I installed and opened the BiocManager package using this code:

install.packages('BiocManager')
library(BiocManager)

BiocManager::install('WGCNA')
BiocManager::install('flashClust')
BiocManager::install("GO.db")
BiocManager::install("impute")
BiocManager::install("preprocessCore")

But then I get this error

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13 ucrt)
Installation paths not writeable, unable to update packages
  path: C:/Program Files (x86)/R/R-4.5.1/library
  packages:
    boot, Matrix

So then i tried to update those two packages

> old.packages()
       Package  LibPath                                    Installed Built   ReposVer
boot   "boot"   "C:/Program Files (x86)/R/R-4.5.1/library" "1.3-31"  "4.5.1" "1.3-32"
Matrix "Matrix" "C:/Program Files (x86)/R/R-4.5.1/library" "1.7-3"   "4.5.1" "1.7-4" 
       Repository                            
boot   "https://cran.rstudio.com/src/contrib"
Matrix "https://cran.rstudio.com/src/contrib"
> update.packages(ask = FALSE)
Warning: package 'boot' in library 'C:/Program Files (x86)/R/R-4.5.1/library' will not be updated
Warning: package 'Matrix' in library 'C:/Program Files (x86)/R/R-4.5.1/library' will not be updated
# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session

Here is the session info.

sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default
LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] BiocManager_1.30.26

loaded via a namespace (and not attached):
[1] compiler_4.5.1 cli_3.6.5 tools_4.5.1

I am running this on a brand new windows laptop. When I update these packages from the packages tab it seems to go through but when I try to install the other packages they are still out of date.

I need to be able to use WGCNA for my phd work and it is frustrating I can't use it. Yesterday it was an issue with "broom" but that seems to have gone away and now the biggest problem is with "Go.db" which doesn't load at all and "boot" and "Matrix". I have deleted r from my laptop multiple times and completely wiped all files related to r. I have then redownloaded it and started from scratch over and over again. How can I fix this?

You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As an aside, those two packages (boot and Matrix) are recommended packages that come as part of the R installation. You installed R using administrator privileges, which means those two packages were installed using higher privileges than you are using as a regular user, which is why you cannot update them. You could do so if you ran R as an administrator, but that's orthogonal to the point, and you should never run R as an administrator unless you are just updating recommended packages.

It appears that WGCNA and GO.db were installed, because you are not providing any output that says that they were not.

If you plan to use R to any extent, you will need to learn to read the output and interpret what it means. You got output saying that boot and Matrix were not updated, and your response was to assume that WGCNA and GO.db were not installed, and to repeatedly remove and reinstall R and Bioconductor packages. Did you try loading either WGCNA or GO.db? The output from R (or any software, really) tends to be terse, but almost always contains sufficient information for you to proceed, so long as you interpret the information correctly. The message said that some unrelated packages were not updated. That's it! There was nothing about WGCNA or GO.db failing to install, and in fact you most likely got something that looks like this:

> install(c("WGCNA","GO.db"), force = TRUE)
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.20
  (BiocManager 1.30.25), R 4.4.1
  (2024-06-14 ucrt)
Installing package(s) 'WGCNA',
  'GO.db'
also installing the dependencies 'dynamicTreeCut', 'fastcluster'

trying URL 'https://cran.rstudio.org/bin/windows/contrib/4.4/dynamicTreeCut_1.63-1.zip'
Content type 'application/zip' length 92583 bytes (90 KB)
downloaded 90 KB

trying URL 'https://cran.rstudio.org/bin/windows/contrib/4.4/fastcluster_1.3.0.zip'
Content type 'application/zip' length 236791 bytes (231 KB)
downloaded 231 KB

trying URL 'https://cran.rstudio.org/bin/windows/contrib/4.4/WGCNA_1.73.zip'
Content type 'application/zip' length 3304090 bytes (3.2 MB)
downloaded 3.2 MB

package 'dynamicTreeCut' successfully unpacked and MD5 sums checked
package 'fastcluster' successfully unpacked and MD5 sums checked
package 'WGCNA' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\jmacdon\AppData\Local\Temp\Rtmp0kaJIJ\downloaded_packages
installing the source package 'GO.db'

trying URL 'https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz'
Content type 'application/gzip' length 26341489 bytes (25.1 MB)
downloaded 25.1 MB

* installing *source* package 'GO.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
package 'IRanges' was built under R version 4.4.2 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: package 'IRanges' was built under R version 4.4.2
** testing if installed package can be loaded from final location
Warning: package 'IRanges' was built under R version 4.4.2
** testing if installed package keeps a record of temporary installation path
* DONE (GO.db)

The downloaded source packages are in
    'C:\Users\jmacdon\AppData\Local\Temp\Rtmp0kaJIJ\downloaded_packages'
Installation paths not writeable,
  unable to update packages
  path: C:/Program Files/R/R-4.4.1/library
  packages:
    class, cluster, KernSmooth,
    lattice, mgcv, nnet, rpart,
    spatial, survival

Note that I have even more recommended packages that I did not update. But the part where it says DONE (GO.db), as well as

package 'dynamicTreeCut' successfully unpacked and MD5 sums checked
package 'fastcluster' successfully unpacked and MD5 sums checked
package 'WGCNA' successfully unpacked and MD5 sums checked

tells you that the packages have been installed.