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After updating to R 3.5.0 and Bioconductor 3.7, I discovered that initializing an AnnotationHub object (version 2.12.0) is problematically verbose. I tried wiping the cached annotationhub.sqlite3 and index.rds, but that didn't fix the problem. The verbosity cannot be suppressed by suppressMessages() or suppressWarnings().
Please see an example and my sessionInfo below.
Thank you in advance for your help!
Thank you,
Rob
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
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> > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> library (AnnotationHub)
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, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
> ah = AnnotationHub()
updating metadata: retrieving 1 resource
|======================================================================| 100%
MAPPING START: ((null)) [(null)]
SCALAR: output_dir ((null)) [(null)]
Value: (output_dir), Tag: (str)
SCALAR: output ((null)) [(null)]
Value: (output), Tag: (str)
SCALAR: staging_deploy_root ((null)) [(null)]
Value: (staging_deploy_root), Tag: (str)
SCALAR: biocadmin@staging.bioconductor.org:/loc/www/bioconductor-test.fhcrc.org ((null)) [(null)]
Value: (biocadmin@staging.bioconductor.org:/loc/www/bioconductor-test.fhcrc.org), Tag: (str)
SCALAR: production_deploy_root ((null)) [(null)]
Value: (production_deploy_root), Tag: (str)
SCALAR: webadmin@master.bioconductor.org:/extra/www/bioc ((null)) [(null)]
Value: (webadmin@master.bioconductor.org:/extra/www/bioc), Tag: (str)
SCALAR: release_version ((null)) [(null)]
Value: (release_version), Tag: (str)
SCALAR: 3.7 ((null)) [(null)]
Value: (3.7), Tag: (str)
SCALAR: r_version_associated_with_release ((null)) [(null)]
Value: (r_version_associated_with_release), Tag: (str)
SCALAR: 3.5.0 ((null)) [(null)]
Value: (3.5.0), Tag: (str)
SCALAR: devel_version ((null)) [(null)]
Value: (devel_version), Tag: (str)
SCALAR: 3.8 ((null)) [(null)]
Value: (3.8), Tag: (str)
SCALAR: versions ((null)) [(null)]
Value: (versions), Tag: (str)
SEQUENCE START: ((null)) [(null)]
SCALAR: 3.7 ((null)) [(null)]
Value: (3.7), Tag: (str)
SCALAR: 3.8 ((null)) [(null)]
...output omitted due to limit of field length...
SCALAR: mirroradmin@tuna.tsinghua.edu.cn ((null)) [(null)]
Value: (mirroradmin@tuna.tsinghua.edu.cn), Tag: (str)
SCALAR: mirror_url ((null)) [(null)]
Value: (mirror_url), Tag: (str)
SCALAR: http://mirrors.tuna.tsinghua.edu.cn/bioconductor/ ((null)) [(null)]
Value: (http://mirrors.tuna.tsinghua.edu.cn/bioconductor/), Tag: (str)
SCALAR: https_mirror_url ((null)) [(null)]
Value: (https_mirror_url), Tag: (str)
SCALAR: https://mirrors.tuna.tsinghua.edu.cn/bioconductor/ ((null)) [(null)]
Value: (https://mirrors.tuna.tsinghua.edu.cn/bioconductor/), Tag: (str)
SCALAR: rsync ((null)) [(null)]
Value: (rsync), Tag: (str)
SCALAR: secure_mirror_from_master ((null)) [(null)]
Value: (secure_mirror_from_master), Tag: (str)
SCALAR: country_code ((null)) [(null)]
Value: (country_code), Tag: (str)
SCALAR: cn ((null)) [(null)]
Value: (cn), Tag: (str)
SCALAR: city ((null)) [(null)]
Value: (city), Tag: (str)
SCALAR: Peking ((null)) [(null)]
Value: (Peking), Tag: (str)
MAPPING END
SEQUENCE END
MAPPING END
SEQUENCE END
MAPPING END
snapshotDate(): 2018-04-23
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] AnnotationHub_2.12.0 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 AnnotationDbi_1.42.1
[3] magrittr_1.5 IRanges_2.14.8
[5] bit_1.1-12 xtable_1.8-2
[7] R6_2.2.2 blob_1.1.1
[9] httr_1.3.1 tools_3.5.0
[11] Biobase_2.40.0 DBI_1.0.0
[13] htmltools_0.3.6 yaml_2.1.19
[15] bit64_0.9-7 digest_0.6.15
[17] interactiveDisplayBase_1.18.0 shiny_1.0.5
[19] later_0.7.2 S4Vectors_0.18.1
[21] promises_1.0.1 curl_3.2
[23] memoise_1.1.0 RSQLite_2.1.1
[25] mime_0.5 compiler_3.5.0
[27] BiocInstaller_1.30.0 stats4_3.5.0
[29] httpuv_1.4.3 pkgconfig_2.0.1
My inquiry above is related to, but distinct from, my previous question regarding a "quiet" mode for AnnotationHub:
A: "quiet" mode for AnnotationHub?
As you can see from the response to my question above, suppressMessages() or invisible() was sufficient to prevent the messages. The messages are now much more verbose and cannot be suppressed by suppressMessages() or invisible().