Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

[Shin, Sunyoung]

Hi JIanhong, that did work. Thank you very much!

Best,
Sunyoung

On Apr 29, 2019, at 10:47 AM, Jianhong Ou, Ph.D. 
mailto:jianhong...@duke.edu>> wrote:

Hi Sunyoung,

Sorry for the change of motifStack which makes you struggling. Please have a 
try following codes for plotting:

pushViewport(viewport(y =unit(.5, "npc") - unit(2, "lines"), height = unit(1, 
"npc") - unit(3, "lines")))
  pushViewport(viewport(y=.875, height=.25))
  plotMotifLogo(pcm2pfm(ref_aug_pwm), "Best match to the reference genome", 
yaxis=FALSE,
xaxis=FALSE, xlab="", ylab="PWM", newpage=FALSE, margins = 
c(1.5, 3, 2, 2))
if(motif.match$ref_strand=='+') {
  grid.lines(x=c(convertUnit(unit(3, "lines"), "npc", valueOnly = TRUE), 1 - 
convertUnit(unit(2, "lines"), "npc", valueOnly = TRUE)),
 y=unit(1, "lines"),
   gp=gpar(col = "blue", lwd = 1.5, xpd=NA), arrow=arrow(length = 
unit(0.1, "inches"), angle = 15, ends = "last"))
  grid.text("3'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(.5, "lines"))
  grid.text("5'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(.5, 
"lines"))
} else {
  grid.lines(x=c(convertUnit(unit(3, "lines"), "npc", valueOnly = TRUE), 1 - 
convertUnit(unit(2, "lines"), "npc", valueOnly = TRUE)),
y=unit(1, "lines"), gp=gpar(col = "blue", lwd = 1.5, xpd=NA),
 arrow=arrow(length = unit(0.1, "inches"), angle = 15, ends = 
"first"))
  grid.text("5'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(.5, "lines"))
  grid.text("3'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(.5, 
"lines"))
}
  popViewport()
  pushViewport(viewport(y=.625, height=.25))
  #par(mar = c(4, 3, 1.5, 2))
  plotMotifLogo(pcm2pfm(ref_aug_match_pwm), font="mono,Courier", yaxis=FALSE, 
xlab="",
ylab=paste("(", motif.match$ref_strand, ")", sep=""),  
newpage=FALSE, margins = c(2, 3, 1.5, 2))
  pushViewport(plotViewport(margins = c(2, 3, 1.5, 2)))
  grid.rect(x=(snp_loc+.5)/motif.match$snp_ref_length, width = 
1/motif.match$snp_ref_length, gp=gpar(col="blue", lty=3, lwd=2, fill=NA))
  popViewport()
  if(motif.match$ref_strand=="+")   {
grid.text("3'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(2.5, "lines"))
grid.text("5'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(2.5, 
"lines"))
} else {
  grid.text("5'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(2.5, "lines"))
  grid.text("3'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(2.5, 
"lines"))
}
popViewport()
pushViewport(viewport(y=.375, height=.25))
#par(mar=c(1.5, 3, 4, 2))
plotMotifLogo(pcm2pfm(snp_aug_match_pwm), "Best match to the SNP genome", 
font="mono,Courier",
  yaxis=FALSE, xlab="", ylab=paste("(", motif.match$snp_strand, 
")", sep=""), newpage=FALSE, margins = c(1.5, 3, 2, 2))
pushViewport(plotViewport(margins = c(1.5, 3, 2, 2)))
grid.rect(x=(snp_loc+.5)/motif.match$snp_ref_length, width = 
1/motif.match$snp_ref_length, gp=gpar(col="blue", lty=3, lwd=2, fill=NA))
popViewport()
  if(motif.match$snp_strand=="+")   {
grid.text("3'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(.5, "lines"))
grid.text("5'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(.5, 
"lines"))
} else {
  grid.text("5'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(.5, "lines"))
  grid.text("3'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(.5, 
"lines"))
}
popViewport()
pushViewport(viewport(y=.125, height=.25))
#par(mar=c(4, 3, 1.5, 2))
plotMotifLogo(pcm2pfm(snp_aug_pwm), yaxis=FALSE, xaxis=FALSE, xlab="", 
ylab="PWM", newpage=FALSE, margins = c(2, 3, 1.5, 2))
if(motif.match$snp_strand=='+') {
  grid.lines(x=c(convertUnit(unit(3, "lines"), "npc", valueOnly = TRUE), 1 - 
convertUnit(unit(1, "lines"), "npc", valueOnly = TRUE)),
 y=unit(1.5, "lines"), gp=gpar(col = "blue", lwd = 1.5, xpd=NA),
 arrow=arrow(length = unit(0.1, "inches"), angle = 15, ends = 
"last"))
  grid.text("3'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(1, "lines"))
  grid.text("5'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(1, 
"lines"))
} else {
  grid.lines(x=c(convertUnit(unit(3, "lines"), "npc", valueOnly = TRUE), 1 - 
convertUnit(unit(1, "lines"), "npc", valueOnly = TRUE)),
 y=unit(1.5, "lines"), gp=gpar(col = "blue", lwd = 1.5, xpd=NA),
 arrow=arrow(length = unit(0.1, "inches"), angle = 15, ends = 
"first"))
  grid.text("5'", x=unit(1, "npc") - unit(1, "lines"), gp=gpar(col="blue", 
cex=1), y=unit(1, "lines"))
  grid.text("3'", x=unit(2, "lines"), gp=gpar(col="blue", cex=1), y=unit(1, 
"lines"))
}
popViewport()
popViewport()
  grid.text(label = paste(motif.match$motif, " Motif Scan for ", 
motif.match$snpid, sep=""),
y=unit(1, "npc") - unit(1.5, "lines"),
gp=gpar(cex.main=cex.main, fontface="bold"))

