date:20201019

Re: [Bioc-devel] Update CARNIVAL maintainer

2020-10-19 Thread Turaga, Nitesh

Hi Enio and Olgo,

I’ve taken care of this.

Olga, you should have access to the package as soon as you add your SSH keys to 
your 
git.bioconductor.org/BiocCredentials
  account.

You’ll get a private email from me about your account information.

Best,

Nitesh

On Oct 16, 2020, at 10:42 AM, Enio Gjerga 
mailto:enio.gje...@gmail.com>> wrote:

Hello,

I am Enio Gjerga and I am listed as the maintainer of the CARNIVAL package in 
Bioconductor: 
https://bioconductor.org/packages/release/bioc/html/CARNIVAL.html

I would like to delegate the role of the maintainer to Olga Ivanova (cc'ed). 
for anything needed please let us know.

Cheers,
Enio

--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057
[https://secure-web.cisco.com/1viVTjdj3n2yLkwynAsbmo-vQ8e-HgYE4RG9NiN-JcuVeTb8Cc6APISrZreRnMn9Pw9GBjuezYvrg9VxINkCQlhZzTXyE3OOeri37OOwRmhtwNbQw1a3eoVhpX9mWZOUYmFBb0lmKKT2ehitF91Od2TVdk9CjdMSbKK4sWLmfyc479RWS9ILCm0gGn_-CW_meHj35Ncg8EO1zgUs2xhnrGUzi4dVdQj32EBlhTW1wjPpmlnDG6g4FUJ-gzdrjROZJsg7dCmKrheaxuhJ2NESrtBNwDqobOejEHKTeXIpWVGz_lLLkWoovt4ut3i1dkOvwSAVbFVKyrp-YX5PADujUhg/https%3A%2F%2Fdocs.google.com%2Fuc%3Fexport%3Ddownload%26id%3D0B6mjZ0BJeekOeUgyQmpTQXYwWjg%26revid%3D0B6mjZ0BJeekORUxnZ1VVS1ZjY25UTUc2VUU1dDA4N0lLUlM0PQ]



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Re: [Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

2020-10-19 Thread Nitesh Turaga

Hi Mikhail,

You should have access to your packages now.

Best,

Nitesh 

> On Oct 19, 2020, at 3:13 PM, Mikhail Dozmorov  
> wrote:
> 
> Hello,
> Would it be possible to add me as a co-maintainer to two packages?
> https://bioconductor.org/packages/SpectralTAD/
> https://bioconductor.org/packages/TADCompare/
> 
> It'll be best if both Kellen, the current maintainer, and I will have push
> access.
> 
> Thanks,
> Mikhail
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

2020-10-19 Thread Gordon K Smyth

Sorry, there was mistype in previous email. Here is the reproducible example 
again. This code produces the NOTE when run in a fresh R 4.0.3 for Windows 
session:

  library(Rcpp)
  Rcpp.package.skeleton("TestPack", example_code = TRUE)
  library(devtools)
  check("TestPack")


> -Original Message-
> From: Gordon K Smyth
> Sent: Tuesday, 20 October 2020 7:58 AM
> To: Martin Morgan ; bioc-devel@r-project.org
> Subject: RE: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'
>
> If you're interested, here is a small reproducible example. This example uses
> Rcpp, but I think that any src code will give the same NOTE:
>
>   library(Rcpp)
>   Rcpp.package.skeleton("TestPack", example_code = TRUE)
>   library(devtools)
>   install.package("devtools")
>   check("TestPack")
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Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

2020-10-19 Thread Gordon K Smyth

Hi Martin and Vince,

Thanks for the responses.

I noticed first noticed this issue (false positive R CMD NOTE about abort) when 
it appeared with R-devel for Windows a few months ago. The same behaviour has 
now appeared in R 4.0.3. It is specific to Windows, R 4.0.3 or higher and 
Rtools40. It may also depend on how you run R CMD check. I run R CMD check at 
the Windows command prompt with Rtools40 and R 4.0.3 in the PATH. The NOTE 
appears for any package that contains Fortran, C or C++.

I had a discussion about it on StackOverflow a couple of days ago with two 
other CRAN package authors:
https://stackoverflow.com/questions/64402688/information-on-o-files-for-x64-is-not-available-note-on-r-package-checks-using

I submitted a package to CRAN several days ago and CRAN did not raise this NOTE 
as an issue, even though I can see the NOTE in my own R CMD checks for the same 
package. I have therefore decided to ignore it in future.

