Re: [Bioc-devel] EXTERNAL: Adding one more maintainer - Mergeomicspackage

2018-08-07 Thread Wenting Liu 
Dear Valerie,

May I check with you whether I have been confirmed the co-maintainer title
on the GitHub for "Mergeomics"? Thanks.

Best Regards,
Wenting

2018-07-20 5:26 GMT-07:00 Obenchain, Valerie <
valerie.obench...@roswellpark.org>:

> [image: Boxbe]  Obenchain, Valerie
> (valerie.obench...@roswellpark.org) is not on your Guest List
> 
> | Approve sender
> 
> | Approve domain
> 
>
> Hi,
>
> I don't see a github account under the name of liuwenting ... is  this
> correct?
>
> Valerie
>
>
>
>
> On 07/20/2018 12:55 AM, Zeyneb Kurt wrote:
>
> Dear Bioc team,
>
> I am maintaining the “Mergeomics” package and would like to add one of my
> colleagues as an *additional* maintainer. Her github username is liuwenting 
> (am
> cc’ing her here).
>
> Best,
> Zeyneb Kurt
>
>   [[alternative HTML version deleted]]
>
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>
>
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-- 
Best regards,

Wenting LIU

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[Bioc-devel] Password Reset Help

2018-08-07 Thread Augustin Luna 
I requested a password reset from this site:

https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/

a couple of times and I haven't received it. Not sure what to do.

Thanks,
Augustin Luna

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Re: [Bioc-devel] EXTERNAL: Re: Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

2018-08-07 Thread Leonardo Collado Torres 
Sorry about that Martin. Here's my thank you reply to Hervé from August 2nd.



Thanks Hervé and no problem about the Windows binary.

Richard did get DelayedArray installed today (I think using biocLite)! ^^

Best,
Leo


On Fri, Aug 3, 2018 at 8:27 AM Martin Morgan
 wrote:
>
>
> The large number of people cc'd on this thread causes the mailman
> software to block posts. I'm removing individuals, please respond to
> this message.
>
> On 08/02/2018 01:57 PM, Hervé Pagès wrote:
> > Hi Leonardo,
> >
> > Hope you were able to solve your connection problems.
> > Just to let you that I fixed the DelayedArray timeout on
> > Windows and the zip files are now available for this
> > platform:
> >
> >https://bioconductor.org/packages/DelayedArray
> >
> > Sorry for the inconvenience.
> >
> > Cheers,
> > H.
> >
> >
> > On 08/01/2018 02:23 PM, Leonardo Collado Torres wrote:
> >> Hi,
> >>
> >> Just as a quick update. Everything worked yesterday when Richard used
> >> another PC computer from his home (another network). So it's
> >> definitely not a Bioc problem.
> >>
> >> Yet I have no idea how to troubleshoot it beyond burning it all and
> >> starting from scratch: re-installing R and everything and checking if
> >> that works. Well, or testing using a hotspot wifi connection with one
> >> of our phones and seeing if that works to bypass the wifi network from
> >> work.
> >>
> >> Best,
> >> Leo
> >>
> >> On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr. 
> >> wrote:
> >>>
> >>> are you sure his tmp directory isn't full
> >>>
> >>> --t
> >>>
> >>>
> >>> On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres
> >>>  wrote:
> 
>   From Richard:
> 
> > BiocManager::install("DelayedArray")
> 
>  Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23)
> 
>  Installing package(s) 'BiocVersion', 'DelayedArray'
> 
>  trying URL
>  'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_bin_windows_contrib_3.5_BiocVersion-5F3.7.4.zip=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=RdZdVvOSqc562aHV7-SuXUDX1UWmqQS3vui_2xYItgQ='
> 
> 
>  Content type 'application/zip' length 8649 bytes
> 
>  downloaded 8649 bytes
> 
> 
> 
>  package ‘BiocVersion’ successfully unpacked and MD5 sums checked
> 
> 
> 
>  The downloaded binary packages are in
> 
>  C:\Users\Richard
>  Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages
> 
>  installing the source package ‘DelayedArray’
> 
> 
> 
>  trying URL
>  'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.7_bioc_src_contrib_DelayedArray-5F0.6.2.tar.gz=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=vz1NGwOvFQqQbsZ2yqnCyV188YNc_k7oDMiD78DpRqY='
> 
> 
>  Content type 'application/x-gzip' length 486139 bytes (474 KB)
> 
>  downloaded 474 KB
> 
> 
> 
>  Error in untar2(tarfile, files, list, exdir, restore_times) :
> 
> incomplete block on file
> 
>  In R CMD INSTALL
> 
> 
> 
>  The downloaded source packages are in
> 
>  ‘C:\Users\Richard
>  Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’
> 
>  installation path not writeable, unable to update packages: foreign,
>  MASS, mgcv, survival
> 
>  Update old packages: 'openssl', 'stringi'
> 
>  Update all/some/none? [a/s/n]:
> 
>  n
> 
>  Warning message:
> 
>  In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
> 
> installation of package ‘DelayedArray’ had non-zero exit status
> 
> >
> 
> 
> 
>  Also, at
>  https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_DelayedArray.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=VQqOqRCRgcQL-JkG2jnIvc9WLYZ09mm9gdXpjfDqJos=sIiQvz3aJN2aHqxD1FLQLygGYRequcJnj2ywQlGrkds=
> 
>  I don't see the tar for the Windows binary.
> 
> 
> 
> 
>  On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr.
>   wrote:
> >
> > BiocManager::install(whatever) doesn't work?
> >
> > biocLite is supposed to die, you see...
> >
> >
> > --t
> >
> >
> > On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres
> >  wrote:
> >>
> >> Hi bioc-devel,
> >>
> >> A co-worker of mine (Richard) tried several times to install the
> >> DelayedArray package. We got a couple of errors but it ultimately
> >> looks like it's an internet connection problem. The truth is that
> >> might be something affecting us on our side since I can't access
> >>

