Re: [Bioc-devel] Reopen cfTools issue #2608

[Kern, Lori]

With the recent updates to the branch renaming and given the large gap in time, 
Could you please resubmit as a new issue.



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 RAN HU 

Sent: Tuesday, March 21, 2023 12:51 AM
To: bioc-devel@r-project.org 
Cc: Peter Li 
Subject: [Bioc-devel] Reopen cfTools issue #2608

Hi,

I am the maintainer of cfTools issue #2608. I submitted it last year but
didn't have many updates then. This issue has been closed. Now I have
modified the package and am ready to submit it again. Could you please
reopen the issue? Many thanks!

Best,
Ran

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Re: [Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

[Kern, Lori]

The maintainer for these two packages

IlluminaHumanMethylationEPICmanifest
IlluminaHumanMethylationEPICanno.ilm10b4.hg19

Is actually Kasper Daniel Hansen as listed in the DESCRIPTION file not bioc 
core members.

You could reach out to Kasper to see if there is any intention or efforts that 
have already been made to include v2.

If not you can submit the packages. We have moved away from traditional 
annotation packages and I would suggest moving towards an annotationhub package 
submission where the data is stored elsewhere on a external server like S3 
buckets, Azure Data Lakes, Zenodo, etc (we have an bioconductor azure data 
lake location that can be used;  it just cannot be store on any personal 
location like github or dropbox)
Little modification to an existing package structure is needed. Basically you 
would remove the data to the external location,  include a metadata.csv file in 
the inst/extdata, and include the biocView AnnotationHub. More details can be 
found at
https://bioconductor.org/packages/release/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html
Then submit as normal to the new package submission tracker.


Cheers,



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 Zuguang Gu 

Sent: Saturday, March 18, 2023 3:56 PM
To: bioc-devel 
Subject: [Bioc-devel] Manifest and annotation packages for EPIC methylation 
array v2.0

Hi Bioc-devel,

I recently analyzed a methylation array dataset which is from EPIC array
v2.0 (
https://secure-web.cisco.com/1lqTYM1ya8XGMtHfnsdUpS8GBFfG2-c035Su1G2QlTqVVUgHKjstjf7gJtWM-rIZGvRTc76YuWsBkkII9eMBecVmP2e1A55mf2ahOVb9Nco1iHMg44efGw-SU_hREgUNlB7o5Sy6C-OATItf9L-NsoDSZnhzqs8WSnCWLDCRBlqDX8bOOoHRQ-xf-Ya5ki_CjTKaCuhaKmLon1QLYV-KVUrdfKTBg0FB1HEG1QPS2gNNCCpqGlOaNWCVxFitnlqZQcyJur9d80tL8Nf9Frcm66rjXthUFvP7ZBdhgy6BIvbN_rytmo9nR3tFO-vqJO7nm/https%3A%2F%2Fwww.illumina.com%2Fproducts%2Fby-type%2Fmicroarray-kits%2Finfinium-methylation-epic.html)
and currently there is no manifest nor annotation packages for that one.
The available packages on Bioconductor are only for EPIC array v1.0:

- IlluminaHumanMethylationEPICmanifest
- IlluminaHumanMethylationEPICanno.ilm10b4.hg19

And it is not proper to use the v1 packages for the v2 data.

I've built a manifest package and an annotation package for the EPIC array
v2.0. They are available at:

https://secure-web.cisco.com/1QiOF2zfvxn-NM_D59JEGrLZNxfjlhE96RB2QFStOhZ-M_vbiO6U4EAWhA4DxQl2K4UCyCR2IlwPHsInzW3sJ2AMU8ZGdfx2iG9GgacdRqfiLFso1I8byAAr3GSfV0yC6vYlWWOAcemIIiQmhz2ucGFBPnr6_XM6d-Fu8yoDbXBs4Kgr-BcAl-Pd75iP9-5p892EmkkdxAoDV7gLycQbrWXkoZ_k4OFitm-jojHDyBux8UbuaxsY6o_AM-f-5uji4V325my36EKUam9Fs_BWlQuoEm92wkvrPfLOrfSGs3gNRe_yOUL-xnZE2dgDIlwr_/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2manifest
https://secure-web.cisco.com/1cO_2hmhoc2EdgBhXjFVHzLhg8R28yb3KFaT2NGVp8p93xKzA8PkG-N2DaTdM1tL75mwBskP9Kd-h2MLGiXL85Pfa8uZd6kt11AoYZjhV6ndx7tUFMKrg3Sk4xT-JqpFRKzZe-ZRCbxOZmeF5yN_MNrKtHMi2mb4jSjbH2dsyG4kKc5CsuTh7xJZV91XBDkTbss0G5a2iD_kkpBLsxMAZz8xA5HK7kQBjUJl-fxgJ5-VyNeEuyXCUKbsI3JTNby7p6xyfjXyIBGZRyuCc5Vbr3bAnpChMyTfiSmvQmjLRn3_uUdnJp9FoAwBye9Y2_M6G/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2anno.20a1.hg38

Basically they are built with the scripts in the original v1 packages, with
small adjustment. The scripts for building the two packages are also
included in the two packages.

The two v2 packages can be seamlessly integrated into the minfi analysis.

I also did some simple comparisons between v1 and v2 (
https://secure-web.cisco.com/1tb2XcerFPyKtnWDHASWp4HiJmKkEZQnpQRX0pCr4zdfYKshBWou5hiaQCMU7fxctqgxTJZHcVXeMDCsdYO4DKDTFGvXu1plvlZqOlJL_XL6wrom9PLgn0bYaqHp3f0gwbDwdR6DndCxxxmy7W8prmtZDI4h4hA_zpjZAQXUS3C77vrKmAB0L2oS_JxbGROozS9GRKkh2dTon2-KX8gl0DDiSGfbubl7xv2mtCcwLhlCW-cQ4W5zpEb7wIk7j1uqvHdAC-jwsG9VPm8VyThNbkBNrijwdrCIfHuggvBKfSknu0oFR42VZ9ifm6JaY3GTm/https%3A%2F%2Fjokergoo.github.io%2FIlluminaHumanMethylationEPICv2manifest%2Farticles%2FIlluminaHumanMethylationEPICv2manifest.html
).

Since the v1 packages were developed by the bioc core members, I want to
ask is there any plan to support the EPIC v2 array officially? If there is
no such plan, can I submit the two packages to bioc? If I can, then I will
have some additional questions regarding how to pass BiocCheck (e.g. file
size, lazy loading, ...). But that will be in another email.

Best,
Zuguang

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[Bioc-devel] Bioconductor 3.17 db0s, OrgDbs and TxDbs now available

[Interdonato, Kayla]

Hello Bioconductor Community!

The newest db0s, OrgDbs, and TxDbs annotation packages for the upcoming
Bioconductor 3.17 release are up and available for download in the devel version
of Bioconductor.

The deadline for submitting contributed annotations will be Wednesday April 
12th.

The new db0 packages are:

anopheles.db0_3.17.0.tar.gz
arabidopsis.db0_3.17.0.tar.gz
bovine.db0_3.17.0.tar.gz
canine.db0_3.17.0.tar.gz
chicken.db0_3.17.0.tar.gz
chimp.db0_3.17.0.tar.gz
ecoliK12.db0_3.17.0.tar.gz
ecoliSakai.db0_3.17.0.tar.gz
fly.db0_3.17.0.tar.gz
human.db0_3.17.0.tar.gz
malaria.db0_3.17.0.tar.gz
mouse.db0_3.17.0.tar.gz
pig.db0_3.17.0.tar.gz
rat.db0_3.17.0.tar.gz
rhesus.db0_3.17.0.tar.gz
worm.db0_3.17.0.tar.gz
xenopus.db0_3.17.0.tar.gz
yeast.db0_3.17.0.tar.gz
zebrafish.db0_3.17.0.tar.gz

The new OrgDb packages are:

