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KentonWhite/ProjectTemplate 570

A template utility for R projects that provides a skeletal project.

daqana/tikzDevice 105

A R package for producing graphics output as PGF/TikZ code for use in TeX documents.

johnmyleswhite/log4r 68

A log4j derivative for R.

jefferislab/RANN 38

R package providing fast nearest neighbour search (wraps ANN library)

krlmlr/awesome-vctrs 38

A curated list of amazingly awesome R vector classes

krlmlr/bindr 26

Parametrized active bindings

krlmlr/brushthat 21

Brush up your tests!

krlmlr/bindrcpp 17

An Rcpp interface to active bindings

cynkra/tv 5

Graphical Display For Data Frame Output

cynkra/SwissCommunes 3

Functions for working with the historicized list of communes of Switzerland.

issue commentr-lib/actions

Setup fails on Windows

@jimhester, somewhat related: I noticed the following point in https://github.com/r-lib/actions#common-questions

Does the setup-r action support R-devel? Not currently, as there are not currently any daily R binaries built for R-devel. Though this support is planned in the future.

I guess we are already in the future by now :)

hannesmuehleisen

comment created time in an hour

fork yihui/cpp11

cpp11 is a header-only R package that helps R package developers handle R objects with C++ code.

https://cpp11.r-lib.org/

fork in 3 hours

issue commentyihui/knitr

Should `dev = "svg"` gracefully fall back if `capabilities("cairo")` is not TRUE?

The check results are different now: https://www.stats.ox.ac.uk/pub/bdr/M1mac/cpp11.out You can see a warning about svg not operational:

Warning: The device 'svg' is not operational; falling back to 'png'.

However, I don't understand why only converting.Rmd failed (even though the device seemed to have fallen back to png), but it worked fine for motivations.Rmd:

--- re-building ‘converting.Rmd’ using rmarkdown
Loading required namespace: cpp11test
Failed with error:  'there is no package called 'cpp11test''
Warning: The device 'svg' is not operational; falling back to 'png'.
Quitting from lines 116-129 (converting.Rmd) 
Error: processing vignette 'converting.Rmd' failed with diagnostics:
svg: Cairo-based devices are not available for this platform
--- failed re-building ‘converting.Rmd’

--- re-building ‘motivations.Rmd’ using rmarkdown
Loading required namespace: cpp11test
Failed with error:  'there is no package called 'cpp11test''
Loading required namespace: cpp11test
Failed with error:  'there is no package called 'cpp11test''
Warning: The device 'svg' is not operational; falling back to 'png'.
Loading required namespace: cpp11test
Failed with error:  'there is no package called 'cpp11test''
Warning: The device 'svg' is not operational; falling back to 'png'.
--- finished re-building ‘motivations.Rmd’

SUMMARY: processing the following file failed:
  ‘converting.Rmd’

Error: Vignette re-building failed.
Execution halted

Does anyone have the new Macbook with the M1 chip? Or is there an easy way to deliberately disable Cairo for R so I can test it?

jimhester

comment created time in 3 hours

issue commentyihui/knitr

kable: cannot start first column with [ symbol using latex and booktabs

I'm okay with adding the extra {} (it's indeed safer to always add them after LaTeX commands). Thanks!

jonnypenarth

comment created time in 3 hours

Pull request review commentyihui/knitr

fix setting col in par() with global.pars = TRUE

 if (xfun::loadable('tikzDevice') &&  # https://github.com/yihui/knitr/issues/1166 knit(text = "\\Sexpr{include_graphics('myfigure.pdf', error = FALSE)}", quiet = TRUE)++with_par <- function(expr, ...) {
with_par = function(expr, ...) {
cderv

comment created time in 3 hours

fork jeroen/gdal

GDAL is an open source X/MIT licensed translator library for raster and vector geospatial data formats.

https://gdal.org

fork in 3 hours

startedkrlmlr/dm

started time in 3 hours

issue commentr-lib/devtools

track install_github() installs?

