Re: [Bioc-devel] R version dependency

[Anatoly Sorokin]

Hi,
You can even set 3.5 if your code working with that version of R, but
BiocManager won't load the latest Bioconductor version (3.19) unless you
have R 4.4.

Cheers,
Anatoly

On Tue, Apr 23, 2024 at 2:57 AM Richard Heery 
wrote:

> Hi all,
>
> I'm wondering what we should now list as the R version in the Depends
> section of the description file: the current version 4.3.3 or the
> development version 4.4?
>
> Cheers,
>
> Richard
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

[Anatoly Sorokin]

Great!
Thank you!

On Fri, Apr 19, 2024 at 2:29 AM James W. MacDonald  wrote:

> There was an error in the scripts used to generate the organism packages
> that excluded (among other genes) GRPEL1. We have rectified the error and
> are re-running. The updated packages should be available early next week.
>
> -Original Message-
> From: Bioc-devel  On Behalf Of James W.
> MacDonald
> Sent: Thursday, April 18, 2024 9:30 AM
> To: Anatoly Sorokin ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene
>
> It is the wrong place to send the request. This listserv is for package
> developers. If you want support please use support.bioconductor.org.
>
> -Original Message-----
> From: Bioc-devel  On Behalf Of Anatoly
> Sorokin
> Sent: Thursday, April 18, 2024 12:40 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene
>
> !---|
>   This Message Is From an Untrusted Sender
>   You have not previously corresponded with this sender.
>   See https://itconnect.uw.edu/email-tags for additional
>   information.  Please contact the UW-IT Service Center,
>   h...@uw.edu 206.221.5000, for assistance.
> |---!
>
> Hi,
> sorry if this is the wrong list to send this request, but the landing page
> of the org.Hs.eg.db package contains no reference for the bug report.
>
> The most recent version of the org.Hs.eg.db package (3.19.7) misses the
> GRPEL1 gene (
> https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$
> ). It could not be found either by SYMBOL, or by ENTREZID:
>
> > orgDB = org.Hs.eg.db
> > select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
> keytype=keytype)
> Error in .testForValidKeys(x, keys, keytype, fks) :
>   None of the keys entered are valid keys for 'ENTREZID'. Please use the
> keys method to see a listing of valid arguments.
> > select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
> keytype='SYMBOL')
> Error in .testForValidKeys(x, keys, keytype, fks) :
>   None of the keys entered are valid keys for 'SYMBOL'. Please use the
> keys method to see a listing of valid arguments.
>
> however, in the previous version of the package (3.18.0), it could be
> found by both keys:
>
> > select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
> keytype=keytype)
> 'select()' returned 1:1 mapping between keys and columns
>   ENTREZID SYMBOL   GENENAME
> 180273 GRPEL1 GrpE like 1, mitochondrial
> > select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
> keytype='SYMBOL')
> 'select()' returned 1:1 mapping between keys and columns
>   SYMBOL   GENENAME ENTREZID
> 1 GRPEL1 GrpE like 1, mitochondrial80273
>
> That omission caused an error in our BioNAR package. As this is the only
> missing gene in the network for the time being I've fixed this manually in
> the vignette, but I'd like to understand is it a real mistake or am I using
> the package in the wrong way?
>
> Cheers,
> Anatoly
>
> [[alternative HTML version deleted]]
>
> ___
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>
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Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Dear Henrik,

thank you very much for pointing me to the rig project. It works fine and I
have two independent R versions on my machine at the moment.

Thank you,
Anatoly

On Tue, Apr 9, 2024 at 4:19 AM Henrik Bengtsson 
wrote:

> > ... I'm on Mac OS 12.5.
>
> I've heard good things about 'rig' (The R Installation Manager;
> https://github.com/r-lib/rig). It can install multiple R versions in
> parallel on macOS, Windows, and Linux, without the different versions
> conflicting with each other.  I recommend trying it out, because being
> able to run different versions of R is always useful, even if you're
> not a package maintainer.
>
> /Henrik
>
> On Thu, Apr 4, 2024 at 8:08 PM Anatoly Sorokin  wrote:
> >
> > Hi Henrik,
> >
> > thank you for the prompt reply. I'm on Mac OS 12.5.
> >
> > And regarding the linking version of Bioconductor and R my major
> complaint is the timing, if R 4.4 hasn't been released yet, why not
> postpone this dependency to the October release of Bioconductor?
> >
> > And it is also true that we have a lot of complaints from people working
> on centrally maintained machines or HPC clusters, that they have no access
> to the latest R versions. So sometimes even for demonstration purposes, we
> had to install the package from the GitHub source, rather than from
> BiocManager.
> >
> > Cheers,
> > Anatoly
> >
> > On Fri, Apr 5, 2024 at 11:57 AM Henrik Bengtsson <
> henrik.bengts...@gmail.com> wrote:
> >>
> >> Hello,
> >>
> >> these days, it's quite straight forward to have multiple versions of R
> >> installed in parallel without them conflicting with each other. I know
> >> it works out of the box on MS Windows (just install all versions you'd
> >> like), and I know there are various tools to achieve the same on
> >> macOS.  I'm on Linux, and I build R from source, so that solves it for
> >> me.  What's platform are you working on?  If you share that, I think
> >> you'll get 1-2-3 instructions for how to install R 4.4 pre-release
> >> from users on that operating system.
> >>
> >> Regarding Bioc versions being tied to specific R versions: That is a
> >> design decision that goes back to day one of the Bioconductor project.
> >> It's a rather big thing to change.  That said, I've always been in the
> >> camp that thinks we should move away from that model for many reasons;
> >> one is the friction added to developers, another is the friction added
> >> to end-users, and some people may be stuck with older versions of R
> >> and in no control of updating.
> >>
> >> Hope this helps,
> >>
> >> Henrik
> >>
> >> On Thu, Apr 4, 2024 at 7:29 PM Anatoly Sorokin 
> wrote:
> >> >
> >> > Hi all,
> >> >
> >> > I'm sorry for the complaint, but do you really think it is wise to
> make the
> >> > new release dependent on the R version which has not released yet?
> >> >
> >> > I have a lot of R-related projects going on apart from maintaining the
> >> > Bioconductor package and I'm not comfortable installing the unreleased
> >> > version of R on my machine and spending time debugging it in the case
> of
> >> > possible problems.
> >> >
> >> > At the same time, I have an error, possibly caused by a new version of
> >> > GO.db package, which BioNAR is dependent upon and I can not fix it
> >> > until the R 4.4 release on the 24th of April when I would have less
> than a
> >> > day to fix the possible problem and fit into R CMD build and R CMD
> check by
> >> > the Friday April 26th. Don't you think this is a rather tight time
> frame?
> >> >
> >> >
> >> > Sorry once again, for the complaint.
> >> >
> >> > Cheers,
> >> > Anatoly
> >> >
> >> > On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
> >> > bioc-devel@r-project.org> wrote:
> >> >
> >> > > Import update:  The Bioconductor Release will be May 1 following the
> >> > > release of R 4.4 on April 24.
> >> > >
> >> > > The Bioconductor 3.18 branch will be frozen Monday April 15th.
> After that
> >> > > date, no changes will be permitted ever on that branch.
> >> > >
> >> > > The deadline for devel Bioconductor 3.19 for packages to pass R CMD
> build
> >

[Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

[Anatoly Sorokin]

Hi,
sorry if this is the wrong list to send this request, but the landing page
of the org.Hs.eg.db package contains no reference for the bug report.

The most recent version of the org.Hs.eg.db package (3.19.7) misses
the GRPEL1 gene (https://www.ncbi.nlm.nih.gov/gene/80273). It could not be
found either by SYMBOL, or by ENTREZID:

> orgDB = org.Hs.eg.db
> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'ENTREZID'. Please use the
keys method to see a listing of valid arguments.
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys
method to see a listing of valid arguments.

however, in the previous version of the package (3.18.0), it could be found
by both keys:

> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
'select()' returned 1:1 mapping between keys and columns
  ENTREZID SYMBOL   GENENAME
180273 GRPEL1 GrpE like 1, mitochondrial
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
'select()' returned 1:1 mapping between keys and columns
  SYMBOL   GENENAME ENTREZID
1 GRPEL1 GrpE like 1, mitochondrial80273

That omission caused an error in our BioNAR package. As this is the only
missing gene in the network for the time being I've fixed this manually in
the vignette, but I'd like to understand is it a real mistake or am I using
the package in the wrong way?

Cheers,
Anatoly

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Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Dear Levi,

minor correction: not requiring but working with. Testing against r-devel
and requiring it for development are two different things. If the
development and maintenance of the Bioconductor package would be my only
responsibility, I wouldn't argue. But because this is a voluntary activity
additional restrictions such as maintaining unstable software release,
which is not needed at all, make it less attractive.

