markdown source builds

Auto-generated via {sandpaper}
Source  : 97b9700
Branch  : main
Author  : Zhian N. Kamvar <zkamvar@gmail.com>
Time    : 2023-09-06 13:50:06 +0000
Message : update 26 packages (#73)

03-installing-bioconductor.md

@@ -159,58 +159,8 @@ If everything is up-to-date, the function will simply print `TRUE`.
 BiocManager::valid()
 ```
 
-```{.warning}
-Warning: 16 packages out-of-date; 0 packages too new
-```
-
 ```{.output}
-
-* sessionInfo()
-
-R version 4.3.1 (2023-06-16)
-Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 22.04.3 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=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
- [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
- [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
-[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
-
-time zone: UTC
-tzcode source: system (glibc)
-
-attached base packages:
-[1] stats     graphics  grDevices utils     datasets  methods   base     
-
-other attached packages:
-[1] BiocStyle_2.28.0
-
-loaded via a namespace (and not attached):
- [1] BiocManager_1.30.21 compiler_4.3.1      fastmap_1.1.1      
- [4] cli_3.6.1           htmltools_0.5.5     tools_4.3.1        
- [7] yaml_2.3.7          rmarkdown_2.23      knitr_1.43         
-[10] digest_0.6.33       xfun_0.39           rlang_1.1.1        
-[13] renv_1.0.1          evaluate_0.21      
-
-Bioconductor version '3.17'
-
-  * 16 packages out-of-date
-  * 0 packages too new
-
-create a valid installation with
-
-  BiocManager::install(c(
-    "BiocManager", "bookdown", "bslib", "cpp11", "curl", "DelayedArray", "fs",
-    "htmltools", "MatrixGenerics", "openssl", "renv", "rmarkdown", "S4Arrays",
-    "sass", "tinytex", "xfun"
-  ), update = TRUE, ask = FALSE, force = TRUE)
-
-more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
+[1] TRUE
 ```
 
 Conveniently, if any package can be updated, the function generates and displays the command needed to update those packages.
@@ -286,7 +236,7 @@ length(BiocManager::available())
 ```
 
 ```{.output}
-[1] 23454
+[1] 23382
 ```
 
 Specifically, the current Bioconductor and CRAN repositories can be displayed as follows.

md5sum.txt

@@ -1,18 +1,18 @@
 "file" "checksum" "built" "date"
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-"config.yaml" "136b895030e91653fc32afb614ad6812" "site/built/config.yaml" "2023-08-15"
-"index.md" "6cf23d25cc71edcff0cdd1f6d60039da" "site/built/index.md" "2023-08-15"
-"episodes/01-setup.Rmd" "052eaf8fb2a945b10aafd94e1b906abc" "site/built/01-setup.md" "2023-08-15"
-"episodes/02-introduction-to-bioconductor.Rmd" "95db83520fedb68fb63fc660fb583ff5" "site/built/02-introduction-to-bioconductor.md" "2023-08-15"
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-"episodes/04-getting-help.Rmd" "d6145a8228a881508820e4b95b99b61b" "site/built/04-getting-help.md" "2023-08-15"
-"episodes/05-s4.Rmd" "e97eed7893703ad409eb937d95e357b1" "site/built/05-s4.md" "2023-08-15"
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+"episodes/07-genomic-ranges.Rmd" "1678d11e207781b420e36810e603000b" "site/built/07-genomic-ranges.md" "2023-09-06"
+"instructors/instructor-notes.md" "a848c3b904c16f0840e7ec385de58d7d" "site/built/instructor-notes.md" "2023-09-06"
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