If you're interested, here is a small reproducible example. This example uses 
Rcpp, but I think that any src code will give the same NOTE:

  library(Rcpp)
  Rcpp.package.skeleton("TestPack", example_code = TRUE)
  library(devtools)
  install.package("devtools")
  check("TestPack")

This produces
  > checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 
'C:/Users/smyth/AppData/Local/Temp/RtmpAdefZW/TestPack.Rcheck/TestPack/libs/x64/TestPack.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Session info:
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] devtools_2.3.2 usethis_1.6.3  Rcpp_1.0.5

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11   magrittr_1.5  rcmdcheck_1.3.3   pkgload_1.1.0
 [5] R6_2.4.1  rlang_0.4.8   fansi_0.4.1   tools_4.0.3
 [9] pkgbuild_1.1.0xopen_1.0.0   sessioninfo_1.1.1 cli_2.1.0
[13] withr_2.3.0   ellipsis_0.3.1remotes_2.2.0 assertthat_0.2.1
[17] digest_0.6.25 rprojroot_1.3-2   crayon_1.3.4  processx_3.4.4
[21] callr_3.5.1   fs_1.5.0  ps_1.4.0  testthat_2.3.2
[25] memoise_1.1.0 glue_1.4.2compiler_4.0.3desc_1.2.0
[29] backports_1.1.10  prettyunits_1.1.1

--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research

> -Original Message-
> From: Martin Morgan 
> Sent: Tuesday, 20 October 2020 4:41 AM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'
>
> Just to respond that I don't have a clear answer for you; I would guess that 
> there
> is a change upstream of your package, and that the NOTE is spurious. If this 
> also
> occurs on a non-Bioconductor Windows machine then it would be appropriate
> to bring this up on another forum, R-devel or R-package-devel
> (https://stat.ethz.ch/mailman/listinfo/r-package-devel), especially if the 
> NOTE
> can be elicited by a trivial example package. I would assume that the NOTE is
> safe to ignore, but...
>
> I think the 'Dependency walker' utility could be used to investigate the DLL 
> to
> identify where this comes from, but I don't have easy access to a Windows
> machine for this type of work.
>
> Martin Morgan
>
> On 10/16/20, 7:00 PM, "Bioc-devel on behalf of Gordon K Smyth"  boun...@r-project.org on behalf of sm...@wehi.edu.au> wrote:
>
> This is more an R question than a Bioconductor question, but I would be
> grateful if the Biocore team or other Bioc developers have any insight.
>
> After upgrading to R 4.0.3 or R 4.1.0-devel, I find that running R CMD 
> check
> under Windows now gives a worrying Note about .o files and 'abort'. The same
> warning occurs for all the packages I maintain that contain source code. The
> Note does not appear for R 4.0.2 or earlier.
>
> An example of the Note is:
>
> START QUOTE
> * checking compiled code ... NOTE
> Note: information on .o files for x64 is not available
> File 'c:/Gordon/software/gitbioc/limma.Rcheck/limma/libs/x64/limma.dll':
>   Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
>   Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
>   Found 'printf', possibly from 'printf' (C)
>
> Compiled code should not call entry points which might terminate R nor
> write to stdout/stderr instead of to the console, nor use Fortran I/O
> nor system RNGs. The

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

2020-10-19 Thread Vincent Carey

On Mon, Oct 19, 2020 at 1:41 PM Martin Morgan 
wrote:

> Just to respond that I don't have a clear answer for you; I would guess
> that there is a change upstream of your package, and that the NOTE is
> spurious. If this also occurs on a non-Bioconductor Windows machine then it
> would be appropriate to bring this up on another forum, R-devel or
> R-package-devel (https://stat.ethz.ch/mailman/listinfo/r-package-devel),
> especially if the NOTE can be elicited by a trivial example package. I
> would assume that the NOTE is safe to ignore, but...
>

I was able to reproduce the abort notes using R 4.0.3 with current
rcmdcheck run over the limma_3.44.3.tar.gz on a non-bioconductor
windows machine.  I tried dependency walker on limma.dll there but did not
see any interesting data.  The notes occur with
IRanges on the machine I checked.