You m

Re: [Bioc-devel] pushing changes to an existing package

[Simina Boca]

Thank you, it seems to work now! Do you have any idea of why the ".git" had
been moved to ".g?" Just curious if it was something on my end.

Cheers,
Simina

On Thu, May 2, 2019 at 2:15 PM Turaga, Nitesh 
wrote:

> Once your access works you should see yourself as maintainer with Read and
> Write access on MultiMed and CancerMutationAnalysis.
>
> Best
>
> Nitesh
>
> 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.
>


-- 
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

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Re: [Bioc-devel] pushing changes to an existing package

[Turaga, Nitesh]

No idea Simina.  Maybe a typo? 

Best,

Nitesh 


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Re: [Bioc-devel] pushing changes to an existing package

[Turaga, Nitesh]

Once your access works you should see yourself as maintainer with Read and 
Write access on MultiMed and CancerMutationAnalysis.

Best

Nitesh 

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Re: [Bioc-devel] pushing changes to an existing package

[Turaga, Nitesh]

Hi Simina,

Now that the RELEASE_3_9 branch and pushes are available to everyone, I can 
help you with this.

It seems like your upstream branch is a little funny looking, is this how it 
got pasted in or maybe it's a mistake.

What you gave: (I understand that the mailto: stuff may have been added later 
but auto format settings in email, but the trailing "g" at the end of the line 
is bugging me and I can't help but think it might be that)

upstream
g...@git.bioconductor.org:packages/MultiMed.g
 (fetch)
upstream
g...@git.bioconductor.org:packages/MultiMed.g 
(push)

What it's supposed to be:

upstream   
git@git.bioconductor.org:packages/MultiMed.git 
(fetch)
upstream.  
git@git.bioconductor.org:packages/MultiMed.git 
(push)


You can try first by resetting your upstream,

git remote set-url upstream 
git@git.bioconductor.org:packages/MultiMed.git

Let me know if this works.

Best,

Nitesh


On May 2, 2019, at 1:02 PM, Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:

Hi Simina,

We are going through the release process for Bioc 3.9 now, so all commits are 
blocked until further notice.

I can get back to helping you debug this issue once we are done with the 
release.

https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html

Best,

Nitesh

On May 2, 2019, at 12:58 PM, Simina Boca 
mailto:smb...@georgetown.edu>> wrote:

Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream
g...@git.bioconductor.org:packages/MultiMed.g 
(fetch)
upstream
g...@git.bioconductor.org:packages/MultiMed.g 
(push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T 
g...@git.bioconductor.org | grep MultiMed
Warning: Permanently added 
'git.bioconductor.org,34.192.48.227' (ECDSA) to 
the list of known hosts.
R  packages/MultiMed

Cheers,
Simina



On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi Simina,

http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little 
more please.

Best,

Nitesh

On Apr 30, 2019, at 10:45 AM, Simina Boca 
mailto:smb...@georgetown.edu>> wrote:

Hello,

I am trying to update my package MultiMed
https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html. It's
on Github at https://github.com/SiminaB/MultiMed. I got and updated the SSH
key (since I am using a new computer) but when I try to "git fetch --all" I
still get a permission-related error:

C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
Fetching origin
Fetching upstream
Warning: Permanently added 
'git.bioconductor.org,34.172.43.227'  to
the list of known hosts.
FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the current access rights and the repository
exists.
error: Could not fetch upstream

I appreciate your help!

