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differences for PR #95
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actions-user committed Aug 6, 2024
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50 changes: 2 additions & 48 deletions 03-installing-bioconductor.md
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Expand Up @@ -148,54 +148,8 @@ If everything is up-to-date, the function will simply print `TRUE`.
BiocManager::valid()
```

``` warning
Warning: 1 packages out-of-date; 0 packages too new
```

``` output
* sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 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_2.32.1
loaded via a namespace (and not attached):
[1] BiocManager_1.30.23 compiler_4.4.1 fastmap_1.2.0
[4] cli_3.6.3 htmltools_0.5.8.1 tools_4.4.1
[7] yaml_2.3.10 rmarkdown_2.27 knitr_1.48
[10] digest_0.6.36 xfun_0.46 rlang_1.1.4
[13] renv_1.0.7 evaluate_0.24.0
Bioconductor version '3.19'
* 1 packages out-of-date
* 0 packages too new
create a valid installation with
BiocManager::install("withr", 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.
Expand Down Expand Up @@ -271,7 +225,7 @@ length(BiocManager::available())
```

``` output
[1] 24742
[1] 24752
```

Specifically, the union of current Bioconductor repositories and other repositories on the search path can be displayed as follows.
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87 changes: 0 additions & 87 deletions config.yaml
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38 changes: 19 additions & 19 deletions md5sum.txt
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@@ -1,20 +1,20 @@
"file" "checksum" "built" "date"
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