GO.db_3.17.0.tar.gz
org.Ag.eg.db_3.17.0.tar.gz
org.At.tair.db_3.17.0.tar.gz
org.Bt.eg.db_3.17.0.tar.gz
org.Ce.eg.db_3.17.0.tar.gz
org.Cf.eg.db_3.17.0.tar.gz
org.Dm.eg.db_3.17.0.tar.gz
org.Dr.eg.db_3.17.0.tar.gz
org.EcK12.eg.db_3.17.0.tar.gz
org.EcSakai.eg.db_3.17.0.tar.gz
org.Gg.eg.db_3.17.0.tar.gz
org.Hs.eg.db_3.17.0.tar.gz
org.Mm.eg.db_3.17.0.tar.gz
org.Mmu.eg.db_3.17.0.tar.gz
org.Pt.eg.db_3.17.0.tar.gz
org.Rn.eg.db_3.17.0.tar.gz
org.Sc.eg.db_3.17.0.tar.gz
org.Ss.eg.db_3.17.0.tar.gz
org.Xl.eg.db_3.17.0.tar.gz
Orthology.eg.db_3.17.0.tar.gz
PFAM.db_3.17.0.tar.gz

The new TxDb packages are:

TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz
TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz
TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz

Thank you!

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


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Re: [Bioc-devel] Reopen cfTools issue #2608

[RAN HU]

Hi Lori,

I submitted a new issue #2962. Since I cannot post to the same directory
twice, this issue was also closed. Could you please open it?

Thanks,
Ran

On Tue, Mar 21, 2023 at 04:31 Kern, Lori 
wrote:

> With the recent updates to the branch renaming and given the large gap in
> time, Could you please resubmit as a new issue.
>
>
> 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 RAN HU
> 
> *Sent:* Tuesday, March 21, 2023 12:51 AM
> *To:* bioc-devel@r-project.org 
> *Cc:* Peter Li 
> *Subject:* [Bioc-devel] Reopen cfTools issue #2608
>
> Hi,
>
> I am the maintainer of cfTools issue #2608. I submitted it last year but
> didn't have many updates then. This issue has been closed. Now I have
> modified the package and am ready to submit it again. Could you please
> reopen the issue? Many thanks!
>
> Best,
> Ran
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
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>
>
> 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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Re: [Bioc-devel] Reopen cfTools issue #2608

[Kern, Lori]

 I modified the code and if you try to resubmit again it should work this time.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: RAN HU 
Sent: Tuesday, March 21, 2023 11:32 AM
To: Kern, Lori 
Cc: Peter Li ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Reopen cfTools issue #2608

Hi Lori,

I submitted a new issue #2962. Since I cannot post to the same directory twice, 
this issue was also closed. Could you please open it?

Thanks,
Ran

On Tue, Mar 21, 2023 at 04:31 Kern, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
With the recent updates to the branch renaming and given the large gap in time, 
Could you please resubmit as a new issue.



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 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of RAN HU mailto:hu...@ucla.edu>>
Sent: Tuesday, March 21, 2023 12:51 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: Peter Li mailto:peter.wenyuan...@gmail.com>>
Subject: [Bioc-devel] Reopen cfTools issue #2608

Hi,

I am the maintainer of cfTools issue #2608. I submitted it last year but
didn't have many updates then. This issue has been closed. Now I have
modified the package and am ready to submit it again. Could you please
reopen the issue? Many thanks!

Best,
Ran

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are hereby notified that any disclosure, copying, distribution, or use of this 
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This email message may contain legally privileged and/or confidential 
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[Bioc-devel] surfaltr build on Bioc 3.17 error advice

[Pooja Gangras]

Hi,

I got an email yesterday alerting me of the error in the build in the new
BioC release. Upon looking into the error further I found out that the
error is occurring because a dependency 'msa' package is not being built in
the new release likely due to some issues with the C++ compiler (just
guessing here).

Can you please advice on next steps? Is there anything I need to do here?

Thanks for your help,
Pooja

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Re: [Bioc-devel] Reopen cfTools issue #2608

[RAN HU]

Thank you, Lori! I have successfully opened a new issue.