Cheers,
Simina


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

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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.


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics | 
Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Compreh

[Bioc-devel] Access to Bioc git server resumed

[Turaga, Nitesh]

Dear Maintainers,

Access to Bioc git server is now active again. Maintainers will now have access 
to RELEASE_3_9 and master branch.

Make sure you sync your packages with the latest release changes before making 
any updates. 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.

Thank you,

Best,

Nitesh Turaga
Bioconductor Core team


This email message may contain legally privileged and/or confidential 
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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [Bioc-devel] pushing changes to an existing package

[Simina Boca]

No worries, thanks for letting me know!

Cheers,
Simina

On Thu, May 2, 2019, 1:02 PM Turaga, Nitesh 
wrote:

> Hi Simina,
>
> We are going through the release process for Bioc 3.9 now, so all commits
> are blocked until further notice.
>
> I can get back to helping you debug this issue once we are done with the
> release.
>
> https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html
>
> Best,
>
> Nitesh
>
> On May 2, 2019, at 12:58 PM, Simina Boca  wrote:
>
> Thank you Nitesh and sorry for missing this initially!
>
> This one seems fine:
> C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
> origin  https://github.com/SiminaB/MultiMed.git (fetch)
> origin  https://github.com/SiminaB/MultiMed.git (push)
> upstreamg...@git.bioconductor.org:packages/MultiMed.g (fetch)
> upstreamg...@git.bioconductor.org:packages/MultiMed.g (push)
>
> However, it seems like I only have read, not write access to the package:
> C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T
> g...@git.bioconductor.org | grep MultiMed
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
> to the list of known hosts.
>  R  packages/MultiMed
>
> Cheers,
> Simina
>
>
>
> On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> Hi Simina,
>>
>> http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a
>> little more please.
>>
>> Best,
>>
>> Nitesh
>>
>> On Apr 30, 2019, at 10:45 AM, Simina Boca  wrote:
>>
>> Hello,
>>
>> I am trying to update my package MultiMed
>> https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html.
>> It's
>> on Github at https://github.com/SiminaB/MultiMed. I got and updated the
>> SSH
>> key (since I am using a new computer) but when I try to "git fetch --all"
>> I
>> still get a permission-related error:
>>
>> C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
>> Fetching origin
>> Fetching upstream
>> Warning: Permanently added 'git.bioconductor.org,34.172.43.227' 
>> to
>> the list of known hosts.
>> FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
>> (or you mis-spelled the reponame)
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the current access rights and the repository
>> exists.
>> error: Could not fetch upstream
>>
>> I appreciate your help!
>>
>> Cheers,
>> Simina
>>
>>
>> --
>> Simina M. Boca
>> Assistant Professor
>> Innovation Center for Biomedical Informatics  (ICBI)
>> Departments of Oncology and Biostatistics, Bioinformatics and
>> Biomathematics | Georgetown University Medical Center
>> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>> Center
>>
>> 2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
>> Phone: (202) 687-1545, Fax: (202) 687-5011
>> http://icbi.georgetown.edu/boca
>> https://sites.google.com/georgetown.edu/siminaboca/
>>
>> [[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.
>
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Departments of Oncology and Biostatistics, Bioinformatics and
> Biomathematics | Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
> Phone: (202) 687-1545, Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
> https://sites.google.com/georgetown.edu/siminaboca/
>
>
>
>
> 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] pushing changes to an existing package

[Turaga, Nitesh]

Hi Simina,

We are going through the release process for Bioc 3.9 now, so all commits are 
blocked until further notice.

I can get back to helping you debug this issue once we are done with the 
release.

https://stat.ethz.ch/pipermail/bioc-devel/2019-May/015050.html

Best,

Nitesh

On May 2, 2019, at 12:58 PM, Simina Boca 
mailto:smb...@georgetown.edu>> wrote:

Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream
g...@git.bioconductor.org:packages/MultiMed.g 
(fetch)
upstream
g...@git.bioconductor.org:packages/MultiMed.g 
(push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T 
g...@git.bioconductor.org | grep MultiMed
Warning: Permanently added 
'git.bioconductor.org,34.192.48.227' (ECDSA) to 
the list of known hosts.
 R  packages/MultiMed

Cheers,
Simina



On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi Simina,

http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little 
more please.

Best,

Nitesh

On Apr 30, 2019, at 10:45 AM, Simina Boca 
mailto:smb...@georgetown.edu>> wrote:

Hello,

I am trying to update my package MultiMed
https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html. It's
on Github at https://github.com/SiminaB/MultiMed. I got and updated the SSH
key (since I am using a new computer) but when I try to "git fetch --all" I
still get a permission-related error:

C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
Fetching origin
Fetching upstream
Warning: Permanently added 
'git.bioconductor.org,34.172.43.227'  to
the list of known hosts.
FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the current access rights and the repository
exists.
error: Could not fetch upstream

I appreciate your help!

