From e47f971efd7c54cc67796b201088a882670d4f31 Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Fri, 5 Jun 2020 13:56:54 -0700 Subject: [PATCH 01/14] Updated to r4.0 and packages that work with it. --- r-notebook/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index 641b0ed584..53432e2f2b 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -24,9 +24,9 @@ RUN ln -s /bin/tar /bin/gtar USER $NB_UID # R packages -RUN conda install --quiet --yes \ - 'r-base=3.6.3' \ - 'r-caret=6.0*' \ +RUN conda install --quiet --yes -c conda-forge \ + 'r-base=4.0*' \ + 'r-caret=6.*' \ 'r-crayon=1.3*' \ 'r-devtools=2.3*' \ 'r-forecast=8.12*' \ @@ -39,7 +39,7 @@ RUN conda install --quiet --yes \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ 'r-reshape2=1.4*' \ - 'r-rmarkdown=2.1*' \ + 'r-rmarkdown=2.2 *' \ 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ From 13059e5f0639bd4e22620ee7345fc7ad0e7fc433 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Fri, 5 Jun 2020 14:04:36 -0700 Subject: [PATCH 02/14] removed plyr and reshape2 closes #1103 --- docs/using/selecting.md | 4 ++-- r-notebook/Dockerfile | 2 -- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/using/selecting.md b/docs/using/selecting.md index 6c536b7c78..4b6239a76a 100644 --- a/docs/using/selecting.md +++ b/docs/using/selecting.md @@ -60,9 +60,9 @@ repository. The following sections describe these images including their content [tidyr](http://tidyr.tidyverse.org/), [readr](http://readr.tidyverse.org/), [purrr](http://purrr.tidyverse.org/), [tibble](http://tibble.tidyverse.org/), [stringr](http://stringr.tidyverse.org/), [lubridate](http://lubridate.tidyverse.org/), and [broom](https://cran.r-project.org/web/packages/broom/vignettes/broom.html) from [conda-forge](https://conda-forge.github.io/feedstocks) -* [plyr](https://cran.r-project.org/web/packages/plyr/index.html), [devtools](https://cran.r-project.org/web/packages/devtools/index.html), +* [devtools](https://cran.r-project.org/web/packages/devtools/index.html), [shiny](https://shiny.rstudio.com/), [rmarkdown](http://rmarkdown.rstudio.com/), [forecast](https://cran.r-project.org/web/packages/forecast/forecast.pdf), -[rsqlite](https://cran.r-project.org/web/packages/RSQLite/index.html), [reshape2](https://cran.r-project.org/web/packages/reshape2/reshape2.pdf), +[rsqlite](https://cran.r-project.org/web/packages/RSQLite/index.html), [nycflights13](https://cran.r-project.org/web/packages/nycflights13/index.html), [caret](http://topepo.github.io/caret/index.html), [rcurl](https://cran.r-project.org/web/packages/RCurl/index.html), and [randomforest](https://cran.r-project.org/web/packages/randomForest/randomForest.pdf) packages from [conda-forge](https://conda-forge.github.io/feedstocks) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index 53432e2f2b..b92e21301e 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -35,10 +35,8 @@ RUN conda install --quiet --yes -c conda-forge \ 'r-htmlwidgets=1.5*' \ 'r-irkernel=1.1*' \ 'r-nycflights13=1.0*' \ - 'r-plyr=1.8*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-reshape2=1.4*' \ 'r-rmarkdown=2.2 *' \ 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ From a883ce1794d2421bc6f986b9b6f59dc309dee9d4 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Fri, 5 Jun 2020 14:41:12 -0700 Subject: [PATCH 03/14] versions and tidymodels - added versions to ggplot2 and sparklyr for all-spark-notebook - added tidymodels to r-notebook and docs closes #1102 --- all-spark-notebook/Dockerfile | 2 +- docs/using/selecting.md | 2 +- r-notebook/Dockerfile | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 29c0f0ba65..fe4bc137c0 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -23,7 +23,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=3.6.3' \ + 'r-base=4.0*' \ 'r-ggplot2=3.3*' \ 'r-irkernel=1.1*' \ 'r-rcurl=1.98*' \ diff --git a/docs/using/selecting.md b/docs/using/selecting.md index 4b6239a76a..d61e3c2221 100644 --- a/docs/using/selecting.md +++ b/docs/using/selecting.md @@ -63,7 +63,7 @@ repository. The following sections describe these images including their content * [devtools](https://cran.r-project.org/web/packages/devtools/index.html), [shiny](https://shiny.rstudio.com/), [rmarkdown](http://rmarkdown.rstudio.com/), [forecast](https://cran.r-project.org/web/packages/forecast/forecast.pdf), [rsqlite](https://cran.r-project.org/web/packages/RSQLite/index.html), -[nycflights13](https://cran.r-project.org/web/packages/nycflights13/index.html), [caret](http://topepo.github.io/caret/index.html), +[nycflights13](https://cran.r-project.org/web/packages/nycflights13/index.html), [caret](http://topepo.github.io/caret/index.html), [tidymodels](https://www.tidymodels.org/), [rcurl](https://cran.r-project.org/web/packages/RCurl/index.html), and [randomforest](https://cran.r-project.org/web/packages/randomForest/randomForest.pdf) packages from [conda-forge](https://conda-forge.github.io/feedstocks) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index b92e21301e..9b6be9bba7 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -43,6 +43,7 @@ RUN conda install --quiet --yes -c conda-forge \ 'r-shiny=1.4*' \ 'r-tidyverse=1.3*' \ 'unixodbc=2.3.