{"action":"closed","issue":{"url":"https://api.github.com/repos/conda/conda/issues/7684","repository_url":"https://api.github.com/repos/conda/conda","labels_url":"https://api.github.com/repos/conda/conda/issues/7684/labels{/name}","comments_url":"https://api.github.com/repos/conda/conda/issues/7684/comments","events_url":"https://api.github.com/repos/conda/conda/issues/7684/events","html_url":"https://github.com/conda/conda/issues/7684","id":353520162,"node_id":"MDU6SXNzdWUzNTM1MjAxNjI=","number":7684,"title":"Conda building broken environment","user":{"login":"abalter","id":5349876,"node_id":"MDQ6VXNlcjUzNDk4NzY=","avatar_url":"https://avatars2.githubusercontent.com/u/5349876?v=4","gravatar_id":"","url":"https://api.github.com/users/abalter","html_url":"https://github.com/abalter","followers_url":"https://api.github.com/users/abalter/followers","following_url":"https://api.github.com/users/abalter/following{/other_user}","gists_url":"https://api.github.com/users/abalter/gists{/gist_id}","starred_url":"https://api.github.com/users/abalter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abalter/subscriptions","organizations_url":"https://api.github.com/users/abalter/orgs","repos_url":"https://api.github.com/users/abalter/repos","events_url":"https://api.github.com/users/abalter/events{/privacy}","received_events_url":"https://api.github.com/users/abalter/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-08-23T19:25:42Z","updated_at":"2018-08-23T19:27:50Z","closed_at":"2018-08-23T19:27:50Z","author_association":"NONE","body":"<!--\r\nHi!  Read this; it's important.\r\n\r\nThis is an issue tracker for conda -- the package manager.  File feature requests\r\nfor conda here, as well as bug reports about something conda has messed up.\r\n\r\nIf your issue is a bug report for:\r\n  * a specific conda package from Anaconda ('defaults' channel):\r\n      ==> file at https://github.com/ContinuumIO/anaconda-issues\r\n  * a specific conda package from conda-forge:\r\n      ==> file at the corresponding feedstock under https://github.com/conda-forge\r\n  * repo.anaconda.com access and service:\r\n      ==> file at https://github.com/ContinuumIO/anaconda-issues\r\n  * anaconda.org access and service:\r\n      ==> file at https://anaconda.org/contact/report\r\n  * commands under 'conda build':\r\n      ==> file at https://github.com/conda/conda-build\r\n  * commands under 'conda env':\r\n      ==> please file it here!\r\n  * all other conda commands that start with 'conda':\r\n      ==> please file it here!\r\n\r\nIf you continue on,\r\n\r\n   **please include all requested information below.**\r\n\r\nIf a maintainer determines the information is required to understand \r\nyour issue, and if it is not provided, your issue may be\r\nclosed automatically.\r\n\r\n-->\r\n\r\nNOTE: I've been told that conda-forge and defaults do not play well together, but the bioconda docs say to use the channels shown below.\r\n\r\n## Current Behavior\r\n<!-- What actually happens?\r\n     If you want to include console output, please use \"Steps to Reproduce\" below. -->\r\nI build a fresh conda environment and install packages including R. When I try to run R, I get\r\n\r\n>\r\n\r\nTo build the environment, I am running the following script:\r\n\r\n```\r\n#!/bin/bash\r\n\r\nconda_home=$(which conda | sed 's/\\/bin.*$//')\r\necho \"conda home: $conda_home\"\r\nconda_sh=\"$conda_home/etc/profile.d/conda.sh\"\r\necho \"activating $conda_sh\"\r\nconda_env_dir=\"$conda_home/envs\"\r\n\r\nsource \"$conda_sh\"\r\n\r\nif [[ `conda env list | grep dada2` != '' ]]; then\r\n  echo \"dada2 environment exists -- removing\"\r\n  conda env remove -n dada2 -y\r\nelse\r\n  echo \"no dada2 environment\"\r\nfi\r\n\r\necho \"creating dada2 environment\"\r\nconda create -n dada2 -y\r\n\r\necho \"activating dada2\"\r\nconda activate dada2\r\n\r\necho \"updating environment\"\r\nconda update --all -y\r\n\r\npkg_list=\"r-knitr r-rmarkdown r-ggplot2 r-gridextra r-nlme r-data.table r-dplyr krb5 libcurl libssh2 zlib bioconductor-dada2\"\r\necho \"installing: `echo $pkg_list | sed 's/ /\\n  \\* /g; s/^/\\n  * /'`\"\r\n\r\ncmd=\"conda install $pkg_list -y\"\r\necho \"executing $cmd\"\r\n$cmd\r\n\r\nexit 0\r\n```\r\n\r\n### Steps to Reproduce\r\n<!