Cheers,
Simina


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

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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.


--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics | 
Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/




This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] pushing changes to an existing package

[Simina Boca]

Thank you Nitesh and sorry for missing this initially!

This one seems fine:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstreamg...@git.bioconductor.org:packages/MultiMed.g (fetch)
upstreamg...@git.bioconductor.org:packages/MultiMed.g (push)

However, it seems like I only have read, not write access to the package:
C:\Users\smb310\Documents\GitHub\MultiMed [devel]> ssh -T
g...@git.bioconductor.org | grep MultiMed
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
 R  packages/MultiMed

Cheers,
Simina



On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi Simina,
>
> http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a
> little more please.
>
> Best,
>
> Nitesh
>
> On Apr 30, 2019, at 10:45 AM, Simina Boca  wrote:
>
> Hello,
>
> I am trying to update my package MultiMed
> https://www.bioconductor.org/packages/release/bioc/html/MultiMed.html.
> It's
> on Github at https://github.com/SiminaB/MultiMed. I got and updated the
> SSH
> key (since I am using a new computer) but when I try to "git fetch --all" I
> still get a permission-related error:
>
> C:\Users\smb310\Documents\GitNuh\Multimed [devel]> git fetch --all
> Fetching origin
> Fetching upstream
> Warning: Permanently added 'git.bioconductor.org,34.172.43.227'  to
> the list of known hosts.
> FATAL: R any packages/MultiMed.g SiminaB DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
>
> Please make sure you have the current access rights and the repository
> exists.
> error: Could not fetch upstream
>
> I appreciate your help!
>
> Cheers,
> Simina
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Departments of Oncology and Biostatistics, Bioinformatics and
> Biomathematics | Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
> Phone: (202) 687-1545, Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
> https://sites.google.com/georgetown.edu/siminaboca/
>
> [[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.



-- 
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Departments of Oncology and Biostatistics, Bioinformatics and
Biomathematics | Georgetown University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007
Phone: (202) 687-1545, Fax: (202) 687-5011
http://icbi.georgetown.edu/boca
https://sites.google.com/georgetown.edu/siminaboca/

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Re: [Bioc-devel] permission denied

[ruizhu huang]

Thanks for help! Unfortunately, I can't even login to activate my account
with the email used to maintain the package (ruizh...@gmail.com)
To double check whether there is an account existing with my email address,
I try to use the password reset and never received the email to reset the
password.

Ruizhu

On Thu, May 2, 2019 at 1:19 PM Shepherd, Lori 
wrote:

> Have you checked your ssh keys on the credentials app?  You can add
> additional keys associated with your username there.
>
>
> https://git.bioconductor.org/BiocCredentials
>
>
> 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 ruizhu
> huang 
> *Sent:* Thursday, May 2, 2019 5:01:34 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] permission denied
>
> Hi all,
>
> My package TreeSummarizedExperiment has recently been accepted. I got the
> error about permission denied when following the guidelines in the page (
> https://bioconductor.org/developers/how-to/git/new-package-workflow/) to
> run the following commands
>
> $git remote add upstream g...@git.bioconductor.org:
> packages/TreeSummarizedExperiment.git
> $git fetch upstream
>
> The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
> established.
>
> ECDSA key fingerprint is
> SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
>
> Are you sure you want to continue connecting (yes/no)? yes
>
> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
> the list of known hosts.
>
> Permission denied (publickey).
>
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights and the repository
> exists.
>
>
> $ssh -T g...@git.bioconductor.org
>
> Permission denied (publickey).
>
> Would you mind helping me about this issue. Thanks!
> Ruizhu
>
> [[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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Re: [Bioc-devel] When to use generics?

[Pages Gallego, M.]

Thank you all for the discussion and input. I have decided to use generics for 
the 
time being since I am working with 3 classes and might add a fourth one later 
on.
Also, worst case scenario, reverting from generics to "if statements wrapper"
functions should not be too terrible.

Many thanks,
Marc

On 01/05/2019, 19:30, "Bioc-devel on behalf of Pages, Herve" 
 wrote:

Hi Boris,

AFAICT the ::() syntax also works well with generics. 
Note that people sometimes specify the  that exports some 
specific method for the generic when they should actually specify the 
 where the generic is defined.

