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conda install -c bioconda r-pheatmap breaks rstudio #54

Open Deena-B opened 5 years ago

Deena-B commented 5 years ago

I'm setting up a conda environment with r, rstudio, pheatmap, and plan to add seurat. However, after I install r-pheatmap, I get an error when I try to run rstudio. My steps are below:

I have anaconda3 installed on a macOS Mojave

Please help, thank you

The following NEW packages will be INSTALLED:

  jbig               pkgs/main/osx-64::jbig-2.1-h4d881f8_0
  r-car              pkgs/r/osx-64::r-car-2.1_4-r3.3.2_0
  r-caret            pkgs/r/osx-64::r-caret-6.0_73-r3.3.2_0
  r-colorspace       pkgs/r/osx-64::r-colorspace-1.3_1-r3.3.2_0
  r-data.table       bioconda/osx-64::r-data.table-1.10.4-r3.3.2_0
  r-dichromat        pkgs/r/osx-64::r-dichromat-2.0_0-r3.3.2_2
  r-essentials       pkgs/r/osx-64::r-essentials-1.0-0a
  r-foreach          pkgs/r/osx-64::r-foreach-1.4.3-r3.3.2_0
  r-formatr          pkgs/r/osx-64::r-formatr-1.4-r3.3.2_0
  r-ggplot2          bioconda/osx-64::r-ggplot2-2.2.1-r3.3.2_0
  r-glmnet           pkgs/r/osx-64::r-glmnet-2.0_5-r3.3.2_0
  r-gtable           pkgs/r/osx-64::r-gtable-0.2.0-r3.3.2_0
  r-iterators        pkgs/r/osx-64::r-iterators-1.0.8-r3.3.2_0
  r-labeling         pkgs/r/osx-64::r-labeling-0.3-r3.3.2_2
  r-lme4             pkgs/r/osx-64::r-lme4-1.1_12-r3.3.2_0
  r-matrixmodels     pkgs/r/osx-64::r-matrixmodels-0.4_1-r3.3.2_0
  r-minqa            pkgs/r/osx-64::r-minqa-1.2.4-r3.3.2_2
  r-mnormt           pkgs/r/osx-64::r-mnormt-1.5_5-r3.3.2_0
  r-modelmetrics     pkgs/r/osx-64::r-modelmetrics-1.1.0-r3.3.2_0
  r-munsell          pkgs/r/osx-64::r-munsell-0.4.3-r3.3.2_0
  r-nloptr           pkgs/r/osx-64::r-nloptr-1.0.4-r3.3.2_2
  r-pbkrtest         pkgs/r/osx-64::r-pbkrtest-0.4_6-r3.3.2_0
  r-pheatmap         bioconda/osx-64::r-pheatmap-1.0.8-r3.3.2_0
  r-psych            bioconda/osx-64::r-psych-1.5.8-r3.3.2_0
  r-quantmod         pkgs/r/osx-64::r-quantmod-0.4_7-r3.3.2_0
  r-quantreg         pkgs/r/osx-64::r-quantreg-5.29-r3.3.2_0
  r-randomforest     pkgs/r/osx-64::r-randomforest-4.6_12-r3.3.2_0
  r-rcolorbrewer     pkgs/r/osx-64::r-rcolorbrewer-1.1_2-r3.3.2_3
  r-rcppeigen        pkgs/r/osx-64::r-rcppeigen-0.3.2.9.0-r3.3.2_0
  r-scales           bioconda/osx-64::r-scales-0.4.1-r3.3.2_1
  r-sparsem          pkgs/r/osx-64::r-sparsem-1.74-r3.3.2_0
  r-ttr              pkgs/r/osx-64::r-ttr-0.23_1-r3.3.2_0
  r-xts              pkgs/r/osx-64::r-xts-0.9_7-r3.3.2_2
  r-zoo              pkgs/r/osx-64::r-zoo-1.7_13-r3.3.2_0

The following packages will be REMOVED:

  r-bindr-0.1.1-r351hf348343_0
  r-bindrcpp-0.2.2-r351h32998d9_0
  r-blob-1.1.1-r351hf348343_0
  r-cellranger-1.1.0-r351hf348343_0
  r-cli-1.0.0-r351h6115d3f_0
  r-dbplyr-1.2.2-r351hf348343_0
  r-fansi-0.2.3-r351h6402f54_0
  r-glue-1.3.0-r351h6402f54_0
  r-later-0.7.3-r351h32998d9_0
  r-mongolite-1.6-r351h46e59ec_1
  r-odbc-1.1.5-r351h0a44026_0
  r-pillar-1.3.0-r351hf348343_0
  r-pkgconfig-2.0.1-r351hf348343_0
  r-profvis-0.3.5-r351h6402f54_0
  r-promises-1.0.1-r351h32998d9_0
  r-rematch-1.0.1-r351hf348343_0
  r-rjdbc-0.2_7.1-r351hf348343_0
  r-rlang-0.2.1-r351h6402f54_0
  r-tidyselect-0.2.4-r351h32998d9_0
  r-tinytex-0.6-r351hf348343_0
  r-utf8-1.1.4-r351h6402f54_0
  r-xfun-0.3-r351hf348343_0

