Re: [Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages

2020-02-27 Thread Aaron Lun 

This is a minor RcppAnnoy issue that should be fixed soon, hopefully.

Incidentally, this little episode has highlighted the advantages of 
Bioconductor's release/devel configuration. If the upstream dependency 
was a Bioc package, its updates are unlikely to break downstream 
packages in release. We are only broken in release right now because 
RcppAnnoy is a CRAN package and lies outside the release/devel cycle.


Of course, that is not to say that we shouldn't use CRAN packages. That 
brings me to my second point: BiocNeighbors explicitly serves as a 
wrapper for this dependency, and if I did not have faith in the 
RcppAnnoy maintainers to respond in a timely manner, I could just modify 
BiocNeighbors so that its Annoy functionality diverts to some other 
algorithm. This ensures that downstream packages that were using Annoy 
via BiocNeighbors can continue to operate - albeit with altered results 
due to the change in algorithm, but at least they don't break.


Right now, I do have faith in the RcppAnnoy maintainers so I have 
refrained from modifying BiocNeighbors in BioC-release. But the key 
point is that I can pull the trigger at any time.


-A

On 2/27/20 12:22 PM, Martin Morgan wrote:

You can't use a package version other than the current release, so 
BiocNeighbors needs to be updated (assuming that's the problem); I'm sure it 
will be. Martin

On 2/28/20, 2:51 AM, "Bioc-devel on behalf of Leonardo Collado Torres" 
 wrote:

 Hi,
 
 When installing BiocNeighbors (1.4.1, latest release from Bioconductor

 version 3.10) from source on linux I noticed the issue as a few hours
 ago it all worked fine but now it doesn't. Locally, I noticed that I
 had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I
 can install the BiocNeighbors 1.4.1 binary, I did the actual tests at
 https://github.com/LTLA/BiocNeighbors/issues/10 and noticed that
 RcppAnnoy's change lead to this. I have no idea how RcppAnnoy works,
 but well, maybe if you use it in your package you do.
 
 Now I need to google how to set on my DESCRIPTION to use the CRAN

 archived version of RcppAnnoy 0.0.14 that you can install with
 
 packageurl <- "https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz;

 install.packages(packageurl, repos=NULL, type="source")
 ## From 
https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages
 
 Best,

 Leo
 
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Re: [Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11

2020-02-27 Thread Ludwig Geistlinger 
Great, thanks for the update!


From: Interdonato, Kayla 
Sent: Thursday, February 27, 2020 2:40 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: EXTERNAL: Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11

When generating this annotation package, we believed the data we were 
downloading was stale which is why we chose to deprecate it.  Upon seeing the 
deprecation list email, a user informed us of a different location where the 
data may be more up to date. We are currently working through our annotation 
pipeline with the new data to be sure we can generate all the information 
needed in the org.At.tair.db package. Once we have finished this pipeline and 
compared, we will determine if the package should in fact be deprecated and if 
so, what will the supplement be.

Best,
Kayla

On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" 
 
wrote:

Why will org.At.tair.db be deprecated and by what will it be replaced? It's 
the org package for Arabidopsis and thus central for gene ID mapping when 
working with Arabidopsis data ...

Thanks,
Ludwig

--
Dr. Ludwig Geistlinger
Department of Epidemiology and Biostatistics
CUNY School of Public Health
New York, NY 10027


From: Bioc-devel  on behalf of Shepherd, 
Lori 
Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11

***ATTENTION: This email came from an external source. Do not open 
attachments or click on links from unknown senders or unexpected emails.***

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. The current list of 
deprecated packages for Bioc 3.11 is as follows:

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw

Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)



Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
RCAS
bgafun
lol
M3D
MergeMaid


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 
3.11 but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38


It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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 
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Re: [Bioc-devel] Change citation reference

2020-02-27 Thread Federico Giorgi 
Dear Stan: tahnks but yes, the version was updated a while ago, after the
change in inst/CITATION was done
Dear Lori: thanks a lot for looking into this!