-- If the current behavior is a bug, please provide specific, minimal steps to independently reproduce.\r\n     Include the exact conda commands that reproduce the issue and their output between the ticks below. -->\r\n```\r\n(base) lab@conda-test:~$ ./build-dada2\r\n(dada2) lab@conda-test:~$ conda activate dada2\r\n(dada2) lab@conda-test:~$ R\r\n/home/lab/conda/envs/dada2/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory\r\n```\r\n\r\n\r\n## Expected Behavior\r\n<!-- What do you think should happen? -->\r\nR should run normally\r\n\r\n## Environment Information\r\n<details open><summary><code>`conda info`</code></summary><p>\r\n<!-- between the ticks below, paste the output of 'conda info' -->\r\n\r\n```\r\n(dada2) lab@conda-test:~$ conda info\r\n\r\n     active environment : dada2\r\n    active env location : /home/lab/conda/envs/dada2\r\n            shell level : 2\r\n       user config file : /home/lab/.condarc\r\n populated config files : /home/lab/.condarc\r\n          conda version : 4.5.11\r\n    conda-build version : not installed\r\n         python version : 3.6.6.final.0\r\n       base environment : /home/lab/conda  (writable)\r\n           channel URLs : https://conda.anaconda.org/bioconda/linux-64\r\n                          https://conda.anaconda.org/bioconda/noarch\r\n                          https://conda.anaconda.org/conda-forge/linux-64\r\n                          https://conda.anaconda.org/conda-forge/noarch\r\n                          https://repo.anaconda.com/pkgs/main/linux-64\r\n                          https://repo.anaconda.com/pkgs/main/noarch\r\n                          https://repo.anaconda.com/pkgs/free/linux-64\r\n                          https://repo.anaconda.com/pkgs/free/noarch\r\n                          https://repo.anaconda.com/pkgs/r/linux-64\r\n                          https://repo.anaconda.com/pkgs/r/noarch\r\n                          https://repo.anaconda.com/pkgs/pro/linux-64\r\n                          https://repo.anaconda.com/pkgs/pro/noarch\r\n          package cache : /home/lab/conda/pkgs\r\n                          /home/lab/.conda/pkgs\r\n       envs directories : /home/lab/conda/envs\r\n                          /home/lab/.conda/envs\r\n               platform : linux-64\r\n             user-agent : conda/4.5.11 requests/2.13.0 CPython/3.6.6 Linux/4.15.0-32-generic ubuntu/18.04 glibc/2.27\r\n                UID:GID : 1003:1004\r\n             netrc file : None\r\n           offline mode : False\r\n\r\n```\r\n</p></details>\r\n\r\n\r\n<details open><summary><code>`conda config --show-sources`</code></summary><p>\r\n<!-- between the ticks below, paste the output of 'conda config --show-sources' -->\r\n\r\n```\r\n(dada2) lab@conda-test:~$ conda config --show-sources\r\n==> /home/lab/.condarc <==\r\nchannels:\r\n  - bioconda\r\n  - conda-forge\r\n  - defaults\r\n\r\n```\r\n</p></details>\r\n\r\n\r\n<details><summary><code>`conda list --show-channel-urls`</code></summary><p>\r\n<!