Hello, to learn using topGO I try to follow the associated vignette, however I run into a problem of not finding the ALL library which is necessary in section 3.1 Data preparation.

Please see below the steps I followed from the vignette and response from the terminal for the consequent steps before I encountered the problem:

Section 2 Installation

#copied from the pdf vignette start

> if (!requireNamespace("BiocManager", quietly=TRUE))
+   install.packages("BiocManager")
> BiocManager::install()
#copied from the pdf vignette end

Bioconductor version 3.10
  (BiocManager 1.30.10), R 3.6.3
  (2020-02-29)
Installation path not writeable,
  unable to update packages: boot,
  class, KernSmooth, lattice,
  MASS, nlme, nnet, spatial,
  survival
Old packages: 'openxlsx', 'tidyr'
Update all/some/none? [a/s/n]: 
a

  There are binary versions
  available but the source
  versions are later:
         binary source
openxlsx  4.1.4  4.1.5
tidyr     1.0.2  1.0.3
         needs_compilation
openxlsx              TRUE
tidyr                 TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/openxlsx_4.1.4.zip'
Content type 'application/zip' length 2575544 bytes (2.5 MB)
downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyr_1.0.2.zip'
Content type 'application/zip' length 1298171 bytes (1.2 MB)
downloaded 1.2 MB

package ‘openxlsx’ successfully unpacked and MD5 sums checked
package ‘tidyr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\vladi\AppData\Local\Temp\RtmpAh9g9H\downloaded_packages

"we can install the topGO package by"

#copied from the pdf vignette start
> if (!requireNamespace("BiocManager", quietly=TRUE))
+     + install.packages("BiocManager")
> BiocManager::install("topGO")
#copied from the pdf vignette end

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'topGO'
Warning: package ‘topGO’ is in use and will not be installed
Installation path not writeable, unable to update packages: boot, class, KernSmooth,
  lattice, MASS, nlme, nnet, spatial, survival
Old packages: 'openxlsx', 'tidyr'
Update all/some/none? [a/s/n]: 
n
> 

section 3.1 Data preparation

> library(topGO)
> library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
> data(ALL)
Warning message:
In data(ALL) : data set ‘ALL’ not found

Session info

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel 
[3] stats     graphics 
[5] grDevices utils    
[7] datasets  methods  
[9] base     

other attached packages:
[1] topGO_2.38.1        
[2] SparseM_1.78        
[3] GO.db_3.10.0        
[4] AnnotationDbi_1.48.0
[5] IRanges_2.20.2      
[6] S4Vectors_0.24.4    
[7] Biobase_2.46.0      
[8] graph_1.64.0        
[9] BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       
 [2] bit_1.1-15.2       
 [3] lattice_0.20-38    
 [4] rlang_0.4.6        
 [5] blob_1.2.1         
 [6] tools_3.6.3        
 [7] grid_3.6.3         
 [8] packrat_0.5.0      
 [9] DBI_1.1.0          
[10] matrixStats_0.56.0 
[11] bit64_0.9-7        
[12] digest_0.6.25      
[13] BiocManager_1.30.10
[14] vctrs_0.2.4        
[15] memoise_1.1.0      
[16] RSQLite_2.2.0      
[17] compiler_3.6.3     
[18] pkgconfig_2.0.3    
> 

Thank you very much for your help, I am very new in the field, so please excuse and let me know of any breaches of etiquette. Best Regards Vladimir

Any time you see a message that there is no package named (in this instance ALL), that simply means that it hasn't been installed yet.