Best,
Ran

On Tue, Mar 21, 2023 at 8:36 AM Kern, Lori 
wrote:

>  I modified the code and if you try to resubmit again it should work this
> time.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* RAN HU 
> *Sent:* Tuesday, March 21, 2023 11:32 AM
> *To:* Kern, Lori 
> *Cc:* Peter Li ; bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> *Subject:* Re: [Bioc-devel] Reopen cfTools issue #2608
>
> Hi Lori,
>
> I submitted a new issue #2962. Since I cannot post to the same directory
> twice, this issue was also closed. Could you please open it?
>
> Thanks,
> Ran
>
> On Tue, Mar 21, 2023 at 04:31 Kern, Lori 
> wrote:
>
> With the recent updates to the branch renaming and given the large gap in
> time, Could you please resubmit as a new issue.
>
>
> 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 RAN HU
> 
> *Sent:* Tuesday, March 21, 2023 12:51 AM
> *To:* bioc-devel@r-project.org 
> *Cc:* Peter Li 
> *Subject:* [Bioc-devel] Reopen cfTools issue #2608
>
> Hi,
>
> I am the maintainer of cfTools issue #2608. I submitted it last year but
> didn't have many updates then. This issue has been closed. Now I have
> modified the package and am ready to submit it again. Could you please
> reopen the issue? Many thanks!
>
> Best,
> Ran
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
>
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>
>
> 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.
>
>
> 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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Re: [Bioc-devel] download stats not accessible

[Luo Weijun via Bioc-devel]

 Thanks for the clarification. I have a analytics plot, which receives the 
download stats from these pages and has not been updated for months. I thought 
this is the cause, but could be something else. Anyway, thanks for working on 
the problem.
Weijun



 On Monday, March 20, 2023, 01:06:26 PM EDT, Sarvesh Nikumbh 
 wrote:  
 
 While I too wondered why the OP mentions unavailability "for months", now 
re-reading the OP's email, may be they meant "for months" granularity which is 
(now temporarily un)available! :D 

Cheers,
  Sarvesh

On Mon, 20 Mar 2023 at 16:50, Hervé Pagès  wrote:

Not for months, only since last week. They should be back in the next 
12-18 hours. Thanks for reporting this.

Cheers,

H.

On 19/03/2023 11:00, Luo Weijun wrote:
> Dear BioC team,
> I noticed that download stats for BioC packages are not accessible for months:
> https://bioconductor.org/packages/stats/bioc/pathview/
> https://bioconductor.org/packages/stats/bioc/BiocGenerics/
>
> can you check on this? thanks.
> Weijun Luo

-- 
Hervé Pagès

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

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-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

  
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Re: [Bioc-devel] Single Package Builder package dependency issue

[Kern, Lori]

This issue should now be resolved.
Thank you for your patience

Cheers,


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 Kern, Lori 

Sent: Monday, March 20, 2023 2:00 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Single Package Builder package dependency issue

We recently updated R on the devel builders. Some of the recent updates have 
temporarily caused issues with finding package dependencies on the Single 
Package Builder for new submission.  We are aware of the issue and are working 
on a fix. We are sorry for the inconvenience and will have it remedied soon




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

[Hervé Pagès]

Hi Pooja,

Generally speaking there are 3 things you can do when a dep breaks your 
package:


1. Consider getting rid of that dep.

2. Contact the author/maintainers of the dep to let them know about the 
problem. If you can suggest a fix (e.g. by sending a PR on GitHub), 
that's even better, as I'm sure it will help get the issue resolved more 
quickly.


3. Do nothing and hope that the dep will get fixed in time for the 3.17 
release (scheduled for end of April, see our release schedule here 
https://bioconductor.org/developers/release-schedule/ for the details). 
But that's risky ;-)


In the case of msa's compilation error, it seems to be due to the R 
developers switching to the C++17 compiler by default for C++ package 
code in recent version of R devel (4.3 series). This is documented in 
the R devel NEWS file here: 
https://cran.r-project.org/doc/manuals/r-devel/NEWS.html


Note that BioC 3.16 is based on R 4.2 which uses the C++14 compiler by 
default for C++ package code. Therefore, in BioC 3.16, msa compiles fine 
on all platforms: 
https://bioconductor.org/checkResults/3.16/bioc-LATEST/msa/


So one option for the msa folks is to stick to the C++14 compiler by 
adding C++14 to they 'SystemRequirements' field. Although I don't know 
how that would play with Rcpp which gets compiled with the C++17 
compiler, and which they depend on. So maybe that's a little bit risky? 
Maybe something to check with the Rcpp experts.