-- between the ticks below, paste the output of 'conda list --show-channel-urls' -->\r\n\r\n```\r\n(dada2) lab@conda-test:~$ conda list --show-channel-urls\r\n# packages in environment at /home/lab/conda/envs/dada2:\r\n#\r\n# Name                    Version                   Build  Channel\r\n_r-mutex                  1.0.0               anacondar_1    defaults\r\nbioconductor-biobase      2.34.0                 r3.3.2_0    bioconda\r\nbioconductor-biocgenerics 0.22.0                 r3.3.2_0    bioconda\r\nbioconductor-biocparallel 1.6.6                  r3.3.2_1    bioconda\r\nbioconductor-biostrings   2.42.1                 r3.3.2_0    bioconda\r\nbioconductor-dada2        1.4.0                  r3.3.2_0    bioconda\r\nbioconductor-genomeinfodb 1.10.3                 r3.3.2_0    bioconda\r\nbioconductor-genomicalignments 1.10.0                 r3.3.2_0    bioconda\r\nbioconductor-genomicranges 1.26.4                 r3.3.2_0    bioconda\r\nbioconductor-iranges      2.8.2                  r3.3.2_0    bioconda\r\nbioconductor-rsamtools    1.26.1                 r3.3.2_0    bioconda\r\nbioconductor-s4vectors    0.12.2                 r3.3.2_0    bioconda\r\nbioconductor-shortread    1.32.0                 r3.3.2_0    bioconda\r\nbioconductor-summarizedexperiment 1.4.0                  r3.3.2_2    bioconda\r\nbioconductor-xvector      0.14.1                 r3.3.2_0    bioconda\r\nbioconductor-zlibbioc     1.20.0                 r3.3.2_1    bioconda\r\nbzip2                     1.0.6                h470a237_2    conda-forge\r\nca-certificates           2018.8.13            ha4d7672_0    conda-forge\r\ncairo                     1.14.8                        0    defaults\r\ncurl                      7.52.1                        0    conda-forge\r\nfontconfig                2.12.1                        3    defaults\r\nfreetype                  2.5.5                         2    defaults\r\nglib                      2.50.2                        1    defaults\r\ngsl                       2.1                           2    conda-forge\r\nharfbuzz                  0.9.39                        2    defaults\r\nicu                       54.1                          0    defaults\r\njpeg                      9c                   h470a237_0    conda-forge\r\nkrb5                      1.16.1               hbb41f41_0    conda-forge\r\nlibcurl                   7.61.0               h1ad7b7a_0    defaults\r\nlibedit                   3.1.20170329                  0    conda-forge\r\nlibffi                    3.2.1                hfc679d8_4    conda-forge\r\nlibgcc                    7.2.0                h69d50b8_2    conda-forge\r\nlibgcc-ng                 7.2.0                hdf63c60_3    conda-forge\r\nlibiconv                  1.14                          4    conda-forge\r\nlibpng                    1.6.35               ha92aebf_0    conda-forge\r\nlibssh2                   1.8.0                h5b517e9_2    conda-forge\r\nlibstdcxx-ng              7.2.0                hdf63c60_3    conda-forge\r\nlibtiff                   4.0.9                he6b73bb_1    conda-forge\r\nlibxcb                    1.13                 h470a237_2    conda-forge\r\nlibxml2                   2.9.4                         0    defaults\r\nncurses                   5.9                          10    conda-forge\r\nopenssl                   1.0.2o               h470a237_1    conda-forge\r\npango                     1.40.3                        1    defaults\r\npcre                      8.39                          0    conda-forge\r\npixman                    0.34.0                        2    conda-forge\r\npthread-stubs             0.4                  h470a237_1    conda-forge\r\nr-assertthat              0.2.0                  r3.3.2_0    conda-forge\r\nr-base                    3.3.2                         1    defaults\r\nr-bh                      1.60.0_2               r3.3.2_0    bioconda\r\nr-bitops                  1.0_6                  r3.3.2_0    conda-forge\r\nr-catools                 1.17.1                 r3.3.2_1    bioconda\r\nr-colorspace              1.3_2                  r3.3.2_0    conda-forge\r\nr-data.table              1.10.4                 r3.3.2_0    bioconda\r\nr-dbi                     0.8                    r3.3.2_0    conda-forge\r\nr-dichromat               2.0_0                  