[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

Here you go ...

sessionInfo()

R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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

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

other attached packages:
[1] AnnotationHub_1.99.72 BiocInstaller_1.17.5

loaded via a namespace (and not attached):
  [1] Rcpp_0.11.5                  IRanges_2.1.43
  [3] digest_0.6.8                 bitops_1.0-6
  [5] mime_0.2                     GenomeInfoDb_1.3.13
  [7] R6_2.0.1                     xtable_1.7-4
  [9] DBI_0.3.1                    stats4_3.2.0
[11] RSQLite_1.0.0                httr_0.6.1
[13] S4Vectors_0.5.22             RJSONIO_1.3-0
[15] stringr_0.6.2                Biobase_2.27.2
[17] RCurl_1.95-4.5               shiny_0.11.1
[19] httpuv_1.3.2                 parallel_3.2.0
[21] BiocGenerics_0.13.6          AnnotationDbi_1.29.17
[23] htmltools_0.2.6              interactiveDisplayBase_1.5.1

Please provide sessionInfo()

The class is defined in AnnotationHub in devel.  Perhaps it is not
suitably
exported.

On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

Hi,

As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)

docker run -ti bioconductor/release_core R

and then executed

library(AnnotationHub)
hub <- AnnotationHub()

and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter, April 2015)

h <- hub[hub$rdataclass == "ExpressionSet"]
h

AnnotationHub with 1 record
# snapshotDate(): 2015-03-26
# names(): AH28855
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from
The
C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
tum...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944
#
$sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["AH28855"]]'

and then tried to retrieve the record with either

h[["AH28855"]]

or

h[[1]]

I received the following error:

Error in value[[3L]](cond) :
   failed to create a 'AnnotationHubResource' instance for hub resource
     ???RNA-Sequencing and clinical data for 7706 tumor samples from The
     Cancer Genome Atlas??? of class ExpressionSet; reason:
     ???ExpressionSetResource??? is not a defined class


Did I do something wrong?
Thank you for your help,
Ludwig


--
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit f??r Bioinformatik
Institut f??r Informatik
Ludwig-Maximilians-Universit??t M??nchen
Amalienstrasse 17, 2. Stock, B??ro A201
80333 M??nchen

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de