable because it requires > └─ libuuid >=2.38.1,<3.0a0 , which conflicts with any installable versions previously reported. > > Looking for: ['blast', 'prinseq=0.20.4', 'cutadapt'] > > pkgs/main/linux-64 Using cache > pkgs/main/noarch Using cache > pkgs/r/linux-64 Using cache > pkgs/r/noarch Using cache > Could not solve for environment specs > The following packages are incompatible > ├─ blast does not exist (perhaps a typo or a missing channel); > ├─ cutadapt does not exist (perhaps a typo or a missing channel); > └─ prinseq 0.20.4** does not exist (perhaps a typo or a missing channel). > > Looking for: ['mafft=7.471', 'openpyxl', 'pandas'] > > pkgs/main/linux-64 Using cache > pkgs/main/noarch Using cache > pkgs/r/linux-64 Using cache > pkgs/r/noarch Using cache > Could not solve for environment specs > The following package could not be installed > └─ mafft 7.471** does not exist (perhaps a typo or a missing channel). > > Looking for: ['taxopy', 'krona'] > > pkgs/main/linux-64 Using cache > pkgs/main/noarch Using cache > pkgs/r/linux-64 Using cache > pkgs/r/noarch Using cache > Could not solve for environment specs > The following packages are incompatible > ├─ krona does not exist (perhaps a typo or a missing channel); > └─ taxopy does not exist (perhaps a typo or a missing channel). > bash: ktUpdateTaxonomy.sh: command not found > install.sh: line 30: cd: scripts/Porechop/: No such file or directory > make: *** No targets specified and no makefile found. Stop.