date:20180913

Re: [Bioc-devel] Access permissions for DMRcate

2018-09-13 Thread Tim Peters

Thanks Valerie, much obliged.

Cheers,
Tim

On 14/09/18 06:06, Obenchain, Valerie wrote:
Hi Tim,

We had 2 accounts for you, one under 
tim.pet...@csiro.au and one under 
t.pet...@garvan.org.au. I've removed the 
@csiro.au account and your information (i.e., package permissions) should by 
synced up.

Valerie






On 09/11/2018 08:14 PM, Tim Peters wrote:

Hi BioC,

I'm attempting to sync the my repo https://github.com/timpeters82/DMRcate-devel 
with Bioconductor using the process here: 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.

However I'm encountering the following error at Step 9:

timpet@goodnow-lab:~/Documents/DMRcate$ git push upstream master
FATAL: W any packages/DMRcate timpeters82 DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists

Here are my remotes:

timpet@goodnow-lab:~/Documents/DMRcate$ git remote -v
originhttps://github.com/timpeters82/DMRcate-devel/ (fetch)
originhttps://github.com/timpeters82/DMRcate-devel/ (push)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (push)


Possibly related, I noticed that my Bioconductor Git Credentials page 
https://git.bioconductor.org/BiocCredentials/permissions_by_user/ only gives me 
access to my newer package "consensus", but not "DMRcate". Can I add DMRcate 
myself through some process, or alternatively can I get an admin to do so 
please?

Best,

Tim

--

===

Tim Peters, PhD

Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

E: 
t.pet...@garvan.org.au
 | W: http://www.garvan.org.au | P: +612 9295 8325


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===

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Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

E: t.pet...@garvan.org.au | W: 
http://www.garvan.org.au | P: +612 9295 8325


NOTICE
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Re: [Bioc-devel] iClusterPlus/iChip/iSeq packages

2018-09-13 Thread Mo, Qianxing

Hi Valerie,

Thank you so much for your prompt reply.

Best,

Quincy


From: "Obenchain, Valerie" 
Date: Thursday, September 13, 2018 at 4:28 PM
To: "Mo, Qianxing" , "bioc-devel@r-project.org" 

Subject: EXT: Re: [Bioc-devel] iClusterPlus/iChip/iSeq packages

Hi Quincy,

Your email has been updated. Please visit

  
https://git.bioconductor.org/BiocCredentials

and activate your account with the 
qianxing...@moffitt.org address. Once activated 
you can login and see the SSH keys we have on file for you.

Valerie





On 09/13/2018 11:47 AM, Mo, Qianxing wrote:

Dear Sir/Madam,



My name is Qianxing Mo, the maintainer of iClusterPlus, iSeq and iChip packages.

Previously, I worked at Baylor College of Medicine and my email address was 
q...@bcm.edu.

However, my email address 
q...@bcm.edu is 
no longer valid because I have left Baylor.  Therefore, I could not reset my 
password and update my packages.



Now, I am working at H. Lee Moffitt Cancer Center and my email is 
qianxing...@moffitt.org.
  Could you change my former email 
q...@bcm.edu to 
my current email 
qianxing...@moffitt.org
 so that I could receive email from Bioconductor to update my packages?



Thank you very much!



Best,



Quincy





Qianxing Mo, Ph.D.

Associate Member

Department of Biostatistics & Bioinformatics

H. Lee Moffitt Cancer Center & Research Institute

12902 Magnolia Drive, Tampa, FL 33612



Phone: 813-745-2252

Email: qianxing...@moffitt.org







Please consider the environment before printing this email.



This transmission may be confidential or protected from disclosure and is only 
for review and use by the intended recipient. Access by anyone else is 
unauthorized. Any unauthorized reader is hereby notified that any review, use, 
dissemination, disclosure or copying of this information, or any act or 
omission taken in reliance on it, is prohibited and may be unlawful. If you 
received this transmission in error, please notify the sender immediately. 
Thank you.



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Re: [Bioc-devel] Access permissions for DMRcate

2018-09-13 Thread Obenchain, Valerie

Hi Tim,

We had 2 accounts for you, one under 
tim.pet...@csiro.au and one under 
t.pet...@garvan.org.au. I've removed the 
@csiro.au account and your information (i.e., package permissions) should by 
synced up.

Valerie






On 09/11/2018 08:14 PM, Tim Peters wrote:

Hi BioC,

I'm attempting to sync the my repo https://github.com/timpeters82/DMRcate-devel 
with Bioconductor using the process here: 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.

However I'm encountering the following error at Step 9:

timpet@goodnow-lab:~/Documents/DMRcate$ git push upstream master
FATAL: W any packages/DMRcate timpeters82 DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists

Here are my remotes:

timpet@goodnow-lab:~/Documents/DMRcate$ git remote -v
originhttps://github.com/timpeters82/DMRcate-devel/ (fetch)
originhttps://github.com/timpeters82/DMRcate-devel/ (push)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (push)


Possibly related, I noticed that my Bioconductor Git Credentials page 
https://git.bioconductor.org/BiocCredentials/permissions_by_user/ only gives me 
access to my newer package "consensus", but not "DMRcate". Can I add DMRcate 
myself through some process, or alternatively can I get an admin to do so 
please?

Best,

Tim

--

===

Tim Peters, PhD

Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

E: 
t.pet...@garvan.org.au
 | W: http://www.garvan.org.au | P: +612 9295 8325


NOTICE
Please consider the environment before printing this email. This message and 
any attachments are intended for the addressee named and may contain legally 
privileged/confidential/copyright information. If you are not the intended 
recipient, you should not read, use, disclose, copy or distribute this 
communication. If you have received this message in error please notify us at 
once by return email and then delete both messages. We accept no liability for 
the distribution of viruses or similar in electronic communications. This 
notice should not be removed.

