I have an error in ArrayExpressHTS that comes from BioBase. I can't figure out how to tag BioBase in that post, so I'm reposting with the relevant tag here.

ArrayExpressHTS emits this error on loading:

No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’

This results in failure of ArrayExpressHTS(), as reported here: https://support.bioconductor.org/p/128736/

Both R and Bioconductor are up to date, and I rebuilt all my packages in a new site library. Here is the full output of 'library(ArrayExpressHTS):

> library(ArrayExpressHTS)
Loading required package: sampling
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: snow

Attaching package: ‘snow’

The following objects are masked from ‘package:BiocGenerics’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’
Wed Mar  4 11:03:07 2020 [AEHTS] Setting Options Step 1
Wed Mar  4 11:03:07 2020 [AEHTS] Setting Options Step 2
Wed Mar  4 11:03:07 2020 [AEHTS] Setting Options Step 3
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/fasta_formatter
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/fastx-toolkit-0.0.13 defined in the 'ArrayExpressHTS.fasta_formatter' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/cufflinks
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/cufflinks-1.1.0.Linux_x86_64 defined in the 'ArrayExpressHTS.cufflinks' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/samtools
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/samtools-0.1.18 defined in the 'ArrayExpressHTS.samtools' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/bwa
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/bwa-0.5.9 defined in the 'ArrayExpressHTS.bwa' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     mmseq not found
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Mar  4 11:03:07 2020 [AEHTS] Use .Rprofile to make options persistent.
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     bam2hits not found
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Mar  4 11:03:07 2020 [AEHTS] Use .Rprofile to make options persistent.
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/bowtie
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/bowtie-0.12.7 defined in the 'ArrayExpressHTS.bowtie' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS] Found /usr/bin/tophat
Wed Mar  4 11:03:07 2020 [AEHTS] *** WARNING ***
Wed Mar  4 11:03:07 2020 [AEHTS] 
Wed Mar  4 11:03:07 2020 [AEHTS]     /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/tophat-1.3.2.Linux_x86_64 defined in the 'ArrayExpressHTS.tophat' option
Wed Mar  4 11:03:07 2020 [AEHTS] 
>

As always, sessionInfo():

> 
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] ArrayExpressHTS_1.36.0 snow_0.4-3             Rsamtools_2.2.3       
 [4] Biostrings_2.54.0      XVector_0.26.0         GenomicRanges_1.38.0  
 [7] GenomeInfoDb_1.22.0    IRanges_2.20.2         S4Vectors_0.24.3      
[10] BiocGenerics_0.32.0    sampling_2.8          

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.55.0         
 [3] R2HTML_2.3.2                bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.2             
 [7] httr_1.4.1                  tools_3.6.3                
 [9] backports_1.1.5             R6_2.4.1                   
[11] rpart_4.1-15                Hmisc_4.3-1                
[13] DBI_1.1.0                   lazyeval_0.2.2             
[15] colorspace_1.4-1            nnet_7.3-13                
[17] tidyselect_1.0.0            gridExtra_2.3              
[19] prettyunits_1.1.1           curl_4.3                   
[21] bit_1.1-15.2                compiler_3.6.3             
[23] sendmailR_1.2-1             Biobase_2.46.0             
[25] htmlTable_1.13.3            DelayedArray_0.12.2        
[27] scales_1.1.0                checkmate_2.0.0            
[29] genefilter_1.68.0           askpass_1.1                
[31] rappdirs_0.3.1              DESeq_1.38.0               
[33] stringr_1.4.0               digest_0.6.25              
[35] foreign_0.8-75              base64enc_0.1-3            
[37] jpeg_0.1-8.1                pkgconfig_2.0.3            
[39] htmltools_0.4.0             limma_3.42.2               
[41] dbplyr_1.4.2                htmlwidgets_1.5.1          
[43] rlang_0.4.5                 rstudioapi_0.11            
[45] RSQLite_2.2.0               hwriter_1.3.2              
[47] BiocParallel_1.20.1         acepack_1.4.1              
[49] dplyr_0.8.4                 RCurl_1.98-1.1             
[51] magrittr_1.5                GenomeInfoDbData_1.2.2     
[53] Formula_1.2-3               Matrix_1.2-18              
[55] Rcpp_1.0.3                  munsell_0.5.0              
[57] lifecycle_0.1.0             edgeR_3.28.1               
[59] stringi_1.4.6               MASS_7.3-51.5              
[61] SummarizedExperiment_1.16.1 zlibbioc_1.32.0            
[63] BiocFileCache_1.10.2        grid_3.6.3                 
[65] blob_1.2.1                  crayon_1.3.4               
[67] lattice_0.20-40             splines_3.6.3              
[69] annotate_1.64.0             hms_0.5.3                  
[71] locfit_1.5-9.1              knitr_1.28                 
[73] pillar_1.4.3                geneplotter_1.64.0         
[75] biomaRt_2.42.0              lpSolve_5.6.15             
[77] XML_3.99-0.3                glue_1.3.1                 
[79] ShortRead_1.44.3            latticeExtra_0.6-29        
[81] data.table_1.12.8           png_0.1-7                  
[83] vctrs_0.2.3                 gtable_0.3.0               
[85] openssl_1.4.1               purrr_0.3.3                
[87] assertthat_0.2.1            ggplot2_3.2.1              
[89] xfun_0.12                   xtable_1.8-4               
[91] svMisc_1.1.0                survival_3.1-8             
[93] tibble_2.1.3                rJava_0.9-11               
[95] GenomicAlignments_1.22.1    AnnotationDbi_1.48.0       
[97] memoise_1.1.0               cluster_2.1.0              
>