In my mind, the requirements mean that the software is not backwards
compatible any more. In my experience, cases when packages are not working
with an R older in major release is rare (for example at the moment all my
code working with R 3.6, due to limitations on some collaborator's
systems). I haven't checked but it would be really interesting to run R Cmd
check on 3.19 packages with R 4.0 and find how many of them will fail.

When we were deciding how to release our code Bioconductor was chosen due
to its stability and user-friendliness in package and dependencies
installation, which is crucial for the adoption of the analysis approach by
biologists who are not so familiar with coding. Forcing them to completely
reinstall the framework is not so convenient.

But anyway it is just my thoughts.

On Fri, Apr 5, 2024 at 12:39 PM Levi Waldron 
wrote:

> Anatoly, delaying dependency on R 4.4 until October would mean 6 months of
> Bioconductor release requiring an old release of R for users. Bioconductor
> developers developing against r-devel means that users get a new
> Bioconductor release that works immediately on the new R. And I think a
> main purpose of a 6 month devel and release cycle is to provide a
> comfortable period for everyone to work out new features and bugs and to
> resolve downstream consequences that may arise.  Delaying the Bioconductor
> release by a week or something might actually encourage a habit of
> last-week bug fixes that should be discouraged 😉. I really can’t see any
> way around requiring developers to test against r-devel without sacrificing
> timeliness and reliability for users. There are also Docker and GitHub
> Actions options that don’t require installing r-devel to test against it.
>

But the recent release of 3.19 version of GO.db package forced me to the
last-minute bug fixing of the code, which was perfectly fine, anyway.

>
> I think many HPC clusters now support Singularity, which is a more
> reliable and easier way to run packages with a compatible version of R.
> Installing from GitHub on an old version of R has no guarantees of being
> tested or working correctly even if it installs without error, and I see as
> a sacrifice of software reliability for convenience that can be avoided
> with Singularity or regular R updates.
>

That's why each package should contain a reliable set of tests. And again,
regular updates of the R are fine for the self-managed machines and skilful
users. Don't fix something, which works!

>
> Henrik, if Bioconductor releases weren’t tied to R releases, how could
> Bioconductor test them? I guess like CRAN where as long as a package says
> it depends on R >= 2.0 then you’re free to try installing on 2.0 even
> though the combination has never been tested? Maybe I worry too much about
> such testing since CRAN seems OK anyways, as far as we know?
>
My point is that too-tight ties make Bioconductor less reliable. When you
test your code against someone's unstable release you are wasting your
time, since you have to debug not only your code but the unstable version
of the platform. I did not sign up as an R beta tester.

Cheers,
Anatoly

--
> *From:* Bioc-devel  on behalf of
> Anatoly Sorokin 
> *Sent:* Thursday, April 4, 2024 10:28:47 PM
> *To:* Kern, Lori 
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] Important Bioconductor Release Deadlines
>
> Hi all,
>
> I'm sorry for the complaint, but do you really think it is wise to make the
> new release dependent on the R version which has not released yet?
>
> I have a lot of R-related projects going on apart from maintaining the
> Bioconductor package and I'm not comfortable installing the unreleased
> version of R on my machine and spending time debugging it in the case of
> possible problems.
>
> At the same time, I have an error, possibly caused by a new version of
> GO.db package, which BioNAR is dependent upon and I can not fix it
> until the R 4.4 release on the 24th of April when I would have less than a
> day to fix the possible problem and fit into R CMD build and R CMD check by
> the Friday April 26th. Don't you think this is a rather tight time frame?
>
>
> Sorry once again, for the complaint.
>
> Cheers,
> Anatoly
>
> On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
> bioc-dev

Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Hi Henrik,

thank you for the prompt reply. I'm on Mac OS 12.5.

And regarding the linking version of Bioconductor and R my major complaint
is the timing, if R 4.4 hasn't been released yet, why not postpone this
dependency to the October release of Bioconductor?

And it is also true that we have a lot of complaints from people working on
centrally maintained machines or HPC clusters, that they have no access to
the latest R versions. So sometimes even for demonstration purposes, we had
to install the package from the GitHub source, rather than from BiocManager.

