From 04060a324746d08e424fadd0b395217be1520771 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 16:11:43 +0530 Subject: [PATCH 01/19] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ed686c8..4267e35 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # Specifying an R environment with a runtime.txt file -Jupyter+R: [![Binder](http://mybinder.org/badge_logo.svg)](http://mybinder.org/v2/gh/binder-examples/r/master?filepath=index.ipynb) +Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?filepath=index.ipynb) -RStudio: [![Binder](http://mybinder.org/badge_logo.svg)](http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=rstudio) +RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?urlpath=rstudio) -RShiny: [![Binder](http://mybinder.org/badge_logo.svg)](http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/) +RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?urlpath=shiny/bus-dashboard/) Binder supports using R and RStudio, with libraries pinned to a specific snapshot on [MRAN](https://mran.microsoft.com/documents/rro/reproducibility). From 6c536051036279c0b468ec091b607044aa4e77b2 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 16:29:11 +0530 Subject: [PATCH 02/19] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4267e35..a1ea299 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # Specifying an R environment with a runtime.txt file -Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?filepath=index.ipynb) +Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)filepath=index.ipynb) -RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?urlpath=rstudio) +RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)urlpath=rstudio) -RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)?urlpath=shiny/bus-dashboard/) +RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)urlpath=shiny/bus-dashboard/) Binder supports using R and RStudio, with libraries pinned to a specific snapshot on [MRAN](https://mran.microsoft.com/documents/rro/reproducibility). From 10df6fdb8e6abf19880d5c8aa21f81d331244f0e Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 16:30:08 +0530 Subject: [PATCH 03/19] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a1ea299..cfae7e3 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # Specifying an R environment with a runtime.txt file -Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)filepath=index.ipynb) +Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?filepath=index.ipynb) -RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)urlpath=rstudio) +RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?urlpath=rstudio) -RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD)urlpath=shiny/bus-dashboard/) +RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?urlpath=shiny/bus-dashboard/) Binder supports using R and RStudio, with libraries pinned to a specific snapshot on [MRAN](https://mran.microsoft.com/documents/rro/reproducibility). From bc40f39a1a1c1f148a8632be8563d527e0465db9 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 17:11:25 +0530 Subject: [PATCH 04/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 6a40cb8..aa017bd 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-3.6-2019-04-12 +r-4.1-2021-05-18 From d8e6c11b21e0cfc1e59bcccc627880529e144af6 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 17:15:18 +0530 Subject: [PATCH 05/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index aa017bd..04f460a 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.1-2021-05-18 +r-4.0.5-2021-03-31 From 61e1544359098d07ba6de22a219bdf182ca07283 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 17:17:38 +0530 Subject: [PATCH 06/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 04f460a..81582fc 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.0.5-2021-03-31 +r-4.0.4-2021-02-15 From 563acd7077b5b5054a8a349a2e8be28e9254b9f8 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 17:19:19 +0530 Subject: [PATCH 07/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 81582fc..cb61ad3 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.0.4-2021-02-15 +r-4.0.3-2020-10-10 From 022b61a837c122551c80ef93bcad727c72a48cba Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 17:21:28 +0530 Subject: [PATCH 08/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index cb61ad3..63e57b5 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.0.3-2020-10-10 +r-4.0.2-2020-06-22 From 942db16f5a0659309b1c03deaf495fc4fb9393e4 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 19:21:57 +0530 Subject: [PATCH 09/19] Create environment.yml --- environment.yml | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..7926caa --- /dev/null +++ b/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge +dependencies: + - r-base=4.1 + - r-tidyverse