[Bioc-devel] Package "rmspc" failing on Bioconductor devel

[Meriem Bahda]

Dear Community,

I have submitted the package rmspc to Bioconductor in July 2021. A
prerequisite for the rmspc package is .NET 5.0. Before installing the
rmspc package,
the program .NET 5.0. should already be installed on the user's computer.
The Bioconductor team added .NET to their builders and the package was
accepted in August 2021.

A few days ago, I received an email saying that the package didn't pass the
platform build check for the host *lconway*. I believe this error may have
occured because .NET isn't installed in  *lconway*.

Who should I contact regarding this issue?

Thank you!

-- 

*Meriem BAHDA*

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Re: [Bioc-devel] Package Classifications via BiocViews

[Hervé Pagès]

On 28/09/2022 16:03, Hervé Pagès wrote:


Hi Burak,

Based on your description of what the package does, this is really a 
software package in nature, so is in the wrong repository. We need to 
fix this.


In 4 steps:

1. Please remove the ExperimentData term from the biocViews field as 
well as any term that belongs to the ExperimentData ontology, that is: 
DiseaseModel, OrganismData, Homo_sapiens_Data, Mus_musculus_Data, 
Rattus_norvegicus_Data, TechnologyData, MicroarrayData, 
SequencingData, and RNASeqData. Yep, most of your terms will go away.


After taking a second look I realize that **all** your current terms are 
from the ExperimentData ontology, instead of being a mix of Software and 
ExperimentData terms as I thought initially. So they should all be removed.




2. Add the Software term, in first position. You're welcome to add new 
terms if you want, from the following vocabulary: 
https://github.com/Bioconductor/biocViews/blob/master/inst/dot/biocViewsVocab.dot. 
Please make sure to pick terms that belong to the Software ontology 
(i.e. are offsprings of the Software term).


You should definitely add new terms from the Software ontology!

Thanks,

H.



3. Bump the package version (only the z part in x.y.z), and push your 
changes to git.bioconductor.org.


4. Let us know when you're done. We'll make the required adjustments 
on our side.


Thanks,

H.

On 28/09/2022 09:37, Burak Ogan Mancarci wrote:

Apologies for the inconvenience.

The change isn't essential on our end and can be avoided or delayed 
if you
think the ExperimentData label can be applied to a package 
responsible for

accessing data from a database rather than storing static data. We were
only worried about misleading use of biocviews terms.

Cheers,
Ogan

On Wed., Sep. 28, 2022, 14:26 Kern, Lori, 


wrote:

Changing the biocviews is not sufficient.  There needs to be work on 
our
end to change the manifest the package belongs to and to clear the 
build
products from the data repositories so it is only found in one 
location.


Are you sure you want to proceed with switching?  It is not trivial 
on our

end.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
--
*From:* Bioc-devel  on behalf of 
Burak

Ogan Mancarci 
*Sent:* Wednesday, September 28, 2022 9:17 AM
*To:* bioc-devel@r-project.org 
*Subject:* [Bioc-devel] Package Classifications via BiocViews

Hi,

I am a developer working on the bioconductor package gemma.R
<
https://secure-web.cisco.com/1wIQY41Mq8CRYqLq1luoPm43XSj6Icl27w6udr35y-BxPHgEP6B5pApAAeBdBeWsydixV0CSwBVIVl2C7mJykPI3ESX7qtp-xJOSvJAu4T1yzHr3CWRc7s6LY_WtIcrnzfyw3MI7z0oqv1hzA1x5oRN1kFZ-KF6tttbi86SwIwZhYADSMaK1xXJxmlZ0Oe8CtJ6jKBrSjnn6fnDONMFHadvspGk8Gxc7N15gdoVzcbADiR0q1V7O973S1e0Fu6CFPAayqcCBKIOs4_xfp6nm1HNupK82P0Bawyi3Bc4Fu2vcDQKLcgU-gyiBMkego3WW4/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.16%2Fdata%2Fexperiment%2Fhtml%2Fgemma.R.html 


.

On publication we have used the ExperimentData biocview to classify the
package but we believe this was not the correct decision since the
package's function is to access a database much like geoquery. I was
wondering if it was safe to change the classification on our end by
changing biocviews directly or if it would cause issues with the
bioconductor infrastructure?

