Last updated: 2022-06-13

Checks: 6 1

Knit directory: rotation2/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20220607)

The command set.seed(20220607) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: absolute

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute relative
~/rotation2/ .

Repository version: 9c733d1

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 9c733d1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


working directory clean

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/misc.Rmd) and HTML (docs/misc.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 9c733d1 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
html 7511e76 chenh19 2022-06-13 Build site.
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Rmd ad7547c chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Routine

Load:

# load
setwd("~/rotation2/")
library(workflowr)

WorkflowR publish:

# workflowR publish
wflow_publish("analysis/*.Rmd")

Cleanup:

# cleanup environment
rm(list = ls())

Git commit and push:

# git pull
#mkdir ~/rotation2/ && cd ~/rotation2/ && git init
#git pull git@github.com:chenh19/rotation2.git

# git push
cd ~/rotation2/
#git remote add origin git@github.com:chenh19/rotation2.git
#git commit -a -m "update"
git push -u origin main

Meetings

  • Xuanyao one-on-one: Tue 1pm and Thur 1pm
  • Liu group meeting: Wed 1pm (Work-in-progress/Journal clubs)
  • Joint lab meeting (Andy & Haky groups): Thurs 2pm (Work-in-progress/Journal clubs)
  • Yang lab journal club: Mon 1pm
  • PBC serminar (Matthew & Xin & John groups): Fri 10:30am
  • Group lunch: Wed 12pm

Git SSH configuration

# check for existing keys
#ls -al ~/.ssh

# create a key if does not exist
ssh-keygen -t ed25519 -C "your_email@example.com"
# when asked "Enter a file in which to save the key," press Enter (default file location)
# input a passphrase (anything you can remember)

# add SSH key to ssh-agent-
eval `ssh-agent -s`
ssh-add ~/.ssh/id_ed25519

# get the key
cat ~/.ssh/id_ed25519.pub
# copy the output key, then navigate to Github account and add the ssh key

Canon printer configuration

# Canon Color ImageCLASS MF735Cdw driver for linux
cd ~/Downloads
wget -q -O linux-UFRII-drv-v550-us-00.tar.gz https://pdisp01.c-wss.com/gdl/WWUFORedirectTarget.do?id=MDEwMDAwOTIzNjEx&cmp=ABR&lang=EN && sleep 10 && 
tar -xf linux-UFRII-drv-v550-us-00.tar.gz && sleep 1 && rm linux-UFRII-drv-v550-us-00.tar.gz
sudo bash ./linux-UFRII-drv-v550-us/install.sh && sleep 1 && rm -rf ./linux-UFRII-drv-v550-us/
sudo apt-get update && sudo apt install -f -y && sudo apt-get autoremove -y && sudo apt-get clean
  • Note: the private IP address is labeled on the printer.
  • Ref: Canon Support

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     highr_0.9        bslib_0.3.1      compiler_4.2.0  
 [5] pillar_1.7.0     later_1.3.0      git2r_0.30.1     jquerylib_0.1.4 
 [9] tools_4.2.0      getPass_0.2-2    digest_0.6.29    jsonlite_1.8.0  
[13] evaluate_0.15    tibble_3.1.7     lifecycle_1.0.1  pkgconfig_2.0.3 
[17] rlang_1.0.2      cli_3.3.0        rstudioapi_0.13  yaml_2.3.5      
[21] xfun_0.31        fastmap_1.1.0    httr_1.4.3       stringr_1.4.0   
[25] knitr_1.39       sass_0.4.1       fs_1.5.2         vctrs_0.4.1     
[29] rprojroot_2.0.3  glue_1.6.2       R6_2.5.1         processx_3.6.0  
[33] fansi_1.0.3      rmarkdown_2.14   callr_3.7.0      magrittr_2.0.3  
[37] whisker_0.4      ps_1.7.0         promises_1.2.0.1 htmltools_0.5.2 
[41] ellipsis_0.3.2   httpuv_1.6.5     utf8_1.2.2       stringi_1.7.6   
[45] crayon_1.5.1