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2362 Commity (0b766082085a0e4f092988aabfeb36cb7ce452b3)

Autor SHA1 Wiadomość Data
YuviPanda 0b76608208 Bump default R version to 4.2 
Been out for a bit now
 2022-07-06 16:39:15 -07:00
Erik Sundell ae8ed290b9
Merge pull request #1161 from yuvipanda/another-r 
Get R from RStudio provided apt packages (.deb files)
 2022-07-01 07:27:19 +02:00
Yuvi Panda 57a95a3614
Merge pull request #1163 from foobarbecue/patch-1 
Add JPL Dataverse
 2022-06-30 16:09:28 -07:00
Aaron Curtis cae431d115
Add JPL Dataverse 
NASA's Jet Propulsion Laboratory recently implemented a dataverse installation and would like to be able to use it with repo2docker / binderhub
 2022-06-28 17:56:55 -07:00
YuviPanda 8af47e9985 Add comment about how r_version is determined 2022-06-23 12:34:48 -07:00
YuviPanda 28035d6426 Make sure our default R version is valid semver 2022-06-23 09:14:34 -07:00
YuviPanda e51eae9287 Don't specify older patchlevel as default R 2022-06-23 03:23:47 -07:00
Yuvi Panda a098f95dc4
Point to a tagged version of rstudio 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2022-06-22 23:37:42 -07:00
YuviPanda 8ed4c96a8e Put simple test date back to where it was 
Let's remove unnecessary changes
 2022-06-22 16:20:58 -07:00
Yuvi Panda 232dddac50
Fix typo 
Co-authored-by: Simon Li <orpheus+devel@gmail.com>
 2022-06-22 13:40:04 -07:00
YuviPanda dfa23f6306 Set custom env vars required for RStudio to work 2022-06-22 08:49:28 -07:00
YuviPanda 9d89d6bd69 Use . instead of source 
As Dockerfile executes with /bin/sh, not /bin/bash
 2022-06-22 08:49:28 -07:00
YuviPanda a9443f04fe Don't hardcode Ubuntu version when fetching R 
This allows us to dynamically change the base image
without having to manually change the version string here
 2022-06-22 08:49:28 -07:00
YuviPanda 2819a6d1b4 Upgrade simple to a newer r snapshot 
2020 had an older version of testthat that ran into issues

> # Error in get(genname, envir = envir) : object 'testthat_print' not found
 2022-06-22 08:49:28 -07:00
YuviPanda 9fa096d0f6 Don't specify distro specific build number 2022-06-22 08:49:28 -07:00
YuviPanda def4009a6b Remove another unneeded R unit test 
We want users to be able to install new versions of R
as soon as they are out, without us having to do anything
special in repo2docker. So we can't actually check for 'invalid'
R versions. This is ok, as we don't have to special case apt repos
or similar when installing R from rstudio's debs
 2022-06-22 08:49:28 -07:00
YuviPanda 9c335a5e9e Cleanup apt-update files after installation 2022-06-22 08:49:28 -07:00
YuviPanda ba82209e67 Remove tests that checked if specific R packages were installed 2022-06-22 08:49:28 -07:00
YuviPanda c1ce8fd189 Use apt rather than debi to install packages 
apt also seems to fetch dependencies when needed
 2022-06-22 08:49:28 -07:00
YuviPanda d72ac15037 Set CRAN mirror URL for R 2022-06-22 08:49:28 -07:00
YuviPanda c123d7bf32 Use new path for Renviron 2022-06-22 08:49:28 -07:00
YuviPanda 4ccbdddeb5 Install package with gdebi 
It fetches dependencies and installs them too, unlike dpkg
 2022-06-22 08:49:28 -07:00
YuviPanda 13250c73d1 Always provide full semver for R version 
Other wise our semver package cries
 2022-06-22 08:49:28 -07:00
YuviPanda 22167c35f0 Actually install the downloaded deb 2022-06-22 08:49:28 -07:00
YuviPanda 965cb15b99 Get R from RStudio managed apt packages 
Might be simpler than getting it from R project managed
apt packages
 2022-06-22 08:49:27 -07:00
Yuvi Panda 0f0fca19a0
Merge pull request #1148 from aplamada/upgrade_rstudio_server_to_2022_02_1 
[MRG] upgrade RStudio Server to v2022.02.1
 2022-06-22 08:36:30 -07:00
Min RK e7524a7b4b
Merge pull request #1156 from CLIP-HPC/fix_server_log 
Fix Read-Only filesystem permission issue for log file
 2022-06-08 11:15:55 +02:00
Yuvi Panda c4e01b3a8d
Merge pull request #1160 from daradib/shallowhead 
[MRG] Shallow clone HEAD
 2022-06-03 22:34:49 +05:30
Dara Adib 56bf03811e Add test for shallow clone HEAD 2022-06-02 20:54:43 -04:00
Dara Adib 991c249141 Remove unused sys import 2022-06-02 20:54:43 -04:00
Dara Adib 49d47b855e Shallow clone HEAD 
Previously repo2docker only performed shallow clones when refspec
was not provided. We now also perform shallow clones if refspec is
explicitly set to HEAD. Binder always specifies a refspec, often
HEAD, so this should improve some build times.