From aaa7c8642281541c87290be2820af1de7045211e Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 19:24:47 +0530 Subject: [PATCH 10/19] Update environment.yml --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 7926caa..a93a3f1 100644 --- a/environment.yml +++ b/environment.yml @@ -1,5 +1,6 @@ channels: - conda-forge + - bioconda dependencies: - r-base=4.1 - r-tidyverse From 0ecd649253ed1616fe9a9152b25f614d512b53b1 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Wed, 2 Jun 2021 19:28:06 +0530 Subject: [PATCH 11/19] Update environment.yml --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index a93a3f1..43470e6 100644 --- a/environment.yml +++ b/environment.yml @@ -4,3 +4,4 @@ channels: dependencies: - r-base=4.1 - r-tidyverse + - r-biocmanager From 54bce25b670ad9aad002beface84a4a84170f1ad Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:24:24 +0530 Subject: [PATCH 12/19] Update environment.yml --- environment.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/environment.yml b/environment.yml index 43470e6..286b8a4 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,3 @@ -channels: - - conda-forge - - bioconda dependencies: - r-base=4.1 - r-tidyverse From a1d464b0c8362be2cdc844244d9519c37a80cf1b Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:25:39 +0530 Subject: [PATCH 13/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 63e57b5..2ee0a4e 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.0.2-2020-06-22 +r-4.1.0-2021-05-18 From 0de6894e9a6cb5784e4fd4c409b7e69b0aea9824 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:29:39 +0530 Subject: [PATCH 14/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 2ee0a4e..63e57b5 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.1.0-2021-05-18 +r-4.0.2-2020-06-22 From 20d30cd4ae51ac683f70c10c7e01171acfbac481 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Thu, 3 Jun 2021 11:32:37 +0530 Subject: [PATCH 15/19] Delete environment.yml --- environment.yml | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 environment.yml diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 286b8a4..0000000 --- a/environment.yml +++ /dev/null @@ -1,4 +0,0 @@ -dependencies: - - r-base=4.1 - - r-tidyverse - - r-biocmanager From 8412da059b7bb8696e4d71e2819b4febd6a9c141 Mon Sep 17 00:00:00 2001 From: davesanjay <43098767+davesanjay@users.noreply.github.com> Date: Thu, 3 Jun 2021 13:35:57 +0530 Subject: [PATCH 16/19] Update install.R --- install.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/install.R b/install.R index 77bdf26..3b40e44 100644 --- a/install.R +++ b/install.R @@ -3,3 +3,5 @@ install.packages("rmarkdown") install.packages("httr") install.packages("shinydashboard") install.packages('leaflet') +install.packages("BiocManager") +BiocManager::install("cBioPortalData") From 9eb9da92dc44ad25893e2dc300153e5c95431657 Mon Sep 17 00:00:00 2001 From: Robin Date: Thu, 5 Aug 2021 08:08:34 +0100 Subject: [PATCH 17/19] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index cfae7e3..42c1522 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # Specifying an R environment with a runtime.txt file -Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?filepath=index.ipynb) +Jupyter+R: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Robinlovelace/rBinder4/HEAD?filepath=index.ipynb) -RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?urlpath=rstudio) +RStudio: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Robinlovelace/rBinder4/HEAD?urlpath=rstudio) -RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davesanjay/r/HEAD?urlpath=shiny/bus-dashboard/) +RShiny: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Robinlovelace/rBinder4/HEAD?urlpath=shiny/bus-dashboard/) Binder supports using R and RStudio, with libraries pinned to a specific snapshot on [MRAN](https://mran.microsoft.com/documents/rro/reproducibility). From a5b5f6c627b05f8da55d8175f3bcb5b851ff9fd7 Mon Sep 17 00:00:00 2001 From: Robin Date: Thu, 5 Aug 2021 08:10:31 +0100 Subject: [PATCH 18/19] Update runtime.txt --- runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/runtime.txt b/runtime.txt index 63e57b5..1ccacb2 100644 --- a/runtime.txt +++ b/runtime.txt @@ -1 +1 @@ -r-4.0.2-2020-06-22 +r-4.1.0-2021-08-05 From 315b2136aa5e46d4405d7906b879d315e49cd63a Mon Sep 17 00:00:00 2001 From: Robin Date: Thu, 5 Aug 2021 08:11:26 +0100 Subject: [PATCH 19/19] Update install.R --- install.R | 6 ------ 1 file changed, 6 deletions(-) diff --git a/install.R b/install.R index 3b40e44..3d51c36 100644 --- a/install.R +++ b/install.R @@ -1,7 +1 @@ -install.packages("tidyverse") install.packages("rmarkdown") -install.packages("httr") -install.packages("shinydashboard") -install.packages('leaflet') -install.packages("BiocManager") -BiocManager::install("cBioPortalData")