[[alternative HTML version deleted]]

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information.  If you are not the intended recipient(s), or the employee or 
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recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] iClusterPlus/iChip/iSeq packages

2018-09-13 Thread Mo, Qianxing

Dear Sir/Madam,

My name is Qianxing Mo, the maintainer of iClusterPlus, iSeq and iChip packages.
Previously, I worked at Baylor College of Medicine and my email address was 
q...@bcm.edu.
However, my email address q...@bcm.edu is no longer valid 
because I have left Baylor.  Therefore, I could not reset my password and 
update my packages.

Now, I am working at H. Lee Moffitt Cancer Center and my email is 
qianxing...@moffitt.org.  Could you change my 
former email q...@bcm.edu to my current email 
qianxing...@moffitt.org so that I could receive 
email from Bioconductor to update my packages?

Thank you very much!

Best,

Quincy


Qianxing Mo, Ph.D.
Associate Member
Department of Biostatistics & Bioinformatics
H. Lee Moffitt Cancer Center & Research Institute
12902 Magnolia Drive, Tampa, FL 33612

Phone: 813-745-2252
Email: qianxing...@moffitt.org



Please consider the environment before printing this email.

This transmission may be confidential or protected from disclosure and is only 
for review and use by the intended recipient. Access by anyone else is 
unauthorized. Any unauthorized reader is hereby notified that any review, use, 
dissemination, disclosure or copying of this information, or any act or 
omission taken in reliance on it, is prohibited and may be unlawful. If you 
received this transmission in error, please notify the sender immediately. 
Thank you.

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[Bioc-devel] GenomeInfoDB SeqInfo function error

2018-09-13 Thread Dario Righelli

Hello everyone,

I'm using in DEScan2 package the GenomeInfoDb::Seqinfo function with 
genome="mm10".

And sometimes it appens to retrieve this error message

"cannot open the connection to 
'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_01635.20_GRCm38/GCF_01635.20_GRCm38_assembly_report.txt'"

Even if the the file is reachable.

I noticed it because I received an ERROR report from the bioconductor test bot.
I have a unit test for my package that doesn't pass on linux, but it works on 
other machines.

Looking on the Internet, this seems like an old (solved) problem.

What do you suggest to do?

thanks,
dario


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Re: [Bioc-devel] Activation failure

2018-09-13 Thread Obenchain, Valerie

Hi Lang,

Thanks for letting us know. There was a bug in the code that checked the github 
username against other usernames (confirming "uniqueness"). This has been fixed 
and I've added your account.

One SSH key was added automatically from your langholee github account. Please 
try again to activate your account, then log in and you can see the key we have 
on file for you.

Valerie




On 09/12/2018 07:35 AM, Lang Ho Lee wrote:

Dear Mr. or Ms.

I am trying to submit my SSH key, since my package, XINA was accepted to
Bioconductor.  However, I couldn't activate my ID and got the following
message.

langho...@gmail.com is not associated with a 
maintainer of a Bioconductor
package. Please check the spelling or contact 
bioc-devel@r-project.org for
help.

My package description for the maintainer is below.

Authors@R: c(person("Lang Ho", "Lee", email = 
"langho...@gmail.com",  role
= c("aut", "cre")), person("Sasha", "Singh", email = "
sasi...@bwh.harvard.edu",  role = c("aut")))

Maintainer: Lang Ho Lee  and 
Sasha A. Singh <
sasi...@bwh.harvard.edu>

Could you help me to activate my account?

Thanks,
Lang

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Re: [Bioc-devel] Activation failure

2018-09-13 Thread Lang Ho Lee

Thanks, Valerie.  It worked and I could see my Github SSH key.   -- Lang

On Wed, Sep 12, 2018 at 1:40 PM Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Lang,
>
> Thanks for letting us know. There was a bug in the code that checked the
> github username against other usernames (confirming "uniqueness"). This has
> been fixed and I've added your account.
>
> One SSH key was added automatically from your langholee github account.
> Please try again to activate your account, then log in and you can see the
> key we have on file for you.
>
> Valerie
>
>
>
>
> On 09/12/2018 07:35 AM, Lang Ho Lee wrote:
>
> Dear Mr. or Ms.
>
> I am trying to submit my SSH key, since my package, XINA was accepted to
> Bioconductor.  However, I couldn't activate my ID and got the following
> message.
> langho...@gmail.com is not associated with a maintainer of a Bioconductor
> package. Please check the spelling or contact bioc-devel@r-project.org for
> help.
>
> My package description for the maintainer is below.
>
> Authors@R: c(person("Lang Ho", "Lee", email = "langho...@gmail.com" 
> ,  role
> = c("aut", "cre")), person("Sasha", "Singh", email = 
> "sasi...@bwh.harvard.edu",  role = c("aut")))
>
> Maintainer: Lang Ho Lee   and Sasha 
> A. Singh 
>
> Could you help me to activate my account?
>
> Thanks,
> Lang
>
>   [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org 
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-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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Re: [Bioc-devel] Access permissions for DMRcate

Re: [Bioc-devel] iClusterPlus/iChip/iSeq packages

Re: [Bioc-devel] Access permissions for DMRcate

[Bioc-devel] iClusterPlus/iChip/iSeq packages

[Bioc-devel] GenomeInfoDB SeqInfo function error

Re: [Bioc-devel] Activation failure

Re: [Bioc-devel] Activation failure

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