Best,

H.

On 21/03/2023 09:18, Pooja Gangras wrote:

Hi,

I got an email yesterday alerting me of the error in the build in the new
BioC release. Upon looking into the error further I found out that the
error is occurring because a dependency 'msa' package is not being built in
the new release likely due to some issues with the C++ compiler (just
guessing here).

Can you please advice on next steps? Is there anything I need to do here?

Thanks for your help,
Pooja

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--
Hervé Pagès

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

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Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

[Pooja Gangras]

Hi Herve,

Thank you for the quick response.

So what surprises me is that msa was compiling and building just fine on
the devel branch until now. And hence so was surfaltr, without any errors.
There was a warning in surfaltr which one can see on the 3.16 release, I
had fixed it in the devel branch. For some reason I was not able to push
changes to the existing 3.16 release branch.

I will go ahead and contact the maintainer for msa but hoping that it will
fix itself before release because it was just fine until yesterday.

Thanks,
Pooja

On Tue, Mar 21, 2023, 2:43 PM Hervé Pagès 
wrote:

> Hi Pooja,
>
> Generally speaking there are 3 things you can do when a dep breaks your
> package:
>
> 1. Consider getting rid of that dep.
>
> 2. Contact the author/maintainers of the dep to let them know about the
> problem. If you can suggest a fix (e.g. by sending a PR on GitHub),
> that's even better, as I'm sure it will help get the issue resolved more
> quickly.
>
> 3. Do nothing and hope that the dep will get fixed in time for the 3.17
> release (scheduled for end of April, see our release schedule here
> https://bioconductor.org/developers/release-schedule/ for the details).
> But that's risky ;-)
>
> In the case of msa's compilation error, it seems to be due to the R
> developers switching to the C++17 compiler by default for C++ package
> code in recent version of R devel (4.3 series). This is documented in
> the R devel NEWS file here:
> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>
> Note that BioC 3.16 is based on R 4.2 which uses the C++14 compiler by
> default for C++ package code. Therefore, in BioC 3.16, msa compiles fine
> on all platforms:
> https://bioconductor.org/checkResults/3.16/bioc-LATEST/msa/
>
> So one option for the msa folks is to stick to the C++14 compiler by
> adding C++14 to they 'SystemRequirements' field. Although I don't know
> how that would play with Rcpp which gets compiled with the C++17
> compiler, and which they depend on. So maybe that's a little bit risky?
> Maybe something to check with the Rcpp experts.
>
> Best,
>
> H.
>
> On 21/03/2023 09:18, Pooja Gangras wrote:
> > Hi,
> >
> > I got an email yesterday alerting me of the error in the build in the new
> > BioC release. Upon looking into the error further I found out that the
> > error is occurring because a dependency 'msa' package is not being built
> in
> > the new release likely due to some issues with the C++ compiler (just
> > guessing here).
> >
> > Can you please advice on next steps? Is there anything I need to do here?
> >
> > Thanks for your help,
> > Pooja
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
>

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Re: [Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

[Zuguang Gu]

I am aware of the AnnotationHub package, but currently I think it is not
possible to integrate with minfi.

In the last several lines in
https://github.com/hansenlab/minfi/blob/master/R/IlluminaMethylationAnnotation-class.R

setMethod(
"getManifest",
signature(object = "IlluminaMethylationAnnotation"),
function(object) {
maniString <- .getManifestString(object@annotation)
if (!require(maniString, character.only = TRUE)) {
stop(sprintf("cannot load manifest package %s", maniString))
}
get(maniString)
}
)

Here `maniString` contains the name of a manifest package,
e.g. IlluminaHumanMethylationEPICmanifest. After loading the manifest
package, minfi directly looks for the variable with the same name as the
manifest package name. So it would be the easiest if just making a new
manifest package taking the IlluminaHumanMethylationEPICmanifest as a
template. Or minfi needs to be adjusted to allow for more flexible
integration of new manifest packages/objects.

