When I tried to use the annotateEset function in affycoretools, it complains and output the following message.

>annotateEset()
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'annotateEset' for signature '"missing", "missing"'

I re-installed the affycoretools package and it appears the annotateEset function is just a holder ...

annotateEset                            html  
Rd warning: /tmp/RtmpE53Lt8/R.INSTALL40a34bd7bc8a/affycoretools/man/annotateEset.Rd:47: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpE53Lt8/R.INSTALL40a34bd7bc8a/affycoretools/man/annotateEset.Rd:50: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic

So it complains about not finding columns and mapIds functions from AnnotationDbi package so re-installed that and checked for existence of the missing two functions below.

> columns
nonstandardGenericFunction for "columns" defined from package "AnnotationDbi"

function (x)
{
    value <- standardGeneric("columns")
    sort(value)
}
<bytecode: 0x563dec99a368>
<environment: 0x563dec9ae258>
Methods may be defined for arguments: x
Use  showMethods("columns")  for currently available ones.
> mapIds
standardGeneric for "mapIds" defined from package "AnnotationDbi"

function (x, keys, column, keytype, ..., multiVals)
standardGeneric("mapIds")
<bytecode: 0x563df0aa2398>
<environment: 0x563df0a9b790>
Methods may be defined for arguments: x
Use  showMethods("mapIds")  for currently available ones.

So both functions exists in AnnotationDbi so I don't know why affycoretools is not able to locate them =/.

Below is my session info if that helps with the diagnostics.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 27 (Twenty Seven)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] affycoretools_1.52.1 AnnotationDbi_1.42.1 IRanges_2.14.10     
[4] S4Vectors_0.18.3     Biobase_2.40.0       BiocGenerics_0.26.0
[7] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            hwriter_1.3.2              
  [3] biovizBase_1.28.0           htmlTable_1.12             
  [5] XVector_0.20.0              GenomicRanges_1.32.3       
  [7] base64enc_0.1-3             dichromat_2.0-0            
  [9] rstudioapi_0.7              affyio_1.50.0              
 [11] bit64_0.9-7                 codetools_0.2-15           
 [13] oligoClasses_1.42.0         splines_3.5.0              
 [15] R.methodsS3_1.7.1           ggbio_1.28.0               
 [17] geneplotter_1.58.0          knitr_1.20                 
 [19] Formula_1.2-3               Rsamtools_1.32.0           
 [21] annotate_1.58.0             cluster_2.0.7-1            
 [23] GO.db_3.6.0                 R.oo_1.22.0                
 [25] graph_1.58.0                compiler_3.5.0             
 [27] httr_1.3.1                  GOstats_2.46.0             
 [29] backports_1.1.2             assertthat_0.2.0           
 [31] Matrix_1.2-14               lazyeval_0.2.1             
 [33] limma_3.36.2                acepack_1.4.1              
 [35] htmltools_0.3.6             prettyunits_1.0.2          
 [37] tools_3.5.0                 gtable_0.2.0               
 [39] GenomeInfoDbData_1.1.0      affy_1.58.0                
 [41] Category_2.46.0             reshape2_1.4.3             
 [43] Rcpp_0.12.17                Biostrings_2.48.0          
 [45] gdata_2.18.0                preprocessCore_1.42.0      
 [47] rtracklayer_1.40.3          iterators_1.0.9            
 [49] stringr_1.3.1               ensembldb_2.4.1            
 [51] gtools_3.5.0                XML_3.98-1.11              
 [53] edgeR_3.22.3                zlibbioc_1.26.0            
 [55] scales_0.5.0                BSgenome_1.48.0            
 [57] VariantAnnotation_1.26.0    hms_0.4.2                  
 [59] ProtGenerics_1.12.0         SummarizedExperiment_1.10.1
 [61] RBGL_1.56.0                 AnnotationFilter_1.4.0     
 [63] RColorBrewer_1.1-2          curl_3.2                   
 [65] memoise_1.1.0               gridExtra_2.3              
 [67] ggplot2_2.2.1               biomaRt_2.36.1             
 [69] rpart_4.1-13                gcrma_2.52.0               
 [71] reshape_0.8.7               latticeExtra_0.6-28        
 [73] stringi_1.2.3               RSQLite_2.1.1              
 [75] genefilter_1.62.0           foreach_1.4.4              
 [77] checkmate_1.8.5             caTools_1.17.1             
 [79] GenomicFeatures_1.32.0      BiocParallel_1.14.1        
 [81] GenomeInfoDb_1.16.0         ReportingTools_2.20.0      
 [83] rlang_0.2.1                 pkgconfig_2.0.1            
 [85] matrixStats_0.53.1          bitops_1.0-6               
 [87] lattice_0.20-35             GenomicAlignments_1.16.0   
 [89] htmlwidgets_1.2             bit_1.1-14                 
 [91] GSEABase_1.42.0             AnnotationForge_1.22.0     
 [93] GGally_1.4.0                plyr_1.8.4                 
 [95] magrittr_1.5                DESeq2_1.20.0              
 [97] R6_2.2.2                    gplots_3.0.1               
 [99] Hmisc_4.1-1                 DelayedArray_0.6.1         
[101] DBI_1.0.0                   pillar_1.2.3               
[103] foreign_0.8-70              survival_2.42-3            
[105] RCurl_1.95-4.10             nnet_7.3-12                
[107] tibble_1.4.2                crayon_1.3.4               
[109] KernSmooth_2.23-15          OrganismDbi_1.22.0         
[111] PFAM.db_3.6.0               progress_1.2.0             
[113] locfit_1.5-9.1              grid_3.5.0                 
[115] data.table_1.11.4           blob_1.1.1                 
[117] Rgraphviz_2.24.0            digest_0.6.15              
[119] xtable_1.8-2                ff_2.2-14                  
[121] R.utils_2.6.0               munsell_0.5.0              
[123] tcltk_3.5.0 

If you try to run a function that has required arguments, but you don't supply any arguments, you should not be surprised that things don't work correctly. What did you think

annotateEset()

Would do? If you don't give it an ExpressionSet to annotate, nor an annotation package to use, I am not sure what the expectation should be.

Also, you are misdiagnosing the warnings you see when installing. Those have to do with the help pages, and won't have any effect on the function at all.