Entering edit mode
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
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