Cheers,
Anatoly

On Fri, Apr 5, 2024 at 11:57 AM Henrik Bengtsson 
wrote:

> Hello,
>
> these days, it's quite straight forward to have multiple versions of R
> installed in parallel without them conflicting with each other. I know
> it works out of the box on MS Windows (just install all versions you'd
> like), and I know there are various tools to achieve the same on
> macOS.  I'm on Linux, and I build R from source, so that solves it for
> me.  What's platform are you working on?  If you share that, I think
> you'll get 1-2-3 instructions for how to install R 4.4 pre-release
> from users on that operating system.
>
> Regarding Bioc versions being tied to specific R versions: That is a
> design decision that goes back to day one of the Bioconductor project.
> It's a rather big thing to change.  That said, I've always been in the
> camp that thinks we should move away from that model for many reasons;
> one is the friction added to developers, another is the friction added
> to end-users, and some people may be stuck with older versions of R
> and in no control of updating.
>
> Hope this helps,
>
> Henrik
>
> On Thu, Apr 4, 2024 at 7:29 PM Anatoly Sorokin  wrote:
> >
> > Hi all,
> >
> > I'm sorry for the complaint, but do you really think it is wise to make
> the
> > new release dependent on the R version which has not released yet?
> >
> > I have a lot of R-related projects going on apart from maintaining the
> > Bioconductor package and I'm not comfortable installing the unreleased
> > version of R on my machine and spending time debugging it in the case of
> > possible problems.
> >
> > At the same time, I have an error, possibly caused by a new version of
> > GO.db package, which BioNAR is dependent upon and I can not fix it
> > until the R 4.4 release on the 24th of April when I would have less than
> a
> > day to fix the possible problem and fit into R CMD build and R CMD check
> by
> > the Friday April 26th. Don't you think this is a rather tight time frame?
> >
> >
> > Sorry once again, for the complaint.
> >
> > Cheers,
> > Anatoly
> >
> > On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
> > bioc-devel@r-project.org> wrote:
> >
> > > Import update:  The Bioconductor Release will be May 1 following the
> > > release of R 4.4 on April 24.
> > >
> > > The Bioconductor 3.18 branch will be frozen Monday April 15th. After
> that
> > > date, no changes will be permitted ever on that branch.
> > >
> > > The deadline for devel Bioconductor 3.19 for packages to pass R CMD
> build
> > > and R CMD check is Friday April 26th. While you will still be able to
> make
> > > commits past this date, This ensures any changes pushed to
> > > git.bioconductor.org are reflected in at least one build report before
> > > the devel branch will be copied to a release 3.19 branch.
> > >
> > > Cheers,
> > >
> > >
> > >
> > > Lori Shepherd - Kern
> > >
> > > Bioconductor Core Team
> > >
> > > Roswell Park Comprehensive Cancer Center
> > >
> > > Department of Biostatistics & Bioinformatics
> > >
> > > Elm & Carlton Streets
> > >
> > > Buffalo, New York 14263
> > >
> > >
> > > 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@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Important Bioconductor Release Deadlines

[Anatoly Sorokin]

Hi all,

I'm sorry for the complaint, but do you really think it is wise to make the
new release dependent on the R version which has not released yet?

I have a lot of R-related projects going on apart from maintaining the
Bioconductor package and I'm not comfortable installing the unreleased
version of R on my machine and spending time debugging it in the case of
possible problems.

At the same time, I have an error, possibly caused by a new version of
GO.db package, which BioNAR is dependent upon and I can not fix it
until the R 4.4 release on the 24th of April when I would have less than a
day to fix the possible problem and fit into R CMD build and R CMD check by
the Friday April 26th. Don't you think this is a rather tight time frame?


Sorry once again, for the complaint.

Cheers,
Anatoly

On Tue, Mar 26, 2024 at 11:06 PM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> Import update:  The Bioconductor Release will be May 1 following the
> release of R 4.4 on April 24.
>
> The Bioconductor 3.18 branch will be frozen Monday April 15th. After that
> date, no changes will be permitted ever on that branch.
>
> The deadline for devel Bioconductor 3.19 for packages to pass R CMD build
> and R CMD check is Friday April 26th. While you will still be able to make
> commits past this date, This ensures any changes pushed to
> git.bioconductor.org are reflected in at least one build report before
> the devel branch will be copied to a release 3.19 branch.
>
> Cheers,
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> 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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] synaptome.db check error

[Anatoly Sorokin]

Dear Jennifer,

Thank you very much!