>
> I think the 'Dependency walker' utility could be used to investigate the
> DLL to identify where this comes from, but I don't have easy access to a
> Windows machine for this type of work.
>
> Martin Morgan
>
> On 10/16/20, 7:00 PM, "Bioc-devel on behalf of Gordon K Smyth" <
> bioc-devel-boun...@r-project.org on behalf of sm...@wehi.edu.au> wrote:
>
> This is more an R question than a Bioconductor question, but I would
> be grateful if the Biocore team or other Bioc developers have any insight.
>
> After upgrading to R 4.0.3 or R 4.1.0-devel, I find that running R CMD
> check under Windows now gives a worrying Note about .o files and 'abort'.
> The same warning occurs for all the packages I maintain that contain source
> code. The Note does not appear for R 4.0.2 or earlier.
>
> An example of the Note is:
>
> START QUOTE
> * checking compiled code ... NOTE
> Note: information on .o files for x64 is not available
> File
> 'c:/Gordon/software/gitbioc/limma.Rcheck/limma/libs/x64/limma.dll':
>   Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
>   Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
>   Found 'printf', possibly from 'printf' (C)
>
> Compiled code should not call entry points which might terminate R nor
> write to stdout/stderr instead of to the console, nor use Fortran I/O
> nor system RNGs. The detected symbols are linked into the code but
> might come from libraries and not actually be called.
> END QUOTE
>
> I am baffled by the Note because my code does not contain any of the
> offending functions (abort, exit or printf) that the Note accuses me of.
> Surprisingly I can't find any recent chatter about this Note on the R-devel
> mailing list. There no mention of it in the Rtools documentation. I have
> also searched the R manual on Writing R Extensions but can't find anything
> that would cause a Windows-specific note.
>
> I see from the build/check reports for Bioconductor 3.12 that I am not
> alone. The same Note appears in the Windows check logs for a very large
> number of Bioconductor packages, for example Biobase:
>
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/riesling1-checksrc.html
>
> I am guessing that the same Note now appears in the Windows check log
> for every Bioconductor package that contains any C or Fortran source code.
> The Note does not appear in the Linux or Mac check logs for the same
> packages.
>
> My questions are:
> 1. Does anyone know what is causing this Note.
> 2. Can I fix the note? If not, can I ignore it?
>
> I also wonder whether this Note will cause the CRAN maintainers to not
> accept my package submissions, but that is perhaps a question for another
> forum.
>
> Thanks for any insights
> Gordon
>
> --
> Professor Gordon K Smyth
> Joint Head, Bioinformatics Division
> Walter and Eliza Hall Institute of Medical Research
>
> ___
>
> The information in this email is confidential and intended solely for
> the addressee.
> You must not disclose, forward, print or use it without the permission
> of the sender.
>
> The Walter and Eliza Hall Institute acknowledges the Wurundjeri people
> of the Kulin
> Nation as the traditional owners of the land where our campuses are
> located and
> the continuing connection to country and community.
> ___
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

2020-10-19 Thread Mikhail Dozmorov

Hello,
Would it be possible to add me as a co-maintainer to two packages?
https://bioconductor.org/packages/SpectralTAD/
https://bioconductor.org/packages/TADCompare/

It'll be best if both Kellen, the current maintainer, and I will have push
access.

Thanks,
Mikhail

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Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

2020-10-19 Thread Martin Morgan

Just to respond that I don't have a clear answer for you; I would guess that 
there is a change upstream of your package, and that the NOTE is spurious. If 
this also occurs on a non-Bioconductor Windows machine then it would be 
appropriate to bring this up on another forum, R-devel or R-package-devel 
(https://stat.ethz.ch/mailman/listinfo/r-package-devel), especially if the NOTE 
can be elicited by a trivial example package. I would assume that the NOTE is 
safe to ignore, but... 

I think the 'Dependency walker' utility could be used to investigate the DLL to 
identify where this comes from, but I don't have easy access to a Windows 
machine for this type of work.

Martin Morgan

On 10/16/20, 7:00 PM, "Bioc-devel on behalf of Gordon K Smyth" 
 wrote:

This is more an R question than a Bioconductor question, but I would be 
grateful if the Biocore team or other Bioc developers have any insight.

After upgrading to R 4.0.3 or R 4.1.0-devel, I find that running R CMD 
check under Windows now gives a worrying Note about .o files and 'abort'. The 
same warning occurs for all the packages I maintain that contain source code. 
The Note does not appear for R 4.0.2 or earlier.

An example of the Note is:

START QUOTE
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'c:/Gordon/software/gitbioc/limma.Rcheck/limma/libs/x64/limma.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
END QUOTE

I am baffled by the Note because my code does not contain any of the 
offending functions (abort, exit or printf) that the Note accuses me of. 
Surprisingly I can't find any recent chatter about this Note on the R-devel 
mailing list. There no mention of it in the Rtools documentation. I have also 
searched the R manual on Writing R Extensions but can't find anything that 
would cause a Windows-specific note.

I see from the build/check reports for Bioconductor 3.12 that I am not 
alone. The same Note appears in the Windows check logs for a very large number 
of Bioconductor packages, for example Biobase:


http://bioconductor.org/checkResults/devel/bioc-LATEST/Biobase/riesling1-checksrc.html

I am guessing that the same Note now appears in the Windows check log for 
every Bioconductor package that contains any C or Fortran source code. The Note 
does not appear in the Linux or Mac check logs for the same packages.

My questions are:
1. Does anyone know what is causing this Note.
2. Can I fix the note? If not, can I ignore it?

I also wonder whether this Note will cause the CRAN maintainers to not 
accept my package submissions, but that is perhaps a question for another forum.

