Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10
Hi Jianhong,
We found that another software package has code in its examples that
is reinstalling org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg18, and
TxDb.Hsapiens.UCSC.hg18.knownGene. This causes problems in the context
of the nightly builds were many packages are checked simultaneously.
After a long hunt, the software package causing these daily
reinstallations has been identified and his maintainer contacted.
Sorry for the inconvenience this has caused so far.
H.
On 6/14/19 07:16, Shepherd, Lori wrote:
> Thank you. We will investigate further and let you know when we have a
> solution on our end.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> From: Jianhong Ou, Ph.D.
> Sent: Friday, June 14, 2019 9:57:47 AM
> To: Shepherd, Lori; Michael Lawrence via Bioc-devel
> Subject: Re: [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
> parseWIG12.81 0.00 12.94
> browseTracks12.04 0.00 12.69
> geneModelFromTxdb7.30 0.319.28
> viewGene 5.15 0.115.26
> ** 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."
> wrote:
>
> It is for a long time. Since last development version (BioC 3.9).
>
> Jianhong.
>
> From: "Shepherd, Lori"
> Date: Friday, June 14, 2019 at 9:29 AM
> To: "Jianhong Ou, Ph.D." , Michael Lawrence via
> Bioc-devel
> 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 on behalf of
> Jianhong Ou, Ph.D.
> 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@r-project.org mailing list
>
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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10
Thank you. We will investigate further and let you know when we have a solution
on our end.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Jianhong Ou, Ph.D.
Sent: Friday, June 14, 2019 9:57:47 AM
To: Shepherd, Lori; Michael Lawrence via Bioc-devel
Subject: Re: [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
parseWIG12.81 0.00 12.94
browseTracks12.04 0.00 12.69
geneModelFromTxdb7.30 0.319.28
viewGene 5.15 0.115.26
** 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."
wrote:
It is for a long time. Since last development version (BioC 3.9).
Jianhong.
From: "Shepherd, Lori"
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via
Bioc-devel
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 on behalf of Jianhong
Ou, Ph.D.
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]]
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Re: [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
parseWIG12.81 0.00 12.94
browseTracks12.04 0.00 12.69
geneModelFromTxdb7.30 0.319.28
viewGene 5.15 0.115.26
** 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."
wrote:
It is for a long time. Since last development version (BioC 3.9).
Jianhong.
From: "Shepherd, Lori"
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via
Bioc-devel
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 on behalf of Jianhong
Ou, Ph.D.
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]]
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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10
It is for a long time. Since last development version (BioC 3.9).
Jianhong.
From: "Shepherd, Lori"
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via
Bioc-devel
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 on behalf of Jianhong Ou,
Ph.D.
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]]
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Re: [Bioc-devel] 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 on behalf of Jianhong Ou,
Ph.D.
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]]
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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
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