Cheers,
Anatoly

On Sat, Sep 2, 2023 at 12:49 AM Jennifer Wokaty <
jennifer.wok...@sph.cuny.edu> wrote:

> Hi Anatoly,
>
> I see we got a few of these on the most recent build. No action is needed
> as the Bioconductor build system will remove the lock files on the next run
> next Wednesday.
>
> Jennifer Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> --
> *From:* Bioc-devel  on behalf of
> Anatoly Sorokin 
> *Sent:* Friday, September 1, 2023 6:34 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] synaptome.db check error
>
> * This email originates from a sender outside of CUNY. Verify the sender
> before replying or clicking on links and attachments. *
>
> Dear all,
> I've found a strange error on *nebbiolo2
> <
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.18%2Fdata-annotation-LATEST%2Fnebbiolo2-NodeInfo.html__%3B!!PxiZbSOawA!OxBOK7v_etZ8bAv-qRxlhci8I2O9RM1QCBFcLfhFFOwov1NvgVB9VmnJfPhHzMCVFo-5mitDjaEDAFDKYYbLP1u8YQ%24&data=05%7C01%7Cjennifer.wokaty%40sph.cuny.edu%7Ca796973f07ed49411b7808dbaad73b31%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638291613648265413%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=v%2BwY9PvGaH64mEpbJowtFOTerNW1EJaQPaOPYmtoLPU%3D&reserved=0
> >*
> check
> server for our package synaptome.db:
>
> * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
> ERROR: failed to lock directory
> ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ for modifying
> Try removing
> ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-metaboliteIDmapping’
>
>
> What should I do to get rid of it?
> Cheers,
> Anatoly
>
> [[alternative HTML version deleted]]
>
> ___
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[Bioc-devel] synaptome.db check error

[Anatoly Sorokin]

Dear all,
I've found a strange error on *nebbiolo2
*
check
server for our package synaptome.db:

* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
ERROR: failed to lock directory
‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ for modifying
Try removing 
‘/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-metaboliteIDmapping’


What should I do to get rid of it?
Cheers,
Anatoly

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Re: [Bioc-devel] Dependence from another New package

[Anatoly Sorokin]

Dear Lori,

It is not strictly the update, as software package newer went through
moderation stage due to problems with large database file. We've split the
original package into software and data part, and now the data part is
under review, but I would not call what happened to the software package as
an update :) as it was newer accepted.

Cheers,
Anatoly


Cheers,


On Mon, Sep 27, 2021 at 11:12 PM Kern, Lori 
wrote:

> Ah okay. So this is an update to an existing software package to include
> the dependency on the new experiment data package.  Sorry I missed that
> part in the original email.   I would just wait until the data package
> makes it through the review.  In the future I would wait to make changes to
> the software package until the data package was accepted.
>
> Cheers
>
> Lori Shepherd
>
> 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
> Anatoly Sorokin 
> *Sent:* Monday, September 27, 2021 5:52 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] Dependence from another New package
>
> Dear Lori, thank you!
>
> I have additional question: our software package is already in the
> bioconductor git, should I add the original github or bioconductor git to
> the AdditionalPackage line to get another package added to the review?
>
> Thank you,
> Anatoly
>
> On Mon, Sep 27, 2021 at 12:26 PM Kern, Lori  >
> wrote:
>
> >
> https://secure-web.cisco.com/1ow-ZDhZ0NTF2PfdRSLQuskm2EA4UHdXlwovzapeXoTOWEzcC-nl0v9wpRPOFKLYduwBFLRlJ4GXsyIVbomFztWS8Nfrcn2x2KMyIDoAmyVUaDYn8Vr3Epdwcuylp2aH9e93s2nYrjmxWIZ1SXnYv28xwk57bE9X1wzSRA7Sdg5KNIgSeEjvZ5KCS70X2GFoSCWR43tSRh2DZ4nIijL9bLtnMQP_hk72VkBD_Cw8pWvSzo_8qvlhBcS6s4IufZiuR0uKcTZ7rsmVVXeoP2CRlLr8Krp1Nmbtv4mgwPavebSIYdrKmNlEsIsALUfXjMeRv/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%23submitting-related-packages
> >
> > In the documentation there is a way to submit related packages under the
> > same review. If they are submitted under the same issue they can be found
> > and reviewed together
> >
> > Get Outlook for iOS <
> https://secure-web.cisco.com/1V9yG0vYO9YdaYbIo5AbK8-ROWQ2XFAY4lkNFl5Kv3B4EZk9Y_ZiYjiDXzm7ktF382AXnOhqxzjrsKm4yu9zuNeJUHkmY2BKWvB5SMDZJOtgP4Fc7fsLM_BQqaxrQWOat-9nikhPY6swF0ziWp74RC2u6hQE35dwtID9CNkfWk7yVIcTLpUDgoah_ojEdn1lAepS5jlYJvIGYtpti1PiYxoIzx6qES3BmTe6sS1AzNcmOZn0HmTY8PeGV_DQUYU7QD82KNCQJaTKFXYzKe_nllnQibScf4TQlPm016hjGRkY_oo5kxGktH3UypVpd2i44/https%3A%2F%2Faka.ms%2Fo0ukef
> >
> > --
> > *From:* Bioc-devel  on behalf of
> > Anatoly Sorokin 
> > *Sent:* Sunday, September 26, 2021 7:59:17 PM
> > *To:* bioc-devel@r-project.org 
> > *Subject:* [Bioc-devel] Dependence from another New package
> >
> > Hi,
> > We have submitted package, that required large data. According to
> > suggestion from bioconductor team, we split the package into two parts,
> > first of which was recently become available on AnnotationHub.
> > Once the data package was on the hub, I've submitted the new version of
> the
> > software package to the git, but validation had failed due to missing
> data
> > package, as it is under review at the moment and not available for on
> > bioconductor yet.
> > Could any one suggest how to resolve this issue, when two packages under
> > review simultaneously?
> >
> > Thank you in advance,
> > Anatoly
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> >
> https://secure-web.cisco.com/1M5jbI1SKUmqRjwEcfvUWB6JZePhaUw1nbM0vVXZV0hZYwgOItbTfNqOR8sa2Cv7GTMkEIWc2vfHa8r8N59UCCWKettR1eIYmSZ4yNSQXxPXeR7jN1yvCyzgyXtMUjyEsyI8W_uXRL7Nm35peDJpVPPy_8Gh9G-RYcCKfgOlVtQy0pjmorfCQsApShSYNHJX5szL7KSekaSpJPGHWYn8ZYwCy6VDIV8OWADq3aw55O5vhBgbq5HVSF5cfCjDbUBW3FdwUwFOQ5tvISsJI9tAp1lhS7paPsH9drmNCBuII06DKQTRVnEM4bLI0k4X35QLN/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
> >
> > 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

Re: [Bioc-devel] Dependence from another New package

[Anatoly Sorokin]

Dear Lori, thank you!

I have additional question: our software package is already in the
bioconductor git, should I add the original github or bioconductor git to
the AdditionalPackage line to get another package added to the review?

Thank you,
Anatoly

On Mon, Sep 27, 2021 at 12:26 PM Kern, Lori 
wrote:

> https://github.com/Bioconductor/Contributions#submitting-related-packages
>
> In the documentation there is a way to submit related packages under the
> same review. If they are submitted under the same issue they can be found
> and reviewed together
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> --
> *From:* Bioc-devel  on behalf of
> Anatoly Sorokin 
> *Sent:* Sunday, September 26, 2021 7:59:17 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* [Bioc-devel] Dependence from another New package
>
> Hi,
> We have submitted package, that required large data. According to
> suggestion from bioconductor team, we split the package into two parts,
> first of which was recently become available on AnnotationHub.
> Once the data package was on the hub, I've submitted the new version of the
> software package to the git, but validation had failed due to missing data
> package, as it is under review at the moment and not available for on
> bioconductor yet.
> Could any one suggest how to resolve this issue, when two packages under
> review simultaneously?
>
> Thank you in advance,
> Anatoly
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
> https://secure-web.cisco.com/1M5jbI1SKUmqRjwEcfvUWB6JZePhaUw1nbM0vVXZV0hZYwgOItbTfNqOR8sa2Cv7GTMkEIWc2vfHa8r8N59UCCWKettR1eIYmSZ4yNSQXxPXeR7jN1yvCyzgyXtMUjyEsyI8W_uXRL7Nm35peDJpVPPy_8Gh9G-RYcCKfgOlVtQy0pjmorfCQsApShSYNHJX5szL7KSekaSpJPGHWYn8ZYwCy6VDIV8OWADq3aw55O5vhBgbq5HVSF5cfCjDbUBW3FdwUwFOQ5tvISsJI9tAp1lhS7paPsH9drmNCBuII06DKQTRVnEM4bLI0k4X35QLN/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> 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.