Thanks for any insights
Gordon

--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research

___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of 
the sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of 
the Kulin
Nation as the traditional owners of the land where our campuses are located 
and
the continuing connection to country and community.
___

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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Leonardo Collado Torres

Thanks! This will also help me ^^ https://orcid.org/-0003-2140-308X

Best,
Leo

Leonardo Collado Torres, Ph. D.
Investigator

LIEBER INSTITUTE for BRAIN DEVELOPMENT
855 N. Wolfe St., Suite 300
Baltimore, MD 21205
lcolladotor.github.io
lcollado...@gmail.com



On Mon, Oct 19, 2020 at 7:43 AM Manders-2, F.M.
 wrote:
>
> Yes, I’ll create a PR.
>
> From: Vincent Carey 
> Date: Monday, 19 October 2020 at 12:36
> To: "Manders-2, F.M." , bioc-devel 
> 
> Subject: Fwd: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
> forwarding to bioc-devel
> -- Forwarded message -
> From: Vincent Carey 
> mailto:st...@channing.harvard.edu>>
> Date: Mon, Oct 19, 2020 at 6:33 AM
> Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
> To: Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
> Cc: Alessandro Lussana via Bioc-devel 
> mailto:Bioc-devel@r-project.org>>
>
> looks like BiocCheck/checks.R:validID <- 
> grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid)
>
> has to change -- do you have time to determine the correct regex for this and 
> file a PR?
>
>
>
> On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
>  wrote:
> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t know 
> why I have an X there and not a number.
>
> From: Vincent Carey 
> mailto:st...@channing.harvard.edu>>
> Date: Monday, 19 October 2020 at 12:20
> To: "Manders-2, F.M." 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
> Cc: Alessandro Lussana via Bioc-devel 
> mailto:Bioc-devel@r-project.org>>
> Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
>  person("Freek", "Manders", email = 
> "f.m.mand...@prinsesmaximacentrum.nl",
>  role = c("aut"),
> comment = c(ORCID = "-0001-6197-347X")),
>
> is what I see in a current checkout.  is "X" at the end correct?  maybe there 
> is an encoding issue?
>
> On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. 
> mailto:f.m.mand...@prinsesmaximacentrum.nl>>
>  wrote:
> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
> for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on the 
> dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
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>
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Re: [Bioc-devel] Bioconductor 3.12 db0s, OrgDbs and TxDbs now available

2020-10-19 Thread Interdonato, Kayla

My apologies - I seem to have a typo in the names of the updated OrgDb 
packages. Please see the following corrected list:



org.Ag.eg.db_3.12.0.tar.gz

org.At.tair.db_3.12.0.tar.gz

org.Bt.eg.db_3.12.0.tar.gz

org.Ce.eg.db_3.12.0.tar.gz

org.Cf.eg.db_3.12.0.tar.gz

org.Dm.eg.db_3.12.0.tar.gz

org.Dr.eg.db_3.12.0.tar.gz

org.EcK12.eg.db_3.12.0.tar.gz

org.EcSakai.eg.db_3.12.0.tar.gz

org.Gg.eg.db_3.12.0.tar.gz

org.Hs.eg.db_3.12.0.tar.gz

org.Mm.eg.db_3.12.0.tar.gz

org.Mmu.eg.db_3.12.0.tar.gz

org.Pf.plasmo.db_3.12.0.tar.gz

org.Pt.eg.db_3.12.0.tar.gz

org.Rn.eg.db_3.12.0.tar.gz

org.Sc.eg.db_3.12.0.tar.gz

org.Ss.eg.db_3.12.0.tar.gz

org.Xl.eg.db_3.12.0.tar.gz

PFAM.db_3.12.0.tar.gz



Best,

Kayla

From: "Interdonato, Kayla" 
Date: Friday, October 16, 2020 at 11:25 AM
To: "bioc-devel@r-project.org" 
Subject: Bioconductor 3.12 db0s, OrgDbs and TxDbs now available

Hello Bioconductor Community!

The newest db0s, OrgDbs, and TxDbs annotation packages for the upcoming
Bioconductor 3.12 release are up and available for download in the devel version
of Bioconductor.

The deadline for submitting contributed annotations will be Wednesday October 
21st.

The new db0 packages are:

anopheles.db0_3.12.0.tar.gz
arabidopsis.db0_3.12.0.tar.gz
bovine.db0_3.12.0.tar.gz
canine.db0_3.12.0.tar.gz
chicken.db0_3.12.0.tar.gz
chimp.db0_3.12.0.tar.gz
ecoliK12.db0_3.12.0.tar.gz
ecoliSakai.db0_3.12.0.tar.gz
fly.db0_3.12.0.tar.gz
human.db0_3.12.0.tar.gz
malaria.db0_3.12.0.tar.gz
mouse.db0_3.12.0.tar.gz
pig.db0_3.12.0.tar.gz
rat.db0_3.12.0.tar.gz
rhesus.db0_3.12.0.tar.gz
worm.db0_3.12.0.tar.gz
xenopus.db0_3.12.0.tar.gz
yeast.db0_3.12.0.tar.gz
zebrafish.db0_3.12.0.tar.gz

The new OrgDb packages are:

