from @diminera:

Dear Ben,

Thank you very much for your patience in advanced.
I have been trying to fix my problem "to push" the changes but I didn´t succeded. I deleted everything and started from zero and the same...stays running but nothing occurs

Do you know what I am doing wrong?

Regards,
Diana

Hi Ben,
I have completed "all" the steps up to section 1.8, but I was having an issue with the Push command. I eventually skipped this step in section 1.5 and continued to section 1.8. But now I am unable to fully complete the Roster in section 1.8: Once I added my details to the csv file, I saved it and made a commit (" + KayleeSmit"), but then the Push is not able to complete in RStudio, it just continues indefinitely (it seems like another participant had the same issue, but I have not been able to resolve it). Thus I am not able to "contribute" to the forked branch and continue to make a pull request.
Please can you help me. I am so close :)

I am having an issue with Knit from step 2.2.2 onward in the Manipulate exercise. I am copying the code from the Manipulate exercise page and pasting it into my own R Markdown file. And I am able to run the code from R Markdown (for this and all following steps) but I am unable to knit any of the steps.

Below is my input and the table I can generate in R Markdown:

And this is the error I get.

So far I have not been able to diagnose the issue with the code due to my limited knowledge of R. Of note, I am running R 3.6.2.

I am having issues with committing from RStudio. I have managed to work around it (I'm not sure what I did) but the error has returned. When trying to commit a change for 1.10 (which I don't think is the issue you wanted us to create) from RStudio I get the following:

#fatal: Unable to create 'C:/Users/corinne.paterson/Documents/R3_course/R3-exercises/.git/index.lock': File exists.

Another git process seems to be running in this repository, e.g.
an editor opened by 'git commit'. Please make sure all processes
are terminated then try again. If it still fails, a git process
may have crashed in this repository earlier:
remove the file manually to continue.

The only things I have open are one instance of RStudio and my repo on GitHub. I am not sure what else would be using the Git process. Are you aware of what the issue might be?

I am also having issues with being able to stage items and an extreme slow down of RStudio that is sometimes fixed after closing RStudio once, but sometimes requires more. I have tried to troubleshoot those issues, but have found that they are just problems with RStudio and Git that are well documents but do not have solutions. Is it possible this is what is hanging up my commit?

Hi Ben,
When doing step 1.5, the push request goes on indefinitely. This past week I've tried restarting the exercise and setting up a PAT using these instructions https://happygitwithr.com/credential-caching.html. I get the following error when trying to store my credentials using gitcreds_set(): "Your current credentials for 'https://github.com':
fatal: Cannot prompt because user interactivity has been disabled"
Is there something I can change in my github or RStudio settings to fix this? Thanks!

When Creating a new Project and using RStudio's git clone, I got this error:

>>> C:/Users/jcoates/AppData/Local/Programs/Git/bin/git.exe clone --progress https://github.com/JuliaCoates/r3-exercises.git r3-exercises
Cloning into 'r3-exercises'...
fatal: unable to access 'https://github.com/JuliaCoates/r3-exercises.git/': error:1408F10B:SSL routines:ssl3_get_record:wrong version number

Hi
I struck at 2.1.5 section to render Rmarkdown with following error. Can anyone help me what could be the problem?

Reference:

• 22.4 Dealing with conflicts | Happy Git and GitHub for the useR

from @lavallef originally as #34 (comment):

Hi Ben,

I'm trying to push, but I am getting this error. I am able to pull fine. Looks like a permission issue?

Thanks,
Flo

I am unsure about this issue and whether the modified local files need to be pushed, or something else has to happen.

When I commit and push files, git tells me everything is up to date.

Yet when I look under the git tab, I still see lots of files?

When I executed this step before, it seemed that the files listed under the git tab disappeared, but not this time.

If I am missing a step, please give me a clue. TIA.

This fails - sst_stck exists in environment with 13M elements, but results here are not produced.

Hi Ben,
I am not succeeded while merging Rmd website. I tried to commit the changes but its not happening. How can resolve this issue? I couldn't understand what to do. My R terminal is not responding also R. Kindly help me.
Thank you

Hello, I have an error message due to the sf package.

shelf(

• NOAA-EDAB/ecodata,
• sf)
  Error: package or namespace load failed for ‘sf’:
  .onLoad failed in loadNamespace() for 'units', details:
  call: udunits_init(path)
  error: function 'Rcpp_precious_remove' not provided by package 'Rcpp'
  I tried to uninstall and reinstall it. But I am still running with the same error.
  