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[Bioc-devel] AnnotationHub is too old on build system

[Anatoly Sorokin]

Hi all,

We have submitted a data package to AnnotationHub, and it was loaded there
around September 20th. Today we've submitted the accompanying software
package, but the automated build system returns an error message:
"error: no records found for the given index" on the line on which we are
extracting data from the Hub. I've noticed that there is a line in the
build report:
"snapshotDate(): 2021-09-10"
which means the AnnotationHub is too old and does not contain our data.
Is it possible to refresh AnnotationHub cache on the building system?

Cheers,
Anatoly

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[Bioc-devel] Dependence from another New package

[Anatoly Sorokin]

Hi,
We have submitted package, that required large data. According to
suggestion from bioconductor team, we split the package into two parts,
first of which was recently become available on AnnotationHub.
Once the data package was on the hub, I've submitted the new version of the
software package to the git, but validation had failed due to missing data
package, as it is under review at the moment and not available for on
bioconductor yet.
Could any one suggest how to resolve this issue, when two packages under
review simultaneously?

Thank you in advance,
Anatoly

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Re: [Bioc-devel] Git lfs support

[Anatoly Sorokin]

Hi, sorry to bother you again, but I'm completely lost: how could I test
that my new package behaves properly?

AnnotationHub by default loads a list of all available Hub data, how can I
add my new package to that list without publishing it in AnnotationHub
first? On the other hand, I don't think that publishing untested packages
is a good idea.

Please, can anyone provide more or less extended documentation? I've read
the CreateAnAnnotationPackage vignette. It is great to understand the
internals of the Annotation package, but there is no clue how to use the
package without publishing it.

Thank you in advance,
Anatoly

On Fri, Sep 10, 2021 at 6:24 PM Kern, Lori 
wrote:

> The paths will be given through the AnnotationHub interface.
>
> I would like to also point out that there is a SQLite  DisplatchClass that
> might be more appropriate? It would load the database automatically using
> AnnotaionDbi::loadDb
> For a Zip DispatchClass, It will get the zipped file, unzip, and provide a
> list of the file paths.
>
> make-data.R should be how you created the sqlite database.  It doesn't
> need to be run again. It could be code, sudo-code, or text but should
> describte how you created the data and any relevant source information for
> the data.
>
> Hope this helps
>
> Cheers,
>
>
> Lori Shepherd
>
> 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
> Anatoly Sorokin 
> *Sent:* Friday, September 10, 2021 5:56 AM
> *To:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] Git lfs support
>
> Hi Hervé,
>
> I've made a new package with metadata.csv, as described in
> CreateAnAnnotationPackage
> vignette.
>
> The data is located on the public service as a zipped SQLite database. So
> I've set both SourceType and DispatchClass as 'Zip'.
> From AnnotationHub::DispatchClassList() I expect that I should have an
> unzipped file path. My first question is: how do I get that path?
>
> The second question is: what should I put into make-data.R? The database is
> already created, cleaned and validated. All I need for the package is to
> download it, unzip and connect.
>
> Thank you,
> Anatoly
>
> On Thu, Aug 26, 2021 at 12:59 PM Hervé Pagès 
> wrote:
>
> > Hi Anatoly,
> >
> > Let's keep this conversation on the bioc-devel mailing list where it
> > started.
> >
> > On 26/08/2021 02:46, Anatoly Sorokin wrote:
> > > Hi Hervé,
> > >
> > > thank you for your answer. Does this mean that the SQLite file will be
> > > downloaded separately and kept in some cache?
> >
> > Yes.
> >
> > >
> > > And another question: does this mean that there should be two packages,
> > > one for code and another one for the database?
> >
> > Yes. One is what we call the software package and the other one the
> > accompanying data package.
> >
> > Cheers,
> > H.
> >
> > >
> > > On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès <
> hpages.on.git...@gmail.com
> > > <mailto:hpages.on.git...@gmail.com >>
> wrote:
> > >
> > > Hi Anatoly,
> > >
> > > What kind of data is in your SQLite database? The Bioconductor
> > approach
> > > for this is to provide the data as a separate data annotation or
> data
> > > experiment package. More precisely, the data itself should go on
> > > AnnotationHub or ExperimentHub. It should be associated with a "Hub
> > > package", that is, a data package that documents it and explains
> how
> > to
> > > retrieve it from AnnotationHub or ExperimentHub. See vignettes in
> the
> > > HubPub package for more information:
> > >
> > > http://bioconductor.org/packages/HubPub
> > > <http://bioconductor.org/packages/HubPub>
> > >
> > > Best,
> > >
> > > H.
> > >
> > > On 24/08/2021 17:53, Nitesh Turaga wrote:
> > >  > Hi,
> > >  >
> > >  > We don’t have LFS support on the Bioconductor git server.
> > >  >
> > >  > I would suggest finding an alternative.
> > >  >
> > >  > Best,
> > >  >
> > >  >
> > >  >
> > >  >
> > >  > Nitesh Turaga
> > >  > Scientist II, Department of Dat

Re: [Bioc-devel] Git lfs support

[Anatoly Sorokin]

Hi Hervé,

I've made a new package with metadata.csv, as described in
CreateAnAnnotationPackage
vignette.