One thing about the "regular function with if (is()) statements" vs 
generic discussion is that it's also about control. The former is fine 
as long as you control the types of object that your function handles 
but it doesn't make it possible for other people to add more types. 
Using a generic facilitate extensibility **by others**. Maybe you want 
that, maybe you don't. But it's an important part of the equation.

H.

On 5/1/19 10:15, Boris Steipe wrote:
> I am more and more emphasizing ::() syntax in my 
teaching, to avoid the issues that library() have wrt. order of 
loading, and clarity of code. It's my understanding that that's a general 
trend. Now, do correct me if I'm wrong but IIRC,  that doesn't work well with 
generics because they don't get registered. If so, that might be another 
consideration.
>
> Cheers,
> Boris
>
>
>
>
>> On 2019-05-01, at 12:18, Michael Lawrence via Bioc-devel 
 wrote:
>>
>> This is good advice. The purpose of the software also matters. The main
>> advantage of a generic is extensibility. If extensibility is important,
>> generics are appropriate, even if there is no immediate need for
>> polymorphism. Bioconductor emphasizes extensibility, and thus generics, 
but
>> it's not the only goal.
>>
>> On Wed, May 1, 2019 at 8:55 AM Kasper Daniel Hansen <
>> kasperdanielhan...@gmail.com> wrote:
>>
>>> This is a common situation. Most packages might have a need for 
something
>>> that looks like a generic, but it really only has a usage inside your 
own
>>> package(s).
>>>
>>> In many ways, the pseudo-generic you define using if() statements is 
often
>>> easier to work with, debugging wise and code-reading wise. However, 
there
>>> is a certain beauty to generics. IME many newcomers to S4 overdo it with
>>> generics. My rule of thumb is don't do a generic unless you have at 
least 3
>>> different classes you're doing dispatch on. Well, you have 3 classes, 
so I
>>> would start thinking about it. For better or worse, this is unlikely to
>>> make much difference so you should choose the one that makes the most 
sense
>>> to you as a writer.
>>>
>>> If you go down the generic route, think hard about the name.
>>>
>>>
>>> On Mon, Apr 29, 2019 at 10:38 AM Michael Lawrence via Bioc-devel <
>>> bioc-devel@r-project.org> wrote:
>>>
 On Mon, Apr 29, 2019 at 6:55 AM Pages Gallego, M. <
 m.pagesgall...@umcutrecht.nl> wrote:

> Dear all,
>
> I am currently developing a package and I am a bit confused in when 
one
> should define a generic. Let me propose an example:
> Suppose I have defined 3 classes: one for proteomics data, one for
> metabolomics data and one for transcriptomics data. I have a function
> “foo(x)” that will do the same to any of the 3 classes, but requires a
> slightly different implementation for each one. I could do something
 like
> that:
>
> ```
> foo <- function(x) {
> if (is(x, ‘proteomics’)) {
>   foo.protein(x)
> } else if (is(x, ‘metabolomics’)) {
>   foo.metabo(x)
> } else if (is(x, ‘transcriptomics’)) {
>   foo.trans(x)
> }
> }
> ```
>
> And then define foo.protein, foo.metabo and foo.trans.
> But this is basically the same as defining the generic “foo” and then
> defining a method for each of the classes.
>
> The problem is that “foo” is not generic “enough” in terms that 
outside
> the package it has no use. Therefore, defining the generic seems like 
a
 big
> responsibility in that it should have a use outside the package. Would
 you
> still define “foo” as generic in this case?

 Not exactly sure what you mean, but if a function has no use outside 
of a
 package, just avoid exporting it.

 Are there any guidelines in when one should or should not define a
 generic?
> From:
>
 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_help_

Re: [Bioc-devel] readVcf problems in package check

[Clark, Lindsay V]

Hi Herve,

Thanks so much for your response!  I realize that you all aren't obligated to 
support CRAN packages.  When I was developing polyRAD I considered submitting 
Bioconductor, but I didn't want to have to convert my 'RADdata' class from S3 
to S4.  The polyRAD package also isn't very deeply integrated with Bioconductor 
and doesn't require users to install VariantAnnotation and its dependencies 
unless they want to import from VCF (there are other import options available). 
 In any event I now have a published manuscript about polyRAD that points to 
CRAN as the repository where it is hosted, so changing repositories would 
probably be confusing for users.

If I look at the checks for the version of polyRAD that is currently on CRAN, 
the errors about an invalid VCFHeader object only show up for Windows.  
However, with the new version that I submitted, CRAN also sends me a Debian 
check with that same error.  Anyway, I will let them know about Rhtslib.

