[Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Jianhong Ou, Ph.D. j|@nhong@ou @end|ng |rom duke@edu
Fri Jun 14 15:57:47 CEST 2019

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks          13.97   0.02   14.84
parseWIG            12.81   0.00   12.94
browseTracks        12.04   0.00   12.69
geneModelFromTxdb    7.30   0.31    9.28
viewGene             5.15   0.11    5.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
> ### ** Examples
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) : 
  there is no package called 'org.Hs.eg.db'
Execution halted

On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." <bioc-devel-bounces using r-project.org on behalf of jianhong.ou using duke.edu> wrote:

    It is for a long time. Since last development version (BioC 3.9).
    From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
    Date: Friday, June 14, 2019 at 9:29 AM
    To: "Jianhong Ou, Ph.D." <jianhong.ou using duke.edu>, Michael Lawrence via Bioc-devel <bioc-devel using r-project.org>
    Subject: Re: CHECK ERROR in tokay1 for BioC 3.10
    How long as this ERROR occurred?
    I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no issues.   Let's wait and see if it clears up on todays build report.  If not we will investigate further.
    Lori Shepherd
    Bioconductor Core Team
    Roswell Park Cancer Institute
    Department of Biostatistics & Bioinformatics
    Elm & Carlton Streets
    Buffalo, New York 14263
    From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jianhong Ou, Ph.D. <jianhong.ou using duke.edu>
    Sent: Thursday, June 13, 2019 2:51:26 PM
    To: Michael Lawrence via Bioc-devel
    Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10
    The package trackViewer get check error in tokay1 (windows) say:
    Error in library(org.Hs.eg.db) :
      there is no package called 'org.Hs.eg.db'
    How could I debug this error? Thank you for your help.
    Yours Sincerely,
    Jianhong Ou
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