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2483 Commity (ae3aeb6dc5dd6deee6d663b7088eb74d225a815f)

Autor SHA1 Wiadomość Data
Sylvain Corlay a0f83c012d Re-add call to clean 2022-01-25 23:58:54 +01:00
YuviPanda 6ab41efd4d Delete /tmp/downloaded_packages after running install.R 
This can often leave ~100-200MB in /tmp that isn't re-used
after the image is set up.
 2022-01-25 21:26:16 +05:30
Simon Li 813d28bfdb
Merge pull request #1115 from minrk/set-user-root 
set USER root after each directive block
 2022-01-25 14:55:11 +00:00
Min RK 3f07830957
Merge pull request #1118 from yuvipanda/no-ggplot2 
Use a smaller R library in our tests
 2022-01-25 15:53:33 +01:00
YuviPanda 9066d079d0 Use testthat, rather than tinytest 
tinytest doesn't exist in older MRAN snapshots
 2022-01-25 19:38:47 +05:30
Min RK 945c45299f set USER root after each directive block 
matches expectations in the directive sequences

not strictly required after preassemble because we have no root steps between preassemble and assemble,
so we could remove the `last_user = "root"` there instead

includes regression test
 2022-01-25 14:48:37 +01:00
YuviPanda f6737cfff5 Use a smaller R library in our tests 
ggplot2 is a big library with a bunch of dependencies,
making our already slow R tests even slower. This PR
switches them to using the tinytest library, which has
no dependencies and is much smaller.
 2022-01-25 18:58:58 +05:30
Yuvi Panda bf99b93dae
Merge pull request #1117 from minrk/r-base-core 
Only get R itself (r-base-core) from apt, not CRAN packages
 2022-01-25 18:39:45 +05:30
Min RK ad0034cb2f note why --no-install-recommends is important for r packages 2022-01-25 13:29:15 +01:00
Min RK 19acf46392 remove r-recommended package 
r-recommended is a collection of common CRAN packages,
which cause conflicts when trying to install older R.

These same packages can be regular dependencies retrieved from CRAN.
 2022-01-25 11:38:35 +01:00
Sylvain Corlay 65a36cc3f7 PR review comments: update micromamba, use MAMBA_EXE environment variable 2022-01-21 13:16:33 +01:00
Sylvain Corlay 374efff3dc Fix CI by calling shell init 2022-01-21 11:21:00 +01:00
Sylvain Corlay 5f82b2c8b0 Update micromamba installation 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 7d4ac3b960 Use micromamba 0.17 and install conda & mamba into base env 2022-01-21 11:21:00 +01:00
Wolf Vollprecht e12ffc4a99 use mamba with fixed zstd linkage 2022-01-21 11:21:00 +01:00
Wolf Vollprecht b6091c9265 use wget better 2022-01-21 11:21:00 +01:00
Wolf Vollprecht c96a230962 try nightly 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 245fc1b939 use 0.16.0 2022-01-21 11:21:00 +01:00
Sylvain Corlay 089f6a87a5 Use micromamba 0.15.2 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 3c2ded30be fix rm targets 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 7c4f2a5b4f fix up urls 2022-01-21 11:21:00 +01:00
Wolf Vollprecht 7ad3c177d2 trigger 2022-01-21 11:21:00 +01:00
Wolf Vollprecht abc1fe98c8 trigger 2022-01-21 11:21:00 +01:00
Madhur Tandon 22d4781809 use strict channel priority 2022-01-21 11:21:00 +01:00
Madhur Tandon 2d27bb2af6 revert back to using install 2022-01-21 11:21:00 +01:00
Madhur Tandon d2a2c070e7 use experimental build of micromamba 2022-01-21 11:21:00 +01:00
Madhur Tandon b08c7dc3b6 use env update instead of install 2022-01-21 11:21:00 +01:00
Madhur Tandon e12c436af2 add MAMBA_EXE environment variable 2022-01-21 11:21:00 +01:00
Madhur Tandon 8926cdc968 minor fixes 2022-01-21 11:21:00 +01:00
Madhur Tandon 9c109f95b4 use latest micromamba and fix MAMBA_ROOT_PREFIX 2022-01-21 11:21:00 +01:00
Madhur Tandon 2e702f0248 rename file and add conda-forge channel to .condarc 2022-01-21 11:21:00 +01:00
Madhur Tandon 3288bca6a4 fix tests + change name of script 2022-01-21 11:21:00 +01:00
Madhur Tandon 6cc7567f2e use micromamba 0.12.2 2022-01-21 11:21:00 +01:00
Madhur Tandon f9388c3200 use latest micromamba 2022-01-21 11:21:00 +01:00
Madhur Tandon 2bfbf44efa adhere to lint 2022-01-21 11:21:00 +01:00
Madhur Tandon f508bf167e replace mamba & conda with micromamba 2022-01-21 11:20:58 +01:00
Simon Li a37a205c0e
Merge pull request #1108 from aplamada/test_R_conda 
[MRG] add tests for R conda
 2022-01-11 10:39:22 +00:00
Simon Li aa17545a9b
Merge pull request #1111 from yuvipanda/no-ppa 
Say 'apt repository' rather than PPA
 2022-01-10 19:02:01 +00:00
YuviPanda c04fff30cd Say 'apt repository' rather than PPA 
PPA is a specific kind of apt repository, hosted on
launchpad.net. We use https://cran.r-project.org/bin/linux/ubuntu/,
which is just a regular apt repository. The PPA terminology
always confused me, so this just clears that up
 2022-01-10 17:43:09 +05:30
Andrei V. Plamada b2b0f758ff
Merge branch 'jupyterhub:main' into test_R_conda 2022-01-08 18:33:59 +01:00
Simon Li 43525352a7
Merge pull request #1107 from yuvipanda/new-r 
Bump default R version to 4.1
 2022-01-08 14:44:37 +00:00
Simon Li 457f718386
Merge pull request #1104 from yuvipanda/rspm 
Get binary R packages from packagemanager.rstudio.com
 2022-01-08 14:43:48 +00:00
Andrei Plamada 8a817eba97 add tests for R conda 2022-01-07 13:37:43 +01:00
YuviPanda 7fd9a3d25f Move 3.6.1 back to 3.6.1-3bionic 
Was accidentally included along with the 3.6.3-1biocnic
upgrade for 3.6
 2022-01-07 11:23:47 +05:30
YuviPanda 3cb3fbf853 Remove unnecessary print() 2022-01-07 11:18:09 +05:30
YuviPanda 05e504a7ce Cleanup some comments 2022-01-07 11:18:02 +05:30
YuviPanda ceb4f8ac4f Hardcode rspm URL as snapshot for IRKernel 2022-01-07 11:17:46 +05:30
YuviPanda e2aefcfbdd Update test to match new default R version 2022-01-05 22:51:27 +05:30
YuviPanda 54636c6ecf Bump default R version to 4.1 
3.6 is almost 4 years old now.
 2022-01-05 22:32:07 +05:30
YuviPanda dbb5ff7c7d Clarify when mran raises valueerror 2022-01-05 21:35:07 +05:30