Best wishes,

Lindsay Clark, Ph.D.
Research Specialist
Department of Crop Sciences
University of Illinois, Urbana-Champaign

-Original Message-
From: Pages, Herve  
Sent: Wednesday, May 1, 2019 11:50 PM
To: Clark, Lindsay V ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] readVcf problems in package check

Hi Lindsay,

Is this issue specific to the Windows CRAN checks?

This Windows-specific error was also affecting several Bioconductor packages 
until recently but has been addressed in the latest version of Rhtslib (v 
1.15.6). What version of Rhtslib are they using for the CRAN checks? They need 
to make sure to use the version that belongs to BioC 3.9:

   http://bioconductor.org/packages/3.9/Rhtslib

which is the version that is known to work with R 3.6.0.

BTW have you considered submitting your package to Bioconductor? We typically 
don't provide support for CRAN packages even if they depend on other 
Bioconductor packages. In other (cruder) words, by submitting to CRAN, you're 
on your own.

Cheers,

H.


On 5/1/19 15:07, Clark, Lindsay V wrote:
> I'm the maintainer of polyRAD, which is hosted on CRAN but dependent on 
> several Bioconductor packages including VariantAnnotation.  I'm not sure if 
> my problem is on CRAN's end or Bioconductor's end, but in any event I have 
> not gotten a response from CRAN yet so I thought I would ask here.
>
> I am running into a package check issue which is causing my CRAN submission 
> to be rejected, but which I cannot reproduce.  I have tried fresh installs of 
> R 3.6 and all package dependencies on three different computers and don't see 
> this same error that CRAN reports.  My vignette uses a function that 
> internally calls VariantAnnotation::readVcf, and when the vignette is run, 
> CRAN reports the errors:
>
>
>Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
>
>invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 
> column DataFrame with names Number, Type, Description
>
>invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 
> column DataFrame with names Number, Type, Description
>
> I can run readVcf on the same file myself and see that the header contains 
> info and geno DataFrames that are formatted exactly as described, so I have 
> no idea how that error is occurring.
>
> More confusing (and this makes me suspect that something is wrong with CRAN's 
> check) are the messages:
>
>[E::bcf_hdr_parse_line] Could not parse the header line: 
> "##contig="
>
>[W::bcf_hdr_parse] Could not parse header line: 
> ##contig=
>
>[W::bcf_hdr_check_sanity] PL should be declared as Number=G
>
> I found these problems with the file (which is contained in inst/extdata), 
> fixed them, resubmitted the package, yet somehow still get the same message 
> from CRAN's checks.
>
> If any of you want to try performing the checks yourselves, my package is 
> hosted here: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lvclark_polyRAD&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=k3YdEzkx33T7tU3oJOCTF75TwVTnKpuZZGVEXnho13A&s=5zn32_iC0gM0KtfttAxA53zxyqFL3XG1NTFdrdQGCRw&e=.
>   The call to VCF2RADdata within the vignette is where these mysterious 
> problems are occurring.
>
> Any help is greatly appreciated.  Perhaps this is just some weird issue with 
> the transition from R 3.5 to 3.6.
>
> Best wishes,
>
> -Lindsay
>
> Lindsay Clark, Ph.D.
> Research Specialist
> Department of Crop Sciences
> University of Illinois, Urbana-Champaign
>
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mail
> man_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=k3YdEzkx33T7tU3oJOCTF75TwVTnKpuZ
> ZGVEXnho13A&s=7_wAV-QI5Ukxt5rkf7brSdbRiI60Rj7g80x40jsEY_M&e=

--
Hervé Pagès

Program in

Re: [Bioc-devel] Bioconductor version 3.9 branching today

[Turaga, Nitesh]

Minor typo, we'll be creating the  Bioconductor 3.9 branch (RELEASE_3_9) 
starting at 11AM. 

> On May 2, 2019, at 9:28 AM, Turaga, Nitesh  
> wrote:
> 
> Dear Bioc developers,
> 
> Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at 
> 11am EST. All commits to git.bioconductor.org 
> will be blocked for a few hours starting at 11AM. We'll post back when push 
> access is restored and you can resume commits.
> 
> Thanks.
> 
> Nitesh Turaga
> Bioconductor team
> 
> 
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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, 
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[Bioc-devel] Bioconductor version 3.9 branching today

[Turaga, Nitesh]

Dear Bioc developers,

Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at 
11am EST. All commits to git.bioconductor.org will 
be blocked for a few hours starting at 11AM. We'll post back when push access 
is restored and you can resume commits.

Thanks.

Nitesh Turaga
Bioconductor team


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] Deleting a branch on Bioconductor git

[Turaga, Nitesh]

Hi Kevin,

I'm actually surprised you were able to push a branch at all.  I'll delete this 
branch. 