GO.db_3.12.0.tar.gz
org.Ag.eg.db_3.12.tar.gz
org.At.tair.db_3.12.tar.gz
org.Bt.eg.db_3.12.tar.gz
org.Ce.eg.db_3.12.tar.gz
org.Cf.eg.db_3.12.tar.gz
org.Dm.eg.db_3.12.tar.gz
org.Dr.eg.db_3.12.tar.gz
org.EcK12.eg.db_3.12.tar.gz
org.EcSakai.eg.db_3.12.tar.gz
org.Gg.eg.db_3.12.tar.gz
org.Hs.eg.db_3.12.tar.gz
org.Mm.eg.db_3.12.tar.gz
org.Mmu.eg.db_3.12.tar.gz
org.Pf.plasmo.db_3.12.tar.gz
org.Pt.eg.db_3.12.tar.gz
org.Rn.eg.db_3.12.tar.gz
org.Sc.eg.db_3.12.tar.gz
org.Ss.eg.db_3.12.tar.gz
org.Xl.eg.db_3.12.tar.gz
PFAM.db_3.12.tar.gz

The new TxDb packages are:

TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz
TxDb.Celegans.UCSC.ce11.ensGene_3.12.0.tar.gz
TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz
TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz
TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz
TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz
TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz
TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz
TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz
TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz
TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz
TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz
TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz

Thank you!

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


This email message may contain legally privileged and/or confidential 
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Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

2020-10-19 Thread Kern, Lori

The latest version is now reflected in the build report and on the package 
landing page.  Please again review timings on this page that the landing pages 
are only updated after a successful build with version bump hence why the full 
update on the build report and landing pages can take up to 48 hours

http://bioconductor.org/developers/how-to/troubleshoot-build-report/



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

Cheers,

From: Xiaowen Chen 
Sent: Saturday, October 17, 2020 2:40 PM
To: Martin Morgan ; Kern, Lori 
; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

Yes, the check report is the one I lately push,
But the epihet on the website" 
bioconductor.org/packages/devel/bioc/html/epihet.html " is not the one latest 
through check the vignettes.

So now I updated the version in DESCRIPTION to 1.5.3, and push again and hope I 
can see the latest version on the website " 
bioconductor.org/packages/devel/bioc/html/epihet.html "

Thank you.
Best,
Xiaowen

On 10/17/20, 10:26 AM, "Martin Morgan"  wrote:

Packages are built nightly, so you must usually wait ~24 - 48 hours for 
your commits to be reflected in the build report.

Sometimes issues prevent the build report from being processed, so on the 
build overview page such as

  
http://secure-web.cisco.com/1Ktwhc-1fOD537-R0w6DZa7xx108gqW4GXONiL_FjB0P1DtGxH_Ts1H15R1oCNf20fTFBPForRU_uweA01_tMeLAiwRSKQ0Q_xCj2Z8jLcpBwyrTHakwW74B7Ej_esnheP6s97mLq0G8HufjxWCAMyPXrqxWK_2H0JRC050653eLkp30aJip-dZMb20BmCg6xzhw1Mqd_Pu4vxReOYEhWo_pazA4USiF82BebUOt0QWntEYAreDEZS0vPfkJgw6aINuP68uLLmrlKKymPFPGzZyK5M0xoICUDwMpvAJBzlGs8GH5WWpS6wQFicGIs3S9K/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2F

compare

  - 'This page generated on...'
  - 'Approx snapshot date...'

and on individual package pages such as

  
http://secure-web.cisco.com/1zdf9ads4VET4y3GW4X3aCfi4cSdGfENmczEK6FJ9MQ-WEKuGct0QO0SntkvNKCDJZ37-wOYUmiXrFyshe1xTL5sQgKZLac_kzk0nrloIqi13Pc10llxMUAxmJ_-ND5PH6hH_TxA9lo4zvnrATrDRn-cFkx-n_mqGlOeOTrj9xBy7o-KJcXDInohJncsDSiEJYNz4sfxfTCnL-eSaoLBf1RhXMP8_nUU8dEbmTm_CFielxiaHfiyL7icRTqu0la8VqPm-a13wu_5O6JShbyKShYvUTZ4vSL14pj0zExjvkRHMMqcjMOpGZbRRGlqt1Rge/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fepihet%2F

look for

  - 'Snapshot date...'
  - 'Last commit...'

If your last commit (`git log --oneline`) was after the snapshot date, then 
changes you made will not be reflected in the build report.

Because of the delay in the nightly builds, it makes sense to do your best 
to ensure that commits are correct, ensuring that your R and Bioconductor 
packages are current for the version that you are committing to, and running

  R CMD build 
  R CMD check 

locally before pushing changes.

Martin



On 10/16/20, 5:08 PM, "Bioc-devel on behalf of Xiaowen Chen" 
 wrote:

Hi Kern,
I checked the epihet on the website 
�bioconductor.org/packages/devel/bioc/html/epihet.html�.
I saw its version is 1.5.2
Unfortunately, it is not the one I push this morning. It is not the 
latest one.
Could you help me check what�s wrong here? I am so sorry about that.