Re: [Bioc-devel] EXTERNAL: SQLForge Question about creating a new species package for Chlamydomonas reinhardtii

2018-08-07 Thread Shepherd, Lori 
Is there a reason one of the existing annotations provided in AnnotationHub 
cannot be used?


> library(AnnotationHub)

> ah = AnnotationHub()
qusnapshotDate(): 2018-08-01

> query(ah, "Chlamydomonas_reinhardtii")
AnnotationHub with 2 records
# snapshotDate(): 2018-08-01
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Chlamydomonas reinhardtii
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH10477"]]'

title
  AH10477 | hom.Chlamydomonas_reinhardtii.inp8.sqlite
  AH62519 | org.Chlamydomonas_reinhardtii.eg.sqlite




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Bijie Ren 

Sent: Wednesday, August 1, 2018 1:50:10 PM
To: bioc-devel@r-project.org
Subject: EXTERNAL: [Bioc-devel] SQLForge Question about creating a new species 
package for Chlamydomonas reinhardtii

Dear all,

I wanna create a new annotation package for Chlamydomonas reinhardtii.
However, sequencing data in NCBI for this species is not updated while
there's a updated version of genome information and annotation in
Phytozyome. I'm wondering can I use phytozome ID as an input to create such
annotation package in R for WGCNA? If so will SQLForge use them to compare
with intermediate?

Best Regards,

Bijie Ren

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Re: [Bioc-devel] EXTERNAL: Updating SSH keys without previous email account

2018-08-07 Thread Anthony Chiu 
Hi Nitesh and Valerie

Thank you both, I've managed to activate my BiocCredentials account now.

Best wishes
Anthony

On 3 August 2018 at 19:52, Turaga, Nitesh 
wrote:

> Try to activate your account now on the BiocCredentials app.
>
> https://git.bioconductor.org/BiocCredentials/account_activation/
>
> Best,
>
> Nitesh
>
> > On Aug 3, 2018, at 2:32 PM, Anthony Chiu  wrote:
> >
> > Hi Nitesh
> >
> > Please could we use ? I think I updated the email
> address everywhere else apart from SSH key management.
> >
> > Many thanks
> > Anthony
> >
> >
> > On Fri, 3 Aug 2018, 19:10 Turaga, Nitesh, 
> wrote:
> > Hi Anthony,
> >
> > What is the new email you want associated with this package?
> >
> > Nitesh
> >
> > > On Aug 2, 2018, at 5:57 AM, Anthony Chiu  wrote:
> > >
> > > Hello
> > >
> > > I maintain the 'twoddpcr' package and I have left my previous
> institute. I
> > > no longer have the SSH keys that I used to push to the Git repository.
> I
> > > never activated my Git credentials account at [1] (I submitted my
> public
> > > key using the Google form during the transition from SVN), and I no
> longer
> > > have access to my old  email
> either.
> > >
> > > Please could someone help me get access to the Git repositories again?
> > >
> > > Thanks
> > > Anthony
> > >
> > > [1]: https://git.bioconductor.org/BiocCredentials/account_activation/
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > This email message may contain legally privileged and/or confidential
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> >
>
>
>
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] EXTERNAL: Updating SSH keys without previous email account

2018-08-07 Thread Turaga, Nitesh 
Try to activate your account now on the BiocCredentials app.

https://git.bioconductor.org/BiocCredentials/account_activation/

Best,

Nitesh

> On Aug 3, 2018, at 2:32 PM, Anthony Chiu  wrote:
> 
> Hi Nitesh
> 
> Please could we use ? I think I updated the email address 
> everywhere else apart from SSH key management.
> 
> Many thanks
> Anthony
> 
> 
> On Fri, 3 Aug 2018, 19:10 Turaga, Nitesh,  
> wrote:
> Hi Anthony,
> 
> What is the new email you want associated with this package? 
> 
> Nitesh 
> 
> > On Aug 2, 2018, at 5:57 AM, Anthony Chiu  wrote:
> > 
> > Hello
> > 
> > I maintain the 'twoddpcr' package and I have left my previous institute. I
> > no longer have the SSH keys that I used to push to the Git repository. I
> > never activated my Git credentials account at [1] (I submitted my public
> > key using the Google form during the transition from SVN), and I no longer
> > have access to my old  email either.
> > 
> > Please could someone help me get access to the Git repositories again?
> > 
> > Thanks
> > Anthony
> > 
> > [1]: https://git.bioconductor.org/BiocCredentials/account_activation/
> > 
> >   [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://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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