Best,

Nitesh 
> On May 2, 2019, at 7:52 AM, Kevin Wang  wrote:
> 
> Hi all,
> I accidentally pushed a branch called “RELEASE_3_9” to the “scMerge" package 
> that I am maintaining on Bioconductor. I now understand that this is not the 
> correct way to manage this Bioconductor package and may interfere with the 
> upcoming release. However, when I tried to delete this branch via “git push 
> upstream --delete RELEASE_3_9”, I got a fatal error and denied access. Could 
> I maybe get some help from the administrator to correct this?
> 
> Thank you
> Best Wishes
> Kevin
> 
>   [[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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Re: [Bioc-devel] 'MoonlightR' Bioconductor package ERROR

[Shepherd, Lori]

Yes that should be a good tutorial to follow to sync to Bioconductor.  As of 
right now there is no RELEASE branch to sync too because the RELEASE_3_8 branch 
was frozen on April 15. but as of tomorrow the release branch will be 
RELEASE_3_9 and the devel branch is the master branch.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Antonio Colaprico 
Sent: Thursday, May 2, 2019 8:16:04 AM
To: Shepherd, Lori
Cc: Catharina Olsen; Morrell, Kayla; bioc-devel@r-project.org
Subject: Re: 'MoonlightR' Bioconductor package ERROR

Dear Lori,
Thank you for your prompt response. I am working on it to fix now. Quick 
question after that I commit to GitHub of Moonlight for syncing with 
Bioconductor Can I follow this tutorial ?

https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

Or there are some updates instructions?

Thank you,
best,
Antonio.


On Thu, May 2, 2019 at 7:24 AM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Please fix the ERROR as soon as possible to avoid potential deprecation.  We 
will temporarily be freezing the master (devel) branch later today (for an hour 
or two)  to create the new release 3.9 branch in preparation for tomorrows 
Bioc3.9 release.  Once this branching happens, the ERROR will need to be fixed 
on both of these branches once we reestablish contributors connection.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Antonio Colaprico 
mailto:antonio.colapr...@gmail.com>>
Sent: Wednesday, May 1, 2019 9:54:22 PM
To: bioc-devel@r-project.org; Morrell, Kayla; 
Catharina Olsen; Shepherd, Lori
Subject: Re: 'MoonlightR' Bioconductor package ERROR

Dear Kayla,

thank you for writing us about the MoonlightR package.

I am one of the maintainer of the package, I got this mail from Catharina.

Please as I changed University can you update my contact mail to 
axc1...@med.miami.edu ?

I am currently out of the office for a conference, I will come back in Miami 
tomorrow.

Are we still in time to check and fix this error?

Best,

Antonio Colaprico, PhD.






 Original Message 
Subject: 'MoonlightR' Bioconductor package ERROR
Date: 26.04.2019 19:19
 From: "Morrell, Kayla" 
To: "col...@ulb.ac.be" 
mailto:col...@ulb.ac.be>>
Cc: "Shepherd, Lori" 



The next Bioconductor release 3.9 is scheduled for May 3rd, and the last
day to commit to the devel branch is April 29th.

We like to make an effort to have all Bioconductor packages building and
checking without ERROR or TIMEOUT in the devel version. It seems your
package is still having an ERROR for all three of the platforms in the
devel version of Bioconductor. Could you please investigate this as soon
as possible.

https://www.bioconductor.org/checkResults/3.9/bioc-LATEST/MoonlightR/
[1]

If you need any assistance please feel free to ask questions at
bioc-devel@r-project.org.

Thank you,

KAYLA E. MORRELL, 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
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.

Links:
--
[1]
https://www.bioconductor.org/checkResults/3.9/bioc-LATEST/MoonlightR/


--

Antonio Colaprico, Ph.D.

Assistant Scientist (University of Miami)
Post doc researcher in Bioinformatics (Universit� Libre de Bruxelles)
Ph.D. in Bioinformatics (University of Sannio, Italy)
Telecommunications Engineer (University of Sannio,Italy)


Dr. Chen Lab
University of Miami Health System (UHealth),
Department of Public Health Sciences,
Sylvester Comprehensive Cancer Center (SCCC),
Clinical Research Building (CRB),
1120 NW 14th 
Street,
Office: Room 1050
33136 Miami, Florida, United States

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 messa

[Bioc-devel] Deleting a branch on Bioconductor git

[Kevin Wang]

Hi all,
I accidentally pushed a branch called “RELEASE_3_9” to the “scMerge" package 
that I am maintaining on Bioconductor. I now understand that this is not the 
correct way to manage this Bioconductor package and may interfere with the 
upcoming release. However, when I tried to delete this branch via “git push 
upstream --delete RELEASE_3_9”, I got a fatal error and denied access. Could I 
maybe get some help from the administrator to correct this?