*' \ + 'r-tidymodels=0.1*' \ && \ conda clean --all -f -y && \ fix-permissions $CONDA_DIR From acc96442765ec58724f32a73906de57fb01037b3 Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Sat, 6 Jun 2020 21:31:07 -0700 Subject: [PATCH 04/14] Update all-spark-notebook/Dockerfile Co-authored-by: Romain --- all-spark-notebook/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index fe4bc137c0..3ad5154f62 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -23,7 +23,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.0*' \ + 'r-base=4.0.0' \ 'r-ggplot2=3.3*' \ 'r-irkernel=1.1*' \ 'r-rcurl=1.98*' \ From bc26d1a77675c35fdb45b798a6a089fc1876ac6d Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Sat, 6 Jun 2020 21:31:43 -0700 Subject: [PATCH 05/14] Update r-notebook/Dockerfile Co-authored-by: Romain --- r-notebook/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index 9b6be9bba7..58bd48a0dd 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -37,7 +37,7 @@ RUN conda install --quiet --yes -c conda-forge \ 'r-nycflights13=1.0*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-rmarkdown=2.2 *' \ + 'r-rmarkdown=2.2*' \ 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ From 017040d78548e7e6e962e6e8deda9e706dae79af Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Sat, 6 Jun 2020 21:31:59 -0700 Subject: [PATCH 06/14] Update r-notebook/Dockerfile Co-authored-by: Romain --- r-notebook/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index 58bd48a0dd..f2ddb1abef 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -24,7 +24,7 @@ RUN ln -s /bin/tar /bin/gtar USER $NB_UID # R packages -RUN conda install --quiet --yes -c conda-forge \ +RUN conda install --quiet --yes \ 'r-base=4.0*' \ 'r-caret=6.*' \ 'r-crayon=1.3*' \ From 6c8db49d8a142158b4c8e5634d56581065526433 Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Sat, 6 Jun 2020 21:32:08 -0700 Subject: [PATCH 07/14] Update r-notebook/Dockerfile Co-authored-by: Romain --- r-notebook/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index f2ddb1abef..f07ac8beaf 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -25,7 +25,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.0*' \ + 'r-base=4.0.0' \ 'r-caret=6.*' \ 'r-crayon=1.3*' \ 'r-devtools=2.3*' \ From f639340c465096b629dd01ea87f7468c6c054acf Mon Sep 17 00:00:00 2001 From: ttimbers Date: Mon, 15 Jun 2020 22:30:54 -0700 Subject: [PATCH 08/14] reverting back to r3.6.3 for all-spark-notebook --- all-spark-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 3ad5154f62..d56ede694e 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -23,7 +23,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.0.0' \ + 'r-base=3.6.3' \ 'r-ggplot2=3.3*' \ 'r-irkernel=1.1*' \ 'r-rcurl=1.98*' \ @@ -48,4 +48,4 @@ RUN conda install --quiet --yes 'spylon-kernel=0.4*' && \ python -m spylon_kernel install --sys-prefix && \ rm -rf /home/$NB_USER/.local && \ fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER + fix-permissions /home/$NB_USER \ No newline at end of file From 07fd9af54e3655041916ea2fc405b6d491dedad0 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Mon, 15 Jun 2020 22:34:37 -0700 Subject: [PATCH 09/14] updated R here as well --- datascience-notebook/Dockerfile | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index c798924502..7c14bd4100 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -45,8 +45,8 @@ USER $NB_UID # R packages including IRKernel which gets installed globally. RUN conda install --quiet --yes \ - 'r-base=3.6.3' \ - 'r-caret=6.0*' \ + 'r-base=4.0.0' \ + 'r-caret=6.*' \ 'r-crayon=1.3*' \ 'r-devtools=2.3*' \ 'r-forecast=8.12*' \ @@ -55,20 +55,23 @@ RUN conda install --quiet --yes \ 'r-htmlwidgets=1.5*' \ 'r-irkernel=1.1*' \ 'r-nycflights13=1.0*' \ - 'r-plyr=1.8*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-reshape2=1.4*' \ - 'r-rmarkdown=2.1*' \ + 'r-rmarkdown=2.2*' \ + 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ 'r-tidyverse=1.3*' \ - 'rpy2=3.1*' \ + 'unixodbc=2.3.