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              

I don't see that output in my session. I'd guess that this comes from these lines of AnnotationHub code

    library(httr); library(yaml)
    yaml <- content(GET("http://bioconductor.org/config.yaml"), 
                    encoding="UTF-8", as="text")
    obj <- yaml.load(yaml)

It seems to come from the yaml library, installed with the 'DEBUG' flag set:

> download.package("yaml", ".", repos = BiocInstaller::biocinstallRepos(), type = "source")
> quit()
$ tar xzf yaml_*gz
$ cd yaml
yaml$ grep -C2 -r "SCALAR:" *
src/r_parse.c-        case YAML_SCALAR_EVENT:
src/r_parse.c-#if DEBUG
src/r_parse.c:          Rprintf("SCALAR: %s (%s) [%s]\n", event.data.scalar.value, event.data.scalar.tag, event.data.scalar.anchor);
src/r_parse.c-#endif
src/r_parse.c-          err = handle_scalar(&event, &s_stack_tail, s_handlers, eval_expr, eval_warning);
yaml$

If you installed from source on your end, then disable the DEBUG flag, otherwise it's an upstream problem for the yaml maintainer; let me know and I'll follow up with them.