Best,
Xiaowen
From: "Kern, Lori" 
Date: Friday, October 16, 2020 at 9:54 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: A question about r package update

We apologize.  It was announced on the Bioconductor slack but we forgot 
to post on the bioc-devel mailing list. There was an issue with the builders 
and there was no report generated yesterday Thursday October 15.  The issue 
should be resolved and we expect a build report today.
I do see 1.5.2 in our git repository so it should be reflected in the 
report today.
We apologize for the confusion and the inconvenience


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 
Xiaowen Chen 
Sent: Friday, October 16, 2020 9:49 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] A question about r package update

Hi bioc-devel,
I am sorry for email you so often, this morning I checked the check 
report website, it did not change.
And I noticed that the data is �This page was generated on 2020-10-14 
11:07:41 -0400 (Wed, 14 Oct 2020).�

Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 
1.5.1 shown in the website.
Even it is not the one I pushed, now it have been two days.

So

Re: [Bioc-devel] VERSO issue #1689

2020-10-19 Thread Kern, Lori

We are sorry for the delay. We try to get to package reviews within 2 weeks of 
submission.  Package reviews are only part of the core team task and as you can 
imagine release time is busy.  Nitesh will have a review for you shortly.

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 Kasper Daniel 
Hansen 
Sent: Monday, October 19, 2020 6:01 AM
To: Davide Maspero 
Cc: Alex Graudenzi ; bioc-devel 
; Nitesh ; 
daniele.ramazzo...@unimib.it 
Subject: Re: [Bioc-devel] VERSO issue #1689

I can't speak for the reviewer, but the package currently has 2 WARNINGS.
If I were you, I would fix those warnings and push the fixes to Github, at
which point the package will be re-built and re-checked. You're not
supposed to have any ERRORS / WARNINGS when you submit. I would also look
at the NOTES, at least the following should be fixed

* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.

* Checking coding practice...
  *NOTE: Avoid 1:...; use seq_len() or seq_along()

Best,
Kasper

On Mon, Oct 19, 2020 at 11:14 AM Davide Maspero 
wrote:

> Dear Bioconductor Staff,
>
> We have submitted a new package VERSO, by opening a new issue (
> https://secure-web.cisco.com/1RpJPkbPrN4WjcPn84a9-dwD7JvdUFas1ZByK2A0RsoCLLTLVuCW7dMEEgOsCHjv1xyUmPACUccvtLbf2_Qd8QdTNvhCpqfX_5dfWqtNUMCOdejERh-b_o-8_CIKkWZe1jrJQbElCvpQWljLiJlHcmAKD8s3ORjA8d5Buy-fnpyRwIFPuX3YoLutUAvCl1j4q1xgWCbbISHWrxMr0XyPJt_PhwmIAbPjnNlstH2XXiuqu9stKVNdQ0rEsrHvPEcocKUvq_HCSuwfdLnKtZI8Y13octl7B5PD1vidb9yXVtFEoBga-k5oVZsAVAKpo5Xsm/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1689)
>  and a moderator
> (CCed) was assigned 17 days ago. Since that, we did not receive any
> feedback. As the submission deadline is approaching we are wondering if you
> can help us to complete the submission procedure.
>
> Thank you very much for your help.
>
> Best regards,
> Davide Maspero
>
> --
> __
> Davide Maspero
> Ph.D student
>
> Dept. of Informatics, Systems and Communication, University of Milan �
> Bicocca.
> Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle
> Ricerche (IBFM-CNR)
>
> [[alternative HTML version deleted]]
>
> ___
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--
Best,
Kasper

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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Manders-2, F.M.

Yes, I’ll create a PR.

From: Vincent Carey 
Date: Monday, 19 October 2020 at 12:36
To: "Manders-2, F.M." , bioc-devel 

Subject: Fwd: [Bioc-devel] Orchid ID invalid according to BiocCheck

forwarding to bioc-devel
-- Forwarded message -
From: Vincent Carey 
mailto:st...@channing.harvard.edu>>
Date: Mon, Oct 19, 2020 at 6:33 AM
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
To: Manders-2, F.M. 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
Cc: Alessandro Lussana via Bioc-devel 
mailto:Bioc-devel@r-project.org>>

looks like BiocCheck/checks.R:validID <- 
grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid)

has to change -- do you have time to determine the correct regex for this and 
file a PR?

On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
 wrote:
Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t know why 
I have an X there and not a number.

From: Vincent Carey 
mailto:st...@channing.harvard.edu>>
Date: Monday, 19 October 2020 at 12:20
To: "Manders-2, F.M." 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
Cc: Alessandro Lussana via Bioc-devel 
mailto:Bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

 person("Freek", "Manders", email = 
"f.m.mand...@prinsesmaximacentrum.nl",
 role = c("aut"),
comment = c(ORCID = "-0001-6197-347X")),

is what I see in a current checkout.  is "X" at the end correct?  maybe there 
is an encoding issue?

On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
 wrote:
Hi all,

BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
for Freek Manders").
However, I see nothing wrong with the ID. It also seems to work well on the dev 
page of my package (MutationalPatterns)
Clicking on the green ID circle, sends me to my page just fine.
Is there a mistake in BiocCheck? Should I just ignore this?