r3.3.2_0    conda-forge\r\nr-digest                  0.6.12                 r3.3.2_0    bioconda\r\nr-dplyr                   0.5.0                  r3.3.2_1    bioconda\r\nr-evaluate                0.10.1                 r3.3.2_0    conda-forge\r\nr-formatr                 1.5                    r3.3.2_0    conda-forge\r\nr-futile.logger           1.4.1                  r3.3.2_0    bioconda\r\nr-futile.options          1.0.0                  r3.3.2_0    bioconda\r\nr-ggplot2                 2.2.1                  r3.3.2_0    bioconda\r\nr-gridextra               2.3                    r3.3.2_0    conda-forge\r\nr-gtable                  0.2.0                  r3.3.2_0    conda-forge\r\nr-highr                   0.6                    r3.3.2_0    conda-forge\r\nr-htmltools               0.3                    r3.3.2_0    bioconda\r\nr-hwriter                 1.3.2                  r3.3.2_0    bioconda\r\nr-knitr                   1.12.3                 r3.3.2_0    bioconda\r\nr-labeling                0.3                    r3.3.2_0    conda-forge\r\nr-lambda.r                1.1.7                  r3.3.2_0    bioconda\r\nr-lattice                 0.20_34                r3.3.2_0    conda-forge\r\nr-latticeextra            0.6_28                 r3.3.2_0    conda-forge\r\nr-lazyeval                0.2.1                  r3.3.2_0    conda-forge\r\nr-magrittr                1.5                    r3.3.2_0    conda-forge\r\nr-markdown                0.8                    r3.3.2_1    conda-forge\r\nr-mass                    7.3_48                 r3.3.2_0    conda-forge\r\nr-matrix                  1.2_14                 r3.3.2_0    conda-forge\r\nr-mime                    0.5                    r3.3.2_0    conda-forge\r\nr-munsell                 0.4.3                  r3.3.2_0    conda-forge\r\nr-nlme                    3.1_131                r3.3.2_0    conda-forge\r\nr-plyr                    1.8.4                  r3.3.2_0    conda-forge\r\nr-r6                      2.2.2                  r3.3.2_0    conda-forge\r\nr-rcolorbrewer            1.1_2                  r3.3.2_0    conda-forge\r\nr-rcpp                    0.12.16                r3.3.2_0    conda-forge\r\nr-rcppparallel            4.3.20                 r3.3.2_1    bioconda\r\nr-rcurl                   1.95_4.8               r3.3.2_0    conda-forge\r\nr-reshape2                1.4.3                  r3.3.2_0    conda-forge\r\nr-rmarkdown               0.9.5                  r3.3.2_0    bioconda\r\nr-scales                  0.4.1                  r3.3.2_1    bioconda\r\nr-snow                    0.4_1                  r3.3.2_0    bioconda\r\nr-stringi                 1.1.7                  r3.3.2_0    conda-forge\r\nr-stringr                 1.2.0                  r3.3.2_0    conda-forge\r\nr-tibble                  1.2                    r3.3.2_1    bioconda\r\nr-yaml                    2.1.13                 r3.3.2_1    bioconda\r\nreadline                  7.0                           0    conda-forge\r\ntk                        8.6.8                         0    conda-forge\r\nxorg-kbproto              1.0.7                h470a237_2    conda-forge\r\nxorg-libx11               1.6.6                h470a237_0    conda-forge\r\nxorg-libxau               1.0.8                h470a237_6    conda-forge\r\nxorg-libxdmcp             1.1.2                h470a237_7    conda-forge\r\nxorg-libxrender           0.9.10               h470a237_2    conda-forge\r\nxorg-renderproto          0.11.1               h470a237_2    conda-forge\r\nxorg-xproto               7.0.31               h470a237_7    conda-forge\r\nxz                        5.2.4                h470a237_1    conda-forge\r\nzlib                      1.2.11               h470a237_3    conda-forge\r\n\r\n```\r\n</p></details>\r\n"}}
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