Cheers,
Ogan

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--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Package Classifications via BiocViews

[Hervé Pagès]

Hi Burak,

Based on your description of what the package does, this is really a 
software package in nature, so is in the wrong repository. We need to 
fix this.


In 4 steps:

1. Please remove the ExperimentData term from the biocViews field as 
well as any term that belongs to the ExperimentData ontology, that is: 
DiseaseModel, OrganismData, Homo_sapiens_Data, Mus_musculus_Data, 
Rattus_norvegicus_Data, TechnologyData, MicroarrayData, SequencingData, 
and RNASeqData. Yep, most of your terms will go away.


2. Add the Software term, in first position. You're welcome to add new 
terms if you want, from the following vocabulary: 
https://github.com/Bioconductor/biocViews/blob/master/inst/dot/biocViewsVocab.dot. 
Please make sure to pick terms that belong to the Software ontology 
(i.e. are offsprings of the Software term).


3. Bump the package version (only the z part in x.y.z), and push your 
changes to git.bioconductor.org.


4. Let us know when you're done. We'll make the required adjustments on 
our side.


Thanks,

H.

On 28/09/2022 09:37, Burak Ogan Mancarci wrote:

Apologies for the inconvenience.

The change isn't essential on our end and can be avoided or delayed if you
think the ExperimentData label can be applied to a package responsible for
accessing data from a database rather than storing static data. We were
only worried about misleading use of biocviews terms.

Cheers,
Ogan

On Wed., Sep. 28, 2022, 14:26 Kern, Lori, 
wrote:


Changing the biocviews is not sufficient.  There needs to be work on our
end to change the manifest the package belongs to and to clear the build
products from the data repositories so it is only found in one location.

Are you sure you want to proceed with switching?  It is not trivial on our
end.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
--
*From:* Bioc-devel  on behalf of Burak
Ogan Mancarci 
*Sent:* Wednesday, September 28, 2022 9:17 AM
*To:* bioc-devel@r-project.org 
*Subject:* [Bioc-devel] Package Classifications via BiocViews

Hi,

I am a developer working on the bioconductor package gemma.R
<
https://secure-web.cisco.com/1wIQY41Mq8CRYqLq1luoPm43XSj6Icl27w6udr35y-BxPHgEP6B5pApAAeBdBeWsydixV0CSwBVIVl2C7mJykPI3ESX7qtp-xJOSvJAu4T1yzHr3CWRc7s6LY_WtIcrnzfyw3MI7z0oqv1hzA1x5oRN1kFZ-KF6tttbi86SwIwZhYADSMaK1xXJxmlZ0Oe8CtJ6jKBrSjnn6fnDONMFHadvspGk8Gxc7N15gdoVzcbADiR0q1V7O973S1e0Fu6CFPAayqcCBKIOs4_xfp6nm1HNupK82P0Bawyi3Bc4Fu2vcDQKLcgU-gyiBMkego3WW4/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.16%2Fdata%2Fexperiment%2Fhtml%2Fgemma.R.html

.

On publication we have used the ExperimentData biocview to classify the
package but we believe this was not the correct decision since the
package's function is to access a database much like geoquery. I was
wondering if it was safe to change the classification on our end by
changing biocviews directly or if it would cause issues with the
bioconductor infrastructure?

Cheers,
Ogan

 [[alternative HTML version deleted]]

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--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] broken DOI link for SINGLe package

[Jennifer Wokaty]

Hi Rocio,

Thanks for bringing this to our attention. I've fixed the DOI for SINGLe.

Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH


From: Bioc-devel  on behalf of Rocio Espada 
via Bioc-devel 
Sent: Wednesday, September 28, 2022 7:51 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] broken DOI link for SINGLe package

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

Hi,

The DOI link for the package SINGLe (which I uploaded to bioconductor)
is not working. Do you know how I can fix this?
This is the link to the package (that does work):
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_release_bioc_html_single.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=LcpRgSrxEqBnuWyGR3u5fnNwC1rP1Jc5_LkPoFIlWRQ=
and this is the DOI's link included there, that does not work:
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_doi-3A10.18129_B9.bioc.single=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=rGiIvVYCzEeKC19nlsEiMeiUG6regDYdLlnGssZaAUk=

Thanks in advance,
Rocio

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Re: [Bioc-devel] Package Classifications via BiocViews

[Kern, Lori]

Changing the biocviews is not sufficient.  There needs to be work on our end to 
change the manifest the package belongs to and to clear the build products from 
the data repositories so it is only found in one location.