Cheers,
Zuguang

On Tue, 21 Mar 2023 at 14:58, Kern, Lori 
wrote:

> The maintainer for these two packages
>
> IlluminaHumanMethylationEPICmanifest
> IlluminaHumanMethylationEPICanno.ilm10b4.hg19
>
> Is actually Kasper Daniel Hansen as listed in the DESCRIPTION file not bioc
> core members.
>
> You could reach out to Kasper to see if there is any intention or efforts
> that have already been made to include v2.
>
> If not you can submit the packages. We have moved away from traditional
> annotation packages and I would suggest moving towards an annotationhub
> package submission where the data is stored elsewhere on a external server
> like S3 buckets, Azure Data Lakes, Zenodo, etc (we have an bioconductor
> azure data lake location that can be used;  it just cannot be store on any
> personal location like github or dropbox)
> Little modification to an existing package structure is needed. Basically
> you would remove the data to the external location,  include a metadata.csv
> file in the inst/extdata, and include the biocView AnnotationHub. More
> details can be found at
>
> https://bioconductor.org/packages/release/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html
> Then submit as normal to the new package submission tracker.
>
>
> Cheers,
>
>
> 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
> Zuguang Gu 
> *Sent:* Saturday, March 18, 2023 3:56 PM
> *To:* bioc-devel 
> *Subject:* [Bioc-devel] Manifest and annotation packages for EPIC
> methylation array v2.0
>
> Hi Bioc-devel,
>
> I recently analyzed a methylation array dataset which is from EPIC array
> v2.0 (
>
> https://secure-web.cisco.com/1lqTYM1ya8XGMtHfnsdUpS8GBFfG2-c035Su1G2QlTqVVUgHKjstjf7gJtWM-rIZGvRTc76YuWsBkkII9eMBecVmP2e1A55mf2ahOVb9Nco1iHMg44efGw-SU_hREgUNlB7o5Sy6C-OATItf9L-NsoDSZnhzqs8WSnCWLDCRBlqDX8bOOoHRQ-xf-Ya5ki_CjTKaCuhaKmLon1QLYV-KVUrdfKTBg0FB1HEG1QPS2gNNCCpqGlOaNWCVxFitnlqZQcyJur9d80tL8Nf9Frcm66rjXthUFvP7ZBdhgy6BIvbN_rytmo9nR3tFO-vqJO7nm/https%3A%2F%2Fwww.illumina.com%2Fproducts%2Fby-type%2Fmicroarray-kits%2Finfinium-methylation-epic.html)
> and currently there is no manifest nor annotation packages for that one.
> The available packages on Bioconductor are only for EPIC array v1.0:
>
> - IlluminaHumanMethylationEPICmanifest
> - IlluminaHumanMethylationEPICanno.ilm10b4.hg19
>
> And it is not proper to use the v1 packages for the v2 data.
>
> I've built a manifest package and an annotation package for the EPIC array
> v2.0. They are available at:
>
>
> https://secure-web.cisco.com/1QiOF2zfvxn-NM_D59JEGrLZNxfjlhE96RB2QFStOhZ-M_vbiO6U4EAWhA4DxQl2K4UCyCR2IlwPHsInzW3sJ2AMU8ZGdfx2iG9GgacdRqfiLFso1I8byAAr3GSfV0yC6vYlWWOAcemIIiQmhz2ucGFBPnr6_XM6d-Fu8yoDbXBs4Kgr-BcAl-Pd75iP9-5p892EmkkdxAoDV7gLycQbrWXkoZ_k4OFitm-jojHDyBux8UbuaxsY6o_AM-f-5uji4V325my36EKUam9Fs_BWlQuoEm92wkvrPfLOrfSGs3gNRe_yOUL-xnZE2dgDIlwr_/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2manifest
>
> https://secure-web.cisco.com/1cO_2hmhoc2EdgBhXjFVHzLhg8R28yb3KFaT2NGVp8p93xKzA8PkG-N2DaTdM1tL75mwBskP9Kd-h2MLGiXL85Pfa8uZd6kt11AoYZjhV6ndx7tUFMKrg3Sk4xT-JqpFRKzZe-ZRCbxOZmeF5yN_MNrKtHMi2mb4jSjbH2dsyG4kKc5CsuTh7xJZV91XBDkTbss0G5a2iD_kkpBLsxMAZz8xA5HK7kQBjUJl-fxgJ5-VyNeEuyXCUKbsI3JTNby7p6xyfjXyIBGZRyuCc5Vbr3bAnpChMyTfiSmvQmjLRn3_uUdnJp9FoAwBye9Y2_M6G/https%3A%2F%2Fgithub.com%2Fjokergoo%2FIlluminaHumanMethylationEPICv2anno.20a1.hg38
>
> Basically they are built with the scripts in the original v1 packages, with
> small adjustment. The scripts for building the two packages are also
> included in the two packages.
>
> The two v2 packages can be seamlessly integrated into the minfi analysis.
>
> I also did some simple comparisons between v1 and v2 (
>
> https://secure-web.cisco.com/1tb2XcerFPyKtnWDHASWp4HiJmKkEZQnpQRX0pCr4zdfYKshBWou5hiaQC

Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

[Hervé Pagès]

On 21/03/2023 12:48, Pooja Gangras wrote:

> Hi Herve,
>
> Thank you for the quick response.
>
> So what surprises me is that msa was compiling and building just fine 
> on the devel branch until now.
As I said, the switch from C++14 to C++17 happened not too long ago in 
the devel version of R. And since we recently updated R on the BioC 3.17 
builders to the most recent R devel, that switch is now reflected on the 
3.17 builds.
> And hence so was surfaltr, without any errors. There was a warning in 
> surfaltr which one can see on the 3.16 release, I had fixed it in the 
> devel branch. For some reason I was not able to push changes to the 
> existing 3.16 release branch.
That's a separate issue but if you provide more details about how you 
tried to do this and what happened, maybe someone on this list will be 
able to help.
>
> I will go ahead and contact the maintainer for msa but hoping that it 
> will fix itself before release because it was just fine until yesterday.

Unfortunately it won't fix itself.

H.

>
> Thanks,
> Pooja
>
> On Tue, Mar 21, 2023, 2:43 PM Hervé Pagès  
> wrote:
>
> Hi Pooja,
>
> Generally speaking there are 3 things you can do when a dep breaks
> your
> package:
>
> 1. Consider getting rid of that dep.
>
> 2. Contact the author/maintainers of the dep to let them know
> about the
> problem. If you can suggest a fix (e.g. by sending a PR on GitHub),
> that's even better, as I'm sure it will help get the issue
> resolved more
> quickly.
>
> 3. Do nothing and hope that the dep will get fixed in time for the
> 3.17
> release (scheduled for end of April, see our release schedule here
> https://bioconductor.org/developers/release-schedule/ for the
> details).
> But that's risky ;-)
>
> In the case of msa's compilation error, it seems to be due to the R
> developers switching to the C++17 compiler by default for C++ package
> code in recent version of R devel (4.3 series). This is documented in
> the R devel NEWS file here:
> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>
> Note that BioC 3.16 is based on R 4.2 which uses the C++14
> compiler by
> default for C++ package code. Therefore, in BioC 3.16, msa
> compiles fine
> on all platforms:
> https://bioconductor.org/checkResults/3.16/bioc-LATEST/msa/
>
> So one option for the msa folks is to stick to the C++14 compiler by
> adding C++14 to they 'SystemRequirements' field. Although I don't
> know
> how that would play with Rcpp which gets compiled with the C++17
> compiler, and which they depend on. So maybe that's a little bit
> risky?
> Maybe something to check with the Rcpp experts.
>
> Best,
>
> H.
>
> On 21/03/2023 09:18, Pooja Gangras wrote:
> > Hi,
> >
> > I got an email yesterday alerting me of the error in the build
> in the new
> > BioC release. Upon looking into the error further I found out
> that the
> > error is occurring because a dependency 'msa' package is not
> being built in
> > the new release likely due to some issues with the C++ compiler
> (just
> > guessing here).
> >
> > Can you please advice on next steps? Is there anything I need to
> do here?
> >
> > Thanks for your help,
> > Pooja
> >
> >       [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
-- 
Hervé Pagès

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

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