markdown source builds

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Source  : 192a35f
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2025-08-26 15:38:41 +0000
Message : Merge pull request datacarpentry#313 from datacarpentry/update/packages

Author: actions-user

03-basics-factors-dataframes.md

@@ -687,17 +687,13 @@ install.packages("ggplot2")
 ```
 
 ``` output
-# Downloading packages -------------------------------------------------------
-- Downloading ggplot2 from https://packagemanager.posit.co/cran/__linux__/jammy/latest ... OK [4.8 Mb in 0.39s]
-Successfully downloaded 1 package in 1.8 seconds.
-
 The following package(s) will be installed:
 - ggplot2 [3.5.2]
 These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/linux-ubuntu-jammy/R-4.5/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
-- Installing ggplot2 ...                        OK [installed binary and cached in 0.71s]
-Successfully installed 1 package in 0.78 seconds.
+- Installing ggplot2 ...                        OK [linked from cache]
+Successfully installed 1 package in 4.9 milliseconds.
 ```
 
 ``` r
@@ -711,7 +707,7 @@ These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/
 
 # Installing packages --------------------------------------------------------
 - Installing dplyr ...                          OK [linked from cache]
-Successfully installed 1 package in 4.4 milliseconds.
+Successfully installed 1 package in 4 milliseconds.
 ```
 
 These two packages are among the most popular add on packages used in R, and they are part of a large set of very useful packages called the [tidyverse](https://www.tidyverse.org). Packages in the tidyverse are designed to work well together and are made to work with tidy data (which we described earlier in this lesson).

05-dplyr.md

@@ -778,16 +778,16 @@ variants %>%
 # A tibble: 801 × 4
    sample_id      POS  QUAL POLPROB
    <chr>        <dbl> <dbl>   <dbl>
- 1 SRR2584863    9972    91    1.00
- 2 SRR2584863  263235    85    1.00
- 3 SRR2584863  281923   217    1   
- 4 SRR2584863  433359    64    1.00
- 5 SRR2584863  473901   228    1   
- 6 SRR2584863  648692   210    1   
- 7 SRR2584863 1331794   178    1   
- 8 SRR2584863 1733343   225    1   
- 9 SRR2584863 2103887    56    1.00
-10 SRR2584863 2333538   167    1   
+ 1 SRR2584863    9972    91   1.000
+ 2 SRR2584863  263235    85   1.000
+ 3 SRR2584863  281923   217   1    
+ 4 SRR2584863  433359    64   1.000
+ 5 SRR2584863  473901   228   1    
+ 6 SRR2584863  648692   210   1    
+ 7 SRR2584863 1331794   178   1    
+ 8 SRR2584863 1733343   225   1    
+ 9 SRR2584863 2103887    56   1.000
+10 SRR2584863 2333538   167   1    
 # ℹ 791 more rows
 ```
 

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