Last updated: 2022-06-14

Checks: 7 0

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

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Cache: none

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File paths: relative

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Repository version: b6e0993

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 b6e0993. 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: 


Unstaged changes:
    Modified:   .RData
    Modified:   .Rhistory

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
html 93a27ae chenh19 2022-06-14 Build site.
html 27121a9 chenh19 2022-06-14 Build site.
Rmd fce1ffd chenh19 2022-06-14 wflow_publish("analysis/*.Rmd")
html 44517c1 chenh19 2022-06-13 Build site.
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Rmd 6b42cc9 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 08a2f76 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd c43ae1f chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 6578184 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 6e56d75 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 63f46d2 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 84dc8ba chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd ead84c2 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 2ccaa57 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 9d84983 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
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Rmd 26f455b chenh19 2022-06-13 update
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1. 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 add --all
git push -u origin main

Environment: Kubuntu 22.04 LTS

2. 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): Thur 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

3. 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

4. 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

5. Watering Ran’s plant

  • 6/13/22 10:30am

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     bslib_0.3.1      compiler_4.2.0   pillar_1.7.0    
 [5] later_1.3.0      git2r_0.30.1     jquerylib_0.1.4  tools_4.2.0     
 [9] getPass_0.2-2    digest_0.6.29    jsonlite_1.8.0   evaluate_0.15   
[13] tibble_3.1.7     lifecycle_1.0.1  pkgconfig_2.0.3  rlang_1.0.2     
[17] cli_3.3.0        rstudioapi_0.13  yaml_2.3.5       xfun_0.31       
[21] fastmap_1.1.0    httr_1.4.3       stringr_1.4.0    knitr_1.39      
[25] sass_0.4.1       fs_1.5.2         vctrs_0.4.1      rprojroot_2.0.3 
[29] glue_1.6.2       R6_2.5.1         processx_3.6.0   fansi_1.0.3     
[33] rmarkdown_2.14   callr_3.7.0      magrittr_2.0.3   whisker_0.4     
[37] ps_1.7.0         promises_1.2.0.1 htmltools_0.5.2  ellipsis_0.3.2  
[41] httpuv_1.6.5     utf8_1.2.2       stringi_1.7.6    crayon_1.5.1