With kind regards,
Freek Manders

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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Mike Smith

Well I learnt something new today!

"The final character, which may also be a letter "X" representing the value
"10" [..], is a MOD 11-2 check digit
 conforming to the ISO/IEC
7064:2003  standard." -
https://en.wikipedia.org/wiki/ORCID

I guess the check in BiocCheck isn't aware of this either.  I don't want to
speak for the author of that code, but I suspect you can ignore it for now
and it'll be fixed soon.


On Mon, 19 Oct 2020 at 12:33, Manders-2, F.M. <
f.m.mand...@prinsesmaximacentrum.nl> wrote:

> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t
> know why I have an X there and not a number.
>
> From: Vincent Carey 
> Date: Monday, 19 October 2020 at 12:20
> To: "Manders-2, F.M." 
> Cc: Alessandro Lussana via Bioc-devel 
> Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
>  person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl
> ", role = c("aut"),
> comment = c(ORCID = "-0001-6197-347X")),
>
> is what I see in a current checkout.  is "X" at the end correct?  maybe
> there is an encoding issue?
>
> On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <
> f.m.mand...@prinsesmaximacentrum.nl f.m.mand...@prinsesmaximacentrum.nl>> wrote:
> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID
> ID for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on
> the dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Manders-2, F.M.

It seems to be a valid ID: 
https://support.orcid.org/hc/en-us/articles/360053289173-Why-does-my-ORCID-iD-have-an-X-
Maybe BiocCheck doesn’t realize the ID can end with an X?

From: Vincent Carey 
Date: Monday, 19 October 2020 at 12:20
To: "Manders-2, F.M." 
Cc: Alessandro Lussana via Bioc-devel 
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

 person("Freek", "Manders", email = 
"f.m.mand...@prinsesmaximacentrum.nl",
 role = c("aut"),
comment = c(ORCID = "-0001-6197-347X")),

is what I see in a current checkout.  is "X" at the end correct?  maybe there 
is an encoding issue?

On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
 wrote:
Hi all,

BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
for Freek Manders").
However, I see nothing wrong with the ID. It also seems to work well on the dev 
page of my package (MutationalPatterns)
Clicking on the green ID circle, sends me to my page just fine.
Is there a mistake in BiocCheck? Should I just ignore this?

With kind regards,
Freek Manders

[[alternative HTML version deleted]]

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[Bioc-devel] Fwd: Orchid ID invalid according to BiocCheck

2020-10-19 Thread Vincent Carey

forwarding to bioc-devel

-- Forwarded message -
From: Vincent Carey 
Date: Mon, Oct 19, 2020 at 6:33 AM
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
To: Manders-2, F.M. 
Cc: Alessandro Lussana via Bioc-devel 


looks like BiocCheck/checks.R:validID <-
grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid)

has to change -- do you have time to determine the correct regex for this
and file a PR?



On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. <
f.m.mand...@prinsesmaximacentrum.nl> wrote:

> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t
> know why I have an X there and not a number.
>
>
>
> *From: *Vincent Carey 
> *Date: *Monday, 19 October 2020 at 12:20
> *To: *"Manders-2, F.M." 
> *Cc: *Alessandro Lussana via Bioc-devel 
> *Subject: *Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
>
>
>  person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl",
> role = c("aut"),
> comment = c(ORCID = "-0001-6197-347X")),
>
>
>
> is what I see in a current checkout.  is "X" at the end correct?  maybe
> there is an encoding issue?
>
>
>
> On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <
> f.m.mand...@prinsesmaximacentrum.nl> wrote:
>
> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID
> ID for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on
> the dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> dispose of the e-mail.
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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Vincent Carey

looks like BiocCheck/checks.R:validID <-
grepl("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}", orcid)

has to change -- do you have time to determine the correct regex for this
and file a PR?



On Mon, Oct 19, 2020 at 6:31 AM Manders-2, F.M. <
f.m.mand...@prinsesmaximacentrum.nl> wrote:

> Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t
> know why I have an X there and not a number.
>
>
>
> *From: *Vincent Carey 
> *Date: *Monday, 19 October 2020 at 12:20
> *To: *"Manders-2, F.M." 
> *Cc: *Alessandro Lussana via Bioc-devel 
> *Subject: *Re: [Bioc-devel] Orchid ID invalid according to BiocCheck
>
>
>
>  person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl",
> role = c("aut"),
> comment = c(ORCID = "-0001-6197-347X")),
>
>
>
> is what I see in a current checkout.  is "X" at the end correct?  maybe
> there is an encoding issue?
>
>
>
> On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <
> f.m.mand...@prinsesmaximacentrum.nl> wrote:
>
> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID
> ID for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on
> the dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> dispose of the e-mail.
>

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e-mail
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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Manders-2, F.M.

Yes, the X is correct (https://orcid.org/-0001-6197-347X). I don’t know why 
I have an X there and not a number.