Federico

On Thu, 27 Feb 2020 at 15:30, Stian Lågstad  wrote:

> Hi Federico,
>
> I believe you need to update the package version (in the DESCRIPTION file)
> to trigger a new build for those changes to be visible. If you update the
> version and push that change then a new build will be triggered.
>
> I see from http://bioconductor.org/checkResults/3.10/bioc-LATEST/ (search
> for "vulcan" there) that your package was last built:
> > Last Commit: b5638d5
> > Last Changed Date: 2019-10-29 13:10:48 -0500
>
> On Thu, Feb 27, 2020 at 3:19 PM Federico Giorgi 
> wrote:
>
>> Dear all,
>>
>> I would like to change the citation in the vulcan package.
>>
>> https://bioconductor.org/packages/release/bioc/html/vulcan.html
>>
>> I have changed the reference in the inst/CITATION file within the package
>> a
>> few weeks ago, but the old citation remains, even in the development
>> version:
>> https://bioconductor.org/packages/devel/bioc/html/vulcan.html
>>
>> Should I wait or is there another way to update the citation reference?
>>
>> Thanks,
>>
>> Federico
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Stian Lågstad
> +47 41 80 80 25
>

[[alternative HTML version deleted]]

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Re: [Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages

2020-02-27 Thread Martin Morgan 
You can't use a package version other than the current release, so 
BiocNeighbors needs to be updated (assuming that's the problem); I'm sure it 
will be. Martin

On 2/28/20, 2:51 AM, "Bioc-devel on behalf of Leonardo Collado Torres" 
 wrote:

Hi,

When installing BiocNeighbors (1.4.1, latest release from Bioconductor
version 3.10) from source on linux I noticed the issue as a few hours
ago it all worked fine but now it doesn't. Locally, I noticed that I
had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I
can install the BiocNeighbors 1.4.1 binary, I did the actual tests at
https://github.com/LTLA/BiocNeighbors/issues/10 and noticed that
RcppAnnoy's change lead to this. I have no idea how RcppAnnoy works,
but well, maybe if you use it in your package you do.

Now I need to google how to set on my DESCRIPTION to use the CRAN
archived version of RcppAnnoy 0.0.14 that you can install with

packageurl <- 
"https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz;
install.packages(packageurl, repos=NULL, type="source")
## From 
https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages

Best,
Leo

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Re: [Bioc-devel] EXTERNAL: Re: List of Deprecated Packages Bioc 3.11

2020-02-27 Thread Interdonato, Kayla 
When generating this annotation package, we believed the data we were 
downloading was stale which is why we chose to deprecate it.  Upon seeing the 
deprecation list email, a user informed us of a different location where the 
data may be more up to date. We are currently working through our annotation 
pipeline with the new data to be sure we can generate all the information 
needed in the org.At.tair.db package. Once we have finished this pipeline and 
compared, we will determine if the package should in fact be deprecated and if 
so, what will the supplement be. 

Best,
Kayla

On 2/27/20, 1:24 PM, "Bioc-devel on behalf of Ludwig Geistlinger" 
 
wrote:

Why will org.At.tair.db be deprecated and by what will it be replaced? It's 
the org package for Arabidopsis and thus central for gene ID mapping when 
working with Arabidopsis data ...

Thanks,
Ludwig

--
Dr. Ludwig Geistlinger
Department of Epidemiology and Biostatistics
CUNY School of Public Health
New York, NY 10027


From: Bioc-devel  on behalf of Shepherd, 
Lori 
Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11

***ATTENTION: This email came from an external source. Do not open 
attachments or click on links from unknown senders or unexpected emails.***

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. The current list of 
deprecated packages for Bioc 3.11 is as follows:

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw

Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)



Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
RCAS
bgafun
lol
M3D
MergeMaid


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 
3.11 but