The data is located on the public service as a zipped SQLite database. So
I've set both SourceType and DispatchClass as 'Zip'.
>From AnnotationHub::DispatchClassList() I expect that I should have an
unzipped file path. My first question is: how do I get that path?

The second question is: what should I put into make-data.R? The database is
already created, cleaned and validated. All I need for the package is to
download it, unzip and connect.

Thank you,
Anatoly

On Thu, Aug 26, 2021 at 12:59 PM Hervé Pagès 
wrote:

> Hi Anatoly,
>
> Let's keep this conversation on the bioc-devel mailing list where it
> started.
>
> On 26/08/2021 02:46, Anatoly Sorokin wrote:
> > Hi Hervé,
> >
> > thank you for your answer. Does this mean that the SQLite file will be
> > downloaded separately and kept in some cache?
>
> Yes.
>
> >
> > And another question: does this mean that there should be two packages,
> > one for code and another one for the database?
>
> Yes. One is what we call the software package and the other one the
> accompanying data package.
>
> Cheers,
> H.
>
> >
> > On Wed, Aug 25, 2021 at 6:58 AM Hervé Pagès  > <mailto:hpages.on.git...@gmail.com>> wrote:
> >
> > Hi Anatoly,
> >
> > What kind of data is in your SQLite database? The Bioconductor
> approach
> > for this is to provide the data as a separate data annotation or data
> > experiment package. More precisely, the data itself should go on
> > AnnotationHub or ExperimentHub. It should be associated with a "Hub
> > package", that is, a data package that documents it and explains how
> to
> > retrieve it from AnnotationHub or ExperimentHub. See vignettes in the
> > HubPub package for more information:
> >
> > http://bioconductor.org/packages/HubPub
> > <http://bioconductor.org/packages/HubPub>
> >
> > Best,
> >
> > H.
> >
> > On 24/08/2021 17:53, Nitesh Turaga wrote:
> >  > Hi,
> >  >
> >  > We don’t have LFS support on the Bioconductor git server.
> >  >
> >  > I would suggest finding an alternative.
> >  >
> >  > Best,
> >  >
> >  >
> >  >
> >  >
> >  > Nitesh Turaga
> >  > Scientist II, Department of Data Science,
> >  > Bioconductor Core Team Member
> >  > Dana Farber Cancer Institute
> >  >
> >  >> On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin  > <mailto:lpto...@gmail.com>> wrote:
> >  >>
> >  >> Hi all,
> >  >>
> >  >> we have developed a package that provides access to the data in
> > the locally
> >  >> stored SQLite database. The GitHub Action successfully built the
> > package,
> >  >> but in Bioconductor, it got an error. The only reason for the
> > error is that
> >  >> the database itself is stored on GitHub via git-lfs, and the R
> > code got an
> >  >> lfs placeholder instead of the actual database.
> >  >>
> >  >> Is it possible to activate lfs within Bioconductor automatic
> > building
> >  >> server? The database is tiny (80 Mb), but I don't want to have
> > it as a
> >  >> regular git object.
> >  >>
> >  >> Thank you,
> >  >> Anatoly
> >  >>
> >  >>  [[alternative HTML version deleted]]
> >  >>
> >  >> ___
> >  >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > mailing list
> >  >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >  >
> >  > ___
> >  > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > mailing list
> >  > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >  >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>

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[Bioc-devel] Git lfs support

[Anatoly Sorokin]

Hi all,

we have developed a package that provides access to the data in the locally
stored SQLite database. The GitHub Action successfully built the package,
but in Bioconductor, it got an error. The only reason for the error is that
the database itself is stored on GitHub via git-lfs, and the R code got an
lfs placeholder instead of the actual database.

Is it possible to activate lfs within Bioconductor automatic building
server? The database is tiny (80 Mb), but I don't want to have it as a
regular git object.

Thank you,
Anatoly

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