From: Vincent Carey 
Date: Monday, 19 October 2020 at 12:20
To: "Manders-2, F.M." 
Cc: Alessandro Lussana via Bioc-devel 
Subject: Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

 person("Freek", "Manders", email = 
"f.m.mand...@prinsesmaximacentrum.nl",
 role = c("aut"),
comment = c(ORCID = "-0001-6197-347X")),

is what I see in a current checkout.  is "X" at the end correct?  maybe there 
is an encoding issue?

On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. 
mailto:f.m.mand...@prinsesmaximacentrum.nl>>
 wrote:
Hi all,

BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
for Freek Manders").
However, I see nothing wrong with the ID. It also seems to work well on the dev 
page of my package (MutationalPatterns)
Clicking on the green ID circle, sends me to my page just fine.
Is there a mistake in BiocCheck? Should I just ignore this?

With kind regards,
Freek Manders

[[alternative HTML version deleted]]

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Vincent Carey

 person("Freek", "Manders", email = "f.m.mand...@prinsesmaximacentrum.nl",
role = c("aut"),
comment = c(ORCID = "-0001-6197-347X")),

is what I see in a current checkout.  is "X" at the end correct?  maybe
there is an encoding issue?

On Mon, Oct 19, 2020 at 6:14 AM Manders-2, F.M. <
f.m.mand...@prinsesmaximacentrum.nl> wrote:

> Hi all,
>
> BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID
> ID for Freek Manders").
> However, I see nothing wrong with the ID. It also seems to work well on
> the dev page of my package (MutationalPatterns)
> Clicking on the green ID circle, sends me to my page just fine.
> Is there a mistake in BiocCheck? Should I just ignore this?
>
> With kind regards,
> Freek Manders
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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[Bioc-devel] Orchid ID invalid according to BiocCheck

2020-10-19 Thread Manders-2, F.M.

Hi all,

BiocCheck is giving me a note that my ORCID ID is invalid ("Invalid ORCID ID 
for Freek Manders").
However, I see nothing wrong with the ID. It also seems to work well on the dev 
page of my package (MutationalPatterns)
Clicking on the green ID circle, sends me to my page just fine.
Is there a mistake in BiocCheck? Should I just ignore this?

With kind regards,
Freek Manders

[[alternative HTML version deleted]]

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Re: [Bioc-devel] VERSO issue #1689

2020-10-19 Thread Kasper Daniel Hansen

I can't speak for the reviewer, but the package currently has 2 WARNINGS.
If I were you, I would fix those warnings and push the fixes to Github, at
which point the package will be re-built and re-checked. You're not
supposed to have any ERRORS / WARNINGS when you submit. I would also look
at the NOTES, at least the following should be fixed

* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.

* Checking coding practice...
  *NOTE: Avoid 1:...; use seq_len() or seq_along()

Best,
Kasper

On Mon, Oct 19, 2020 at 11:14 AM Davide Maspero 
wrote:

> Dear Bioconductor Staff,
>
> We have submitted a new package VERSO, by opening a new issue (
> https://github.com/Bioconductor/Contributions/issues/1689) and a moderator
> (CCed) was assigned 17 days ago. Since that, we did not receive any
> feedback. As the submission deadline is approaching we are wondering if you
> can help us to complete the submission procedure.
>
> Thank you very much for your help.
>
> Best regards,
> Davide Maspero
>
> --
> __
> Davide Maspero
> Ph.D student
>
> Dept. of Informatics, Systems and Communication, University of Milan –
> Bicocca.
> Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle
> Ricerche (IBFM-CNR)
>
> [[alternative HTML version deleted]]
>
> ___
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>

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Best,
Kasper

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[Bioc-devel] VERSO issue #1689

2020-10-19 Thread Davide Maspero

Dear Bioconductor Staff,

We have submitted a new package VERSO, by opening a new issue (
https://github.com/Bioconductor/Contributions/issues/1689) and a moderator
(CCed) was assigned 17 days ago. Since that, we did not receive any
feedback. As the submission deadline is approaching we are wondering if you
can help us to complete the submission procedure.

Thank you very much for your help.

Best regards,
Davide Maspero

-- 
__
Davide Maspero
Ph.D student

Dept. of Informatics, Systems and Communication, University of Milan –
Bicocca.
Institute of Molecular Bioimaging and Physiology, Consiglio Nazionale delle
Ricerche (IBFM-CNR)

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Re: [Bioc-devel] Update CARNIVAL maintainer

Re: [Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

[Bioc-devel] Co-maintainer for SpectralTAD and TADCompare

Re: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Bioconductor 3.12 db0s, OrgDbs and TxDbs now available

Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

Re: [Bioc-devel] VERSO issue #1689

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

[Bioc-devel] Fwd: Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] Orchid ID invalid according to BiocCheck

[Bioc-devel] Orchid ID invalid according to BiocCheck

Re: [Bioc-devel] VERSO issue #1689

[Bioc-devel] VERSO issue #1689

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