As this is quite an old issue I am going to lock it, thank you all for the feedback!

cklunch

comment created time in 3 hours

issue commentr-lib/devtools

track install_github() installs?

install_github() does not clone the repository, it downloads the tar.gz, which GitHub does not track. If there was a way to track this through GitHub we would be doing it.

cklunch

comment created time in 3 hours

issue openedcwida/duckdb

Can you provide a row iterator interface in Python for query results?

All of the row result methods here: https://duckdb.org/docs/api/python

  • fetchdf
  • fetchall
  • fetchnumpy will put store the query results into memory. If the DuckDB database is sufficiently large, we will run out of memory.

Can you provide an iterator-based method that won't create a list like fetchall? I would recommend just having fetchall return an iterator. That way, you can still call list(fetchall) if you want a list of results.

created time in 4 hours

issue commentr-dbi/RPostgres

PostgreSQL from WSL1, failed System has not been booted with systemd

It just works after couple of time trying, and certainly this is not ideal for batch processing unless I wrap this in trycatch

armenic

comment created time in 4 hours

issue commentr-dbi/RPostgres

PostgreSQL from WSL1, failed System has not been booted with systemd

I did the following and issue is resolved. Please close if no more information is needed.

sudo apt install postgresql postgresql-contrib

Reference https://docs.microsoft.com/en-us/windows/wsl/tutorials/wsl-database#install-postgresql

armenic

comment created time in 4 hours

issue openedr-dbi/RPostgres

PostgreSQL from WSL1, failed System has not been booted with systemd

I am trying to connect to PostgreSQL from WSL1 (WSL2 does not connect to a network, so can't use it) and I get the following error:

System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to create bus connection: Host is down
Warning message:
In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1

OS info

OS Name:                   Microsoft Windows 10 Enterprise
OS Version:                10.0.18363 N/A Build 18363

R info

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          0.3                         
year           2020                        
month          10                          
day            10                          
svn rev        79318                       
language       R                           
version.string R version 4.0.3 (2020-10-10)
nickname       Bunny-Wunnies Freak Out  

DBI and RPostgres info

> packageVersion("DBI")
[1] ‘1.1.1’
> packageVersion("RPostgres")
[1] ‘1.3.1’

reprex

library(DBI)

# Connect to the default postgres database
con <- dbConnect(
  RPostgres::Postgres(),
  dbname = "sandpit_man",
  host = "rkalvpose01s.kau.rose.com",
  port = "5432",
  user = "my_masked_username",
  password = "my_masked_pass"
)

dbListTables(con)

created time in 4 hours

issue commentr-lib/testthat

testthat subprocess exits when running tests in parallel

I think you're going to have to make us a reprex.

byoung

comment created time in 4 hours

issue commentr-lib/devtools

track install_github() installs?

@bakaburg1 In GitHub settings you can see the Insights tabs which tracks the number of clones that I guess correspond to install_github() installs (?)

cklunch

comment created time in 4 hours

issue openedr-lib/testthat

testthat subprocess exits when running tests in parallel

When running tests in parallel and without any explanation, one of the threads dies on the same file.

Error: testthat subprocess exited in file `my_tests.R`
15747Backtrace:
15748     █
15749  1. └─testthat::test_local(".", reporter = c("progress", "fail"))
15750  2.   └─testthat::test_dir(...)
15751  3.     └─testthat:::test_files(...)
15752  4.       └─testthat:::test_files(...)
15753  5.         ├─testthat::with_reporter(...)
15754  6.         │ ├─base::withRestarts(...)
15755  7.         │ │ └─base:::withOneRestart(expr, restarts[[1L]])
15756  8.         │ │   └─base:::doWithOneRestart(return(expr), restart)
15757  9.         │ └─base::force(code)
15758 10.         └─testthat:::parallel_event_loop_chunky(queue, reporters)
15759 11.           └─queue$poll(Inf)
15760 12.             └─base::lapply(...)
15761 13.               └─testthat:::FUN(X[[i]], ...)
15762 14.                 └─private$handle_error(msg, i)
15763Execution halted
15764The command "docker-compose run --entrypoint="bin/runTests.sh" myproj" exited with 1.
15765
15766
15767Done. Your build exited with 1.

created time in 5 hours

PR opened yihui/knitr

fix setting col in par() with global.pars = TRUE

This PR fix #1603 by adding the special handling of fg option in par2()

I took the opportunity to add some test for this function - it seems one of the parameters is changed by others when we use the equivalent of par(par(no.readonly = TRUE). There are dependencies between parameters and setting all of them at once seems to have side effect. Usually you do

op = par(x)
# do something
par(op)

and not

par(x)
all = par(no.readonly = TRUE)
# do something
par(all)

It does not seem to be equivalent. But we can't really do the former.