Are you sure you want to proceed with switching?  It is not trivial on our end.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Burak Ogan 
Mancarci 
Sent: Wednesday, September 28, 2022 9:17 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Package Classifications via BiocViews

Hi,

I am a developer working on the bioconductor package gemma.R
.
On publication we have used the ExperimentData biocview to classify the
package but we believe this was not the correct decision since the
package's function is to access a database much like geoquery. I was
wondering if it was safe to change the classification on our end by
changing biocviews directly or if it would cause issues with the
bioconductor infrastructure?

Cheers,
Ogan

[[alternative HTML version deleted]]

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[Bioc-devel] Bioconductor 3.16 db0s, OrgDbs and TxDbs now available

[Interdonato, Kayla]

Hello Bioconductor Community!

The newest db0s, OrgDbs, and TxDbs annotation packages for the upcoming
Bioconductor 3.16 release are up and available for download in the devel version
of Bioconductor.

The deadline for submitting contributed annotations will be Wednesday October 
19th.

The new db0 packages are:

anopheles.db0_3.16.0.tar.gz
arabidopsis.db0_3.16.0.tar.gz
bovine.db0_3.16.0.tar.gz
canine.db0_3.16.0.tar.gz
chicken.db0_3.16.0.tar.gz
chimp.db0_3.16.0.tar.gz
ecoliK12.db0_3.16.0.tar.gz
ecoliSakai.db0_3.16.0.tar.gz
fly.db0_3.16.0.tar.gz
human.db0_3.16.0.tar.gz
malaria.db0_3.16.0.tar.gz
mouse.db0_3.16.0.tar.gz
pig.db0_3.16.0.tar.gz
rat.db0_3.16.0.tar.gz
rhesus.db0_3.16.0.tar.gz
worm.db0_3.16.0.tar.gz
xenopus.db0_3.16.0.tar.gz
yeast.db0_3.16.0.tar.gz
zebrafish.db0_3.16.0.tar.gz

The new OrgDb packages are:

GO.db_3.16.0.tar.gz
org.Ag.eg.db_3.16.0.tar.gz
org.At.tair.db_3.16.0.tar.gz
org.Bt.eg.db_3.16.0.tar.gz
org.Ce.eg.db_3.16.0.tar.gz
org.Cf.eg.db_3.16.0.tar.gz
org.Dm.eg.db_3.16.0.tar.gz
org.Dr.eg.db_3.16.0.tar.gz
org.EcK12.eg.db_3.16.0.tar.gz
org.EcSakai.eg.db_3.16.0.tar.gz
org.Gg.eg.db_3.16.0.tar.gz
org.Hs.eg.db_3.16.0.tar.gz
org.Mm.eg.db_3.16.0.tar.gz
org.Mmu.eg.db_3.16.0.tar.gz
org.Pt.eg.db_3.16.0.tar.gz
org.Rn.eg.db_3.16.0.tar.gz
org.Sc.eg.db_3.16.0.tar.gz
org.Ss.eg.db_3.16.0.tar.gz
org.Xl.eg.db_3.16.0.tar.gz
Orthology.eg.db_3.16.0.tar.gz
PFAM.db_3.16.0.tar.gz

The new TxDb packages are:

TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz

Thank you!

Kayla E. Interdonato, MS
Programmer/Analyst - Morgan Lab
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
(716)845-1300 x4621


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[Bioc-devel] Package Classifications via BiocViews

[Burak Ogan Mancarci]

Hi,

I am a developer working on the bioconductor package gemma.R
.
On publication we have used the ExperimentData biocview to classify the
package but we believe this was not the correct decision since the
package's function is to access a database much like geoquery. I was
wondering if it was safe to change the classification on our end by
changing biocviews directly or if it would cause issues with the
bioconductor infrastructure?

Cheers,
Ogan

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[Bioc-devel] broken DOI link for SINGLe package

[Rocio Espada via Bioc-devel]

Hi,

The DOI link for the package SINGLe (which I uploaded to bioconductor) 
is not working. Do you know how I can fix this?
This is the link to the package (that does work): 
https://www.bioconductor.org/packages/release/bioc/html/single.html
and this is the DOI's link included there, that does not work: 
https://doi.org/doi:10.18129/B9.bioc.single


Thanks in advance,
Rocio

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