The following packages will be SUPERSEDED by a higher-priority channel:

  cairo                 pkgs/main::cairo-1.14.12-hc4e6be7_4 --> pkgs/free::cairo-1.14.8-0
  fontconfig         pkgs/main::fontconfig-2.13.0-h5d5b041~ --> pkgs/free::fontconfig-2.12.1-3
  freetype             pkgs/main::freetype-2.9.1-hb4e5f40_0 --> pkgs/free::freetype-2.5.5-2
  glib                    pkgs/main::glib-2.56.2-hd9629dc_0 --> pkgs/free::glib-2.50.2-1
  harfbuzz             pkgs/main::harfbuzz-1.8.8-hb8d4a28_0 --> pkgs/free::harfbuzz-0.9.39-2
  icu                        pkgs/main::icu-58.2-h4b95b61_1 --> pkgs/free::icu-54.1-0
  jpeg                        pkgs/main::jpeg-9b-he5867d9_2 --> pkgs/free::jpeg-8d-2
  libiconv              pkgs/main::libiconv-1.15-hdd342a3_7 --> pkgs/free::libiconv-1.14-0
  libtiff              pkgs/main::libtiff-4.0.10-hcb84e12_2 --> pkgs/free::libtiff-4.0.6-2
  libxml2               pkgs/main::libxml2-2.9.9-hab757c2_0 --> pkgs/free::libxml2-2.9.4-0
  pango                  pkgs/main::pango-1.42.4-h060686c_0 --> pkgs/free::pango-1.40.3-1
  pcre                      pkgs/main::pcre-8.43-h0a44026_0 --> pkgs/free::pcre-8.39-1
  r-bh                 pkgs/r::r-bh-1.66.0_1-r351hf348343_0 --> bioconda::r-bh-1.60.0_2-r3.3.2_0
  r-catools          pkgs/r::r-catools-1.17.1.1-r351h32998~ --> bioconda::r-catools-1.17.1-r3.3.2_1
  r-dplyr              pkgs/r::r-dplyr-0.7.6-r351h32998d9_0 --> bioconda::r-dplyr-0.5.0-r3.3.2_1
  r-knitr               pkgs/r::r-knitr-1.20-r351hf348343_0 --> bioconda::r-knitr-1.12.3-r3.3.2_0
  r-prettyunits      pkgs/r::r-prettyunits-1.0.2-r351hf348~ --> bioconda::r-prettyunits-1.0.2-r3.3.2_0
  r-rappdirs         pkgs/r::r-rappdirs-0.3.1-r351h6402f54~ --> bioconda::r-rappdirs-0.3-r3.3.2_0
  r-readr              pkgs/r::r-readr-1.1.1-r351h32998d9_0 --> bioconda::r-readr-0.2.2-r3.3.2_0
  r-rmarkdown        pkgs/r::r-rmarkdown-1.10-r351hf348343~ --> bioconda::r-rmarkdown-0.9.5-r3.3.2_0
  r-tibble            pkgs/r::r-tibble-1.4.2-r351h6402f54_0 --> bioconda::r-tibble-1.2-r3.3.2_1

The following packages will be DOWNGRADED:

  gettext                               0.19.8.1-h15daf44_3 --> 0.19.8.1-hb0f4f8b_2
  pixman                                  0.38.0-h1de35cc_0 --> 0.34.0-hca0a616_3
  r                                            3.5.1-r351_0 --> 3.3.2-r3.3.2_0
  r-assertthat                         0.2.0-r351hf348343_0 --> 0.1-r3.3.2_4
  r-backports                          1.1.2-r351h6402f54_0 --> 1.0.4-r3.3.2_0
  r-base                                   3.5.1-h539fb6c_1 --> 3.3.2-0
  r-base64enc                          0.1_3-r351h6402f54_4 --> 0.1_3-r3.3.2_0
  r-bit                               1.1_14-r351h6402f54_0 --> 1.1_12-r3.3.2_0
  r-bit64                              0.9_7-r351h6402f54_0 --> 0.9_5-r3.3.2_0
  r-bitops                             1.0_6-r351h6402f54_4 --> 1.0_6-r3.3.2_2
  r-boot                              1.3_20-r351hf348343_0 --> 1.3_18-r3.3.2_0
  r-broom                              0.5.0-r351hf348343_0 --> 0.4.1-r3.3.2_0
  r-class                             7.3_14-r351h6402f54_4 --> 7.3_14-r3.3.2_0
  r-cluster                          2.0.7_1-r351h0b560c1_0 --> 2.0.5-r3.3.2_0
  r-codetools                         0.2_15-r351hf348343_0 --> 0.2_15-r3.3.2_0
  r-config                               0.3-r351hf348343_0 --> 0.2-r3.3.2_0
  r-crayon                             1.3.4-r351hf348343_0 --> 1.3.2-r3.3.2_0
  r-curl                                 3.2-r351h6402f54_0 --> 2.3-r3.3.2_0
  r-dbi                                1.0.0-r351hf348343_0 --> 0.5_1-r3.3.2_0
  r-digest                            0.6.15-r351h6402f54_0 --> 0.6.10-r3.3.2_0
  r-evaluate                            0.11-r351hf348343_0 --> 0.10-r3.3.2_0
  r-forcats                            0.3.0-r351hf348343_0 --> 0.1.1-r3.3.2_0
  r-foreign                           0.8_71-r351h6402f54_0 --> 0.8_67-r3.3.2_0
  r-haven                              1.1.2-r351h32998d9_0 --> 1.0.0-r3.3.2_0
  r-highr                                0.7-r351hf348343_0 --> 0.6-r3.3.2_0
  r-hms                                0.4.2-r351hf348343_0 --> 0.3-r3.3.2_0
  r-htmltools                          0.3.6-r351h32998d9_0 --> 0.3.5-r3.3.2_0
  r-htmlwidgets                          1.2-r351hf348343_0 --> 0.8-r3.3.2_0
  r-httpuv                             1.4.5-r351h32998d9_0 --> 1.3.3-r3.3.2_0
  r-httr                               1.3.1-r351hf348343_0 --> 1.2.1-r3.3.2_0
  r-jsonlite                             1.5-r351h6402f54_0 --> 1.1-r3.3.2_0
  r-kernsmooth                       2.23_15-r351h0b560c1_4 --> 2.23_15-r3.3.2_0
  r-lattice                          0.20_35-r351h6402f54_0 --> 0.20_34-r3.3.2_0
  r-lazyeval                           0.2.1-r351h6402f54_0 --> 0.2.0-r3.3.2_0
  r-magrittr                             1.5-r351hf348343_4 --> 1.5-r3.3.2_2
  r-markdown                             0.8-r351h6402f54_0 --> 0.7.7-r3.3.2_2
  r-mass                              7.3_50-r351h6402f54_0 --> 7.3_45-r3.3.2_0
  r-matrix                            1.2_14-r351h6402f54_0 --> 1.2_7.1-r3.3.2_0
  r-mgcv                              1.8_24-r351h6402f54_0 --> 1.8_16-r3.3.2_0
  r-mime                                 0.5-r351h6402f54_0 --> 0.5-r3.3.2_0
  r-miniui                           0.1.1.1-r351hf348343_0 --> 0.1.1-r3.3.2_0
  r-nlme                             3.1_137-r351h0b560c1_0 --> 3.1_128-r3.3.2_0
  r-nnet                              7.3_12-r351h6402f54_0 --> 7.3_12-r3.3.2_0
  r-openssl                            1.0.2-r351h46e59ec_1 --> 0.9.5-r3.3.2_0
  r-packrat                          0.4.9_3-r351hf348343_0 --> 0.4.8_1-r3.3.2_0
  r-pki                              0.1_5.1-r351h46e59ec_1 --> 0.1_3-r3.3.2_0
  r-plogr                              0.2.0-r351hf348343_0 --> 0.1_1-r3.3.2_0
  r-plyr                               1.8.4-r351h32998d9_0 --> 1.8.4-r3.3.2_0
  r-purrr                              0.2.5-r351h6402f54_0 --> 0.2.2-r3.3.2_0
  r-r6                                 2.2.2-r351hf348343_0 --> 2.2.0-r3.3.2_0
  r-rcpp                             0.12.18-r351h32998d9_0 --> 0.12.8-r3.3.2_0
  r-rcurl                          1.95_4.11-r351h6402f54_0 --> 1.95_4.8-r3.3.2_0
  r-readxl                             1.1.0-r351h32998d9_0 --> 0.1.1-r3.3.2_0
  r-recommended                                3.5.1-r351_0 --> 3.3.2-r3.3.2_0
  r-reshape2                           1.4.3-r351h32998d9_0 --> 1.4.2-r3.3.2_0
  r-rjava                             0.9_10-r351h6402f54_0 --> 0.9_8-r3.3.2_0
  r-rjsonio                            1.3_0-r351h32998d9_4 --> 1.3_0-r3.3.2_2
  r-rpart                             4.1_13-r351h6402f54_0 --> 4.1_10-r3.3.2_0
  r-rprojroot                          1.3_2-r351hf348343_0 --> 1.1-r3.3.2_0
  r-rsconnect                          0.8.8-r351hf348343_0 --> 0.7-r3.3.2_0
  r-rstudioapi                           0.7-r351hf348343_0 --> 0.6-r3.3.2_0
  r-shiny                              1.1.0-r351hf348343_0 --> 0.14.2-r3.3.2_0
  r-sourcetools                        0.1.7-r351h32998d9_0 --> 0.1.5-r3.3.2_0
  r-sparklyr                           0.8.4-r351hf348343_0 --> 0.5.1-r3.3.2_0
  r-spatial                           7.3_11-r351h6402f54_4 --> 7.3_11-r3.3.2_0
  r-stringi                            1.2.4-r351h32998d9_0 --> 1.1.2-r3.3.2_0
  r-stringr                            1.3.1-r351hf348343_0 --> 1.1.0-r3.3.2_0
  r-survival                          2.42_6-r351h6402f54_0 --> 2.40_1-r3.3.2_0
  r-tidyr                              0.8.1-r351h32998d9_0 --> 0.6.0-r3.3.2_0
  r-withr                              2.1.2-r351hf348343_0 --> 1.0.2-r3.3.2_0
  r-xml2                               1.2.0-r351h32998d9_0 --> 1.0.0-r3.3.2_0
  r-xtable                             1.8_2-r351hf348343_0 --> 1.8_2-r3.3.2_0
  r-yaml                               2.2.0-r351h6402f54_0 --> 2.1.14-r3.3.2_0
  rstudio                                1.1.456-h04f5b5a_1 --> 1.0.44-0
  unixodbc                                 2.3.7-h1de35cc_0 --> 2.3.6-h3efe00b_0
Deena-B commented 5 years ago