+42 -0

0 comment

2 changed files

pr created time in 5 hours

create barnchyihui/knitr

branch : fix/global-pars-col

created branch time in 5 hours

issue commentr-lib/actions

Setup fails on Windows

Nothing has changed recently as far as the action is concerned. So this must be something upstream in the builder image or possibly the current R-devel installer is messed up somehow?

hannesmuehleisen

comment created time in 5 hours

push eventdsbbfinddx/FINDCov19TrackerData

GitHub Action

commit sha 196e38f205142e28d346815876b0ce431cc012fb

update run analysis files for 2021-01-27

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commit sha 3b3fa07155738c95d26908a8eb68e32008c752a5

update files for 2021-01-27

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issue commentr-lib/devtools

track install_github() installs?

As said before probably only releases download can be checked.

devtools code about installing were organized in remotes, you can read it there. I think it just download the source zip from github.

cklunch

comment created time in 6 hours

issue openedtidyverse/dplyr

Unexpected behavior in na_if

Tried using na_if today to turn values in a column that are less than zero to NA. Tried the ifelse alternative and that gave the behavior I expected to see when using na_if.


test <- tibble(Staff.Confirmed = c(0, 1, -999), Residents.Confirmed = c(12, -192, 0))
print(test)

out <-  test %>% 
  mutate(staff_conf_naif = na_if(Staff.Confirmed, Staff.Confirmed < 0),
        staff_conf_ifelse = ifelse(Staff.Confirmed < 0, NA, Staff.Confirmed),
        res_conf_naif = na_if(Residents.Confirmed, Residents.Confirmed < 0),
        res_conf_ifelse = ifelse(Residents.Confirmed < 0, NA, Residents.Confirmed)) %>% 
  select(Staff.Confirmed, staff_conf_naif, staff_conf_ifelse,
         Residents.Confirmed, res_conf_naif, res_conf_ifelse)
print(out)

When I use na_if in this mutate, it only makes changes to values equal to zero in the column referenced. Not sure if this is the intended behavior, but it seems a bit strange

created time in 6 hours

issue commentr-lib/devtools

track install_github() installs?

Hello, I know that the issue is closed (even I didn't understand the CRAN policy problem), but I was wondering if it's possible to check the downloads via github directly, without any action from the R side. Is there any github action or API that can be used for this? Using https://img.shields.io/github/downloads/User/Repo/total.svg doesn't work because it checks only releases downloads. What actions is actually devtools performing when installing from github? (I tried to check install_github code, but it's very nested and got lost)

cklunch

comment created time in 6 hours

push eventdsbbfinddx/FINDCov19TrackerData

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commit sha d0e727872ce0cd310399312575dba7a2616615d1

update 2021-01-27-selenium-tests.csv

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issue openedr-lib/actions

Setup fails on Windows

Describe the bug Error "Error: Failed to get R devel: Failed to get R devel: Failed to install R: Error: spawn UNKNOWN" on Windows

To Reproduce See here: https://github.com/cwida/duckdb/runs/1777121516

Expected behavior Working as it did before.

Here is the relevant piece of my GHA config:

 rstats-windows:
    name: R Package Windows
    runs-on: windows-latest

    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0

    - uses: actions/setup-python@v2
      with:
        python-version: '3.7'

    - uses: r-lib/actions/setup-r@v1
      with:
        r-version: 'devel'

created time in 6 hours

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Joe Thorley

commit sha d112115632107966490787457fb7b770ad3528c3

sort read path messages so that not sensitive to timing order

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Joe Thorley

commit sha 971c2a436482829d2e76df5090e8c42a8b36402d

sort to deal with timing of file processing

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