The instructions for section 2.1.2 in the training Rmd (https://noaa-iea.github.io/r3-train/manipulate.html) is not working now.

https://oceanview.pfeg.noaa.gov/services now takes you to this URL to access the ERDAP files: https://coastwatch.pfeg.noaa.gov/erddap/index.html.

But doing a full text search on "cciea" does returns no results: https://coastwatch.pfeg.noaa.gov/erddap/search/index.html?page=1&itemsPerPage=1000&searchFor=CCIEA+Anthropogenic+Drivers

Listing all data sets and searching the html for "cciea" also returns no results ":https://coastwatch.pfeg.noaa.gov/erddap/info/index.html?page=1&itemsPerPage=1000"

It appears that the CSV file is available here: https://github.com/noaa-iea/r3-train/blob/master/data/cciea_AC.csv

But the instructions in section 2.1.2 do not handle this file correctly:

set variables

#csv_url <- "https://oceanview.pfeg.noaa.gov/erddap/tabledap/cciea_AC.csv"
csv_url <- "https://github.com/noaa-iea/r3-train/blob/master/data/cciea_AC.csv"

dir_data <- "data"

derived variables

csv <- file.path(dir_data, basename(csv_url))

create directory

dir.create(dir_data)

download file

download.file(csv_url, csv)

Read table read.csv()

read csv by skipping first two lines, so no header

d <- read.csv(csv, skip = 2, header = FALSE)

update data frame to original column names

names(d) <- names(read.csv(csv))

Instead I get this after executing the above code in R:
str(d)
'data.frame': 405 obs. of 1 variable:
$ X..DOCTYPE.html.: chr "" "" " " " " ...

Could someone update and correct the code in Section 2.1.2 and the Manipulate lesson so that the data can be re-processed in R. I did not save the data set locally when I first worked with the lessons.

TIA.

Working with @ajanefmc:

C:/Users/aapplegate/AppData/Local/Programs/Git/bin/git.exe push origin HEAD:refs/heads/main

@bbest
When I try to install infographiq I get errors. I do not recognize these errors and am unsure how to troubleshoot.

`> remotes::install_github("marinebon/infographiqR")
Downloading GitHub repo marinebon/infographiqR@HEAD
√ checking for file 'C:\Users\halie.ofarrell\AppData\Local\Temp\RtmpGQD8xb\remotes4270198f62b9\marinebon-infographiqR-6949dcb/DESCRIPTION' (354ms)

• preparing 'infographiqR': (522ms)
  √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
  Omitted 'LazyData' from DESCRIPTION
• building 'infographiqR_0.2.0.tar.gz'
  Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
  storing paths of more than 100 bytes is not portable:
  'infographiqR/inst/template_website/site_libs/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2'

Installing package into ‘C:/Users/halie.ofarrell/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)

• installing source package 'infographiqR' ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'infographiqR'
  finding HTML links ... done
  generate_html_4_rmd html
  get_figure_info html
  get_modal_info html
  glossarize_md html
  infographiq_template html
  insert_tooltip html
  md_caption html
  ocnms_create_link_table html
  ocnms_get_modal_info html
  ocnms_get_sheet html
  render_all_rmd html
  render_figure html
  rmd2html html
  *** copying figures
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  *** arch - i386
  Error : package 'infographiqR' is not installed for 'arch = i386'
  Error: loading failed
  Execution halted
  *** arch - x64
  Error : package 'infographiqR' is not installed for 'arch = x64'
  Error: loading failed
  Execution halted
  ERROR: loading failed for 'i386', 'x64'
• removing 'C:/Users/halie.ofarrell/Documents/R/win-library/4.1/infographiqR'
  Warning message:
  In i.p(...) :
  installation of package ‘C:/Users/HALIE~1.OFA/AppData/Local/Temp/RtmpGQD8xb/file42701aa25aae/infographiqR_0.2.0.tar.gz’ had non-zero exit status`

Hi Ben!

Thank you very much for creating such informative lessons. I followed the collaborate lesson but unfortunately my r3-excercises website is not displaying correctly, please see https://jkumagai96.github.io/r3-excercises/.

When I display the index.html file locally it looks great, just like your example. By chance, do you know what I missed? Thanks very much for your help.

Hi,

When I try to complete section 1.8's fork and pull request, I get the below error message when trying to create the Github RStudio Project for the fork off of https://github.com/noaa-iea/r3-train.

error: invalid path 'docs/figs/collaborate/todo-gh-pat/screen - Github git push denied w: blog .png'
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

When I use "git status", a list of all the files is returned in this format: "deleted: README.md" and the directory where I'm trying to clone the repo is empty. I've been trying to figure out what's going on via Google, but so far all I can think of is that maybe the space between blog and .png or the w: in the file named in the error may be causing this issue?