Thank you
Best Wishes
Kevin

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Re: [Bioc-devel] 'MoonlightR' Bioconductor package ERROR

[Shepherd, Lori]

Please fix the ERROR as soon as possible to avoid potential deprecation.  We 
will temporarily be freezing the master (devel) branch later today (for an hour 
or two)  to create the new release 3.9 branch in preparation for tomorrows 
Bioc3.9 release.  Once this branching happens, the ERROR will need to be fixed 
on both of these branches once we reestablish contributors connection.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Antonio Colaprico 
Sent: Wednesday, May 1, 2019 9:54:22 PM
To: bioc-devel@r-project.org; Morrell, Kayla; Catharina Olsen; Shepherd, Lori
Subject: Re: 'MoonlightR' Bioconductor package ERROR

Dear Kayla,

thank you for writing us about the MoonlightR package.

I am one of the maintainer of the package, I got this mail from Catharina.

Please as I changed University can you update my contact mail to 
axc1...@med.miami.edu ?

I am currently out of the office for a conference, I will come back in Miami 
tomorrow.

Are we still in time to check and fix this error?

Best,

Antonio Colaprico, PhD.






 Original Message 
Subject: 'MoonlightR' Bioconductor package ERROR
Date: 26.04.2019 19:19
 From: "Morrell, Kayla" 
To: "col...@ulb.ac.be" 
mailto:col...@ulb.ac.be>>
Cc: "Shepherd, Lori" 



The next Bioconductor release 3.9 is scheduled for May 3rd, and the last
day to commit to the devel branch is April 29th.

We like to make an effort to have all Bioconductor packages building and
checking without ERROR or TIMEOUT in the devel version. It seems your
package is still having an ERROR for all three of the platforms in the
devel version of Bioconductor. Could you please investigate this as soon
as possible.

https://www.bioconductor.org/checkResults/3.9/bioc-LATEST/MoonlightR/
[1]

If you need any assistance please feel free to ask questions at
bioc-devel@r-project.org.

Thank you,

KAYLA E. MORRELL, 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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e-mail and delete this email message from your computer. Thank you.

Links:
--
[1]
https://www.bioconductor.org/checkResults/3.9/bioc-LATEST/MoonlightR/


--

Antonio Colaprico, Ph.D.

Assistant Scientist (University of Miami)
Post doc researcher in Bioinformatics (Universit� Libre de Bruxelles)
Ph.D. in Bioinformatics (University of Sannio, Italy)
Telecommunications Engineer (University of Sannio,Italy)


Dr. Chen Lab
University of Miami Health System (UHealth),
Department of Public Health Sciences,
Sylvester Comprehensive Cancer Center (SCCC),
Clinical Research Building (CRB),
1120 NW 14th Street,
Office: Room 1050
33136 Miami, Florida, United States


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Re: [Bioc-devel] permission denied

[Shepherd, Lori]

Have you checked your ssh keys on the credentials app?  You can add additional 
keys associated with your username there.


https://git.bioconductor.org/BiocCredentials



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 ruizhu huang 

Sent: Thursday, May 2, 2019 5:01:34 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] permission denied

Hi all,

My package TreeSummarizedExperiment has recently been accepted. I got the
error about permission denied when following the guidelines in the page (
https://bioconductor.org/developers/how-to/git/new-package-workflow/) to
run the following commands

$git remote add upstream g...@git.bioconductor.org:
packages/TreeSummarizedExperiment.git
$git fetch upstream

The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.

ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.

Are you sure you want to continue connecting (yes/no)? yes

Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.

Permission denied (publickey).

fatal: Could not read from remote repository.

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


$ssh -T g...@git.bioconductor.org

Permission denied (publickey).

Would you mind helping me about this issue. Thanks!
Ruizhu

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[Bioc-devel] permission denied

[ruizhu huang]

Hi all,

My package TreeSummarizedExperiment has recently been accepted. I got the
error about permission denied when following the guidelines in the page (
https://bioconductor.org/developers/how-to/git/new-package-workflow/) to
run the following commands

$git remote add upstream g...@git.bioconductor.org:
packages/TreeSummarizedExperiment.git
$git fetch upstream

The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.

ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.

Are you sure you want to continue connecting (yes/no)? yes

Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.

Permission denied (publickey).

fatal: Could not read from remote repository.

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


$ssh -T g...@git.bioconductor.org

Permission denied (publickey).

Would you mind helping me about this issue. Thanks!
Ruizhu

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