*' \ + 'r-tidymodels=0.1*' \ && \ conda clean --all -f -y && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER +# Install e1071 R package (dependency of the caret R package) +RUN conda install --quiet --yes r-e1071 + # Add Julia packages. Only add HDF5 if this is not a test-only build since # it takes roughly half the entire build time of all of the images on Travis # to add this one package and often causes Travis to timeout. From 8a57a05ae74e43a56eda60e02319e852e86d0f49 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Tue, 16 Jun 2020 08:37:40 -0700 Subject: [PATCH 10/14] removed rpy2 as it seems incompatible with r4.0 --- datascience-notebook/Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index f9b0681bab..1da14d6e07 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -63,11 +63,9 @@ RUN conda install --quiet --yes \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ 'r-rmarkdown=2.2*' \ - 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ 'r-tidyverse=1.3*' \ - 'unixodbc=2.3.*' \ 'r-tidymodels=0.1*' \ && \ conda clean --all -f -y && \ From e54c5cb091238673c6f749fe947159b0bc90b2f5 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Tue, 16 Jun 2020 09:08:15 -0700 Subject: [PATCH 11/14] added reticulate --- datascience-notebook/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index 1da14d6e07..d7b8dc138c 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -62,6 +62,7 @@ RUN conda install --quiet --yes \ 'r-nycflights13=1.0*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ + 'r-reticulate=1.16*' \ 'r-rmarkdown=2.2*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ From cdfe98ad8cc3fee66bcd8ce7f310fffe14911896 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Sun, 21 Jun 2020 21:48:22 -0700 Subject: [PATCH 12/14] reverting datascience-notebook back to R 3.6.3 --- datascience-notebook/Dockerfile | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index d7b8dc138c..73d4d3f79b 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -50,8 +50,8 @@ USER $NB_UID # R packages including IRKernel which gets installed globally. RUN conda install --quiet --yes \ - 'r-base=4.0.0' \ - 'r-caret=6.*' \ + 'r-base=3.6.3' \ + 'r-caret=6.0*' \ 'r-crayon=1.3*' \ 'r-devtools=2.3*' \ 'r-forecast=8.12*' \ @@ -60,22 +60,20 @@ RUN conda install --quiet --yes \ 'r-htmlwidgets=1.5*' \ 'r-irkernel=1.1*' \ 'r-nycflights13=1.0*' \ + 'r-plyr=1.8*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-reticulate=1.16*' \ - 'r-rmarkdown=2.2*' \ + 'r-reshape2=1.4*' \ + 'r-rmarkdown=2.1*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.4*' \ 'r-tidyverse=1.3*' \ - 'r-tidymodels=0.1*' \ + 'rpy2=3.1*' \ && \ conda clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" -# Install e1071 R package (dependency of the caret R package) -RUN conda install --quiet --yes r-e1071 - # Add Julia packages. Only add HDF5 if this is not a test-only build since # it takes roughly half the entire build time of all of the images on Travis # to add this one package and often causes Travis to timeout. @@ -92,4 +90,4 @@ RUN julia -e 'import Pkg; Pkg.update()' && \ rm -rf "${HOME}/.local" && \ fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter" -WORKDIR $HOME +WORKDIR $HOME \ No newline at end of file From 6024c327f92b78a119ca290d5fbb94e1ec6218b4 Mon Sep 17 00:00:00 2001 From: ttimbers Date: Sun, 21 Jun 2020 21:53:23 -0700 Subject: [PATCH 13/14] reverting ending on a newline --- all-spark-notebook/Dockerfile | 3 ++- datascience-notebook/Dockerfile | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 9b8e26c384..04df12c162 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -49,4 +49,5 @@ RUN conda install --quiet --yes 'spylon-kernel=0.4*' && \ python -m spylon_kernel install --sys-prefix && \ rm -rf "/home/${NB_USER}/.local" && \ fix-permissions "${CONDA_DIR}" && \ - fix-permissions "/home/${NB_USER}" \ No newline at end of file + fix-permissions "/home/${NB_USER}" + \ No newline at end of file diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index 73d4d3f79b..82803f57cb 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -90,4 +90,4 @@ RUN julia -e 'import Pkg; Pkg.update()' && \ rm -rf "${HOME}/.local" && \ fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter" -WORKDIR $HOME \ No newline at end of file +WORKDIR $HOME From 6939527d3a7c7fd187591287e0f3418d5214098d Mon Sep 17 00:00:00 2001 From: "Tiffany A. Timbers" Date: Sun, 21 Jun 2020 21:55:28 -0700 Subject: [PATCH 14/14] Update all-spark-notebook/Dockerfile --- all-spark-notebook/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 04df12c162..401a2d0a58 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -50,4 +50,3 @@ RUN conda install --quiet --yes 'spylon-kernel=0.4*' && \ rm -rf "/home/${NB_USER}/.local" && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" - \ No newline at end of file