 2022-06-02 20:54:43 -04:00
Ümit Seren 3ee04e34a3 Fix Read-Only filesystem permission issue for log file 2022-05-03 16:05:55 +02:00
Min RK 61247bec16
Merge pull request #1151 from pymonger/handle-logfile-permission-error 
handle permission issue writing .jupyter-server-log.txt in REPO_DIR
 2022-05-02 09:27:54 +02:00
Min RK 5df775aac6
keep server log name 2022-04-28 13:07:11 +02:00
Gerald Manipon c09d66fea6 better comment 2022-04-24 17:19:24 -07:00
Gerald Manipon e75c664edb fix join() call 2022-04-19 07:57:58 -07:00
Gerald Manipon 304b1430a5 fix insert call 2022-04-19 05:46:20 -07:00
Gerald Manipon 051c9d36a3 iterate through different log locations 2022-04-18 17:24:49 -07:00
Gerald Manipon 723e5b6907 handle permission issue 2022-04-15 13:26:04 -07:00
Min RK 1d218afd38
Merge pull request #1149 from yuvipanda/bumpies 
Update base notebook packages
 2022-04-13 10:01:47 +02:00
YuviPanda 76aacbf3ab Update py3.6 environment one last time 
Updated with previous contents of environment.yml file.
From now on, 3.6 will only get security updates
 2022-04-11 12:31:56 -07:00
YuviPanda 5444850bc4 Update base notebook packages 
- We should stop auto updating 3.6 now, so we can move on to
  newer notebook packages - a new notebook version ought to fix
  issues like https://github.com/2i2c-org/infrastructure/issues/1170
  for example.
- No longer explicitly pin nbconvert, as whatever version notebook
  brings in should be sufficient.
- Bump up ipywidgets and jupyterlab while we're at it.
- No longer pin jupyterhub-singleuser either, as that too works
  properly with 3.7
 2022-04-11 12:31:56 -07:00
Min RK 5f86ef6269
Merge pull request #1147 from yuvipanda/r-doc 
Update 'how to get R' section
 2022-04-11 13:46:28 +02:00
Min RK ddcb532a56
Merge pull request #1150 from yuvipanda/moblack 
Update black version
 2022-04-11 13:46:08 +02:00
YuviPanda 672c21ff82 Make black happy 2022-04-08 13:55:06 -07:00
YuviPanda 34a7e33148 Update black version 
Fixes error with click causing current CI failures
 2022-04-08 13:44:55 -07:00
Andrei Plamada 190f4cfba8 upgrade RStudio Server to v2022.02.1 2022-03-28 10:01:55 +02:00
YuviPanda f5759cbdac Update 'how to get R' section 
- Explains https://github.com/jupyterhub/repo2docker/pull/1104
- Advertises that we get RStudio 'for free' when R is installed
 2022-03-25 13:16:00 -07:00
Yuvi Panda 66f608e207
Merge pull request #1133 from manics/post-release-fixes 
Post release fixes
 2022-03-15 00:28:49 -07:00
Simon Li ec993498ab
Merge pull request #1141 from minrk/r-version 
handle r version being unspecified in environment.yml
 2022-03-06 15:35:02 +00:00