Solution: conda install -c conda-forge -c bioconda r-pheatmap

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    r-pheatmap-1.0.12          |   r351h6115d3f_0          87 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          87 KB

The following NEW packages will be INSTALLED:

  r-colorspace       conda-forge/osx-64::r-colorspace-1.4_1-r351h159158b_0
  r-gtable           conda-forge/noarch::r-gtable-0.3.0-r351h6115d3f_0
  r-labeling         conda-forge/noarch::r-labeling-0.3-r351h6115d3f_1001
  r-munsell          conda-forge/noarch::r-munsell-0.5.0-r351h6115d3f_1001
  r-pheatmap         conda-forge/noarch::r-pheatmap-1.0.12-r351h6115d3f_0
  r-rcolorbrewer     conda-forge/noarch::r-rcolorbrewer-1.1_2-r351h6115d3f_1001
  r-scales           conda-forge/osx-64::r-scales-1.0.0-r351h466af19_1001
  r-viridislite      conda-forge/noarch::r-viridislite-0.3.0-r351h6115d3f_1001

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2019.1.23-0 --> conda-forge::ca-certificates-2019.3.9-hecc5488_0
  openssl              pkgs/main::openssl-1.1.1b-h1de35cc_1 --> conda-forge::openssl-1.1.1b-h01d97ff_2

Note that conda search r-pheatmap only returned the table below (it didn't list conda-forge as possible source of the pheatmap package) 

Name                        Version           Build       Channel
r-pheatmap                     1.0.8        r3.2.2_0  bioconda
r-pheatmap                     1.0.8        r3.3.1_0  bioconda
r-pheatmap                     1.0.8        r3.3.2_0  bioconda
Deena-B commented 5 years ago

I'm not sure who's side this problem is on so, I posted the same issue and fix here: https://github.com/conda/conda/issues/8618

mbargull commented 5 years ago

(Copying over the answer from https://github.com/conda/conda/issues/8618#issuecomment-487874829 for ease of use/discoverability)

This command installed a version of r-pheatmap that keep rstudio in working condition: conda install -c conda-forge -c bioconda r-pheatmap

That command has the right and recommend channel priorities for Bioconda, see http://bioconda.github.io/#set-up-channels. Packages from the bioconda channel (often) depend on packages from conda-forge. You should even give conda-forge higher priority than bioconda, see https://github.com/bioconda/bioconda-recipes/pull/10924#issuecomment-421463832 for a rationale for this.