Message-ID: <0F035ADC-B694-44BF-B7D0-5069807DADA6@duke.edu>
Date: 2019-06-14T13:57:47Z
From: Jianhong Ou, Ph.D.
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10
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 at r-project.org on behalf of jianhong.ou at duke.edu> wrote:
It is for a long time. Since last development version (BioC 3.9).
Jianhong.
From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org>
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." <jianhong.ou at duke.edu>, Michael Lawrence via Bioc-devel <bioc-devel at 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 at r-project.org> on behalf of Jianhong Ou, Ph.D. <jianhong.ou at 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
Hi,
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
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=w1a47iv59l8nsY8T-xeFNWhvFbEegIYemPNynykYXbI&s=sS64xiJgMU6JG1EgM1BIVIGx-BznK5d-JXAxiQ_yMjQ&e=<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=LQSP_bwpXYhO_adZGDjjJJ1zSlnIz5xu-a8JKZOSAwA&s=eCgeOhbMl0xJqBOkvcPavnS8VND88QmrFbuyZdO47wY&e=>
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=w1a47iv59l8nsY8T-xeFNWhvFbEegIYemPNynykYXbI&s=sS64xiJgMU6JG1EgM1BIVIGx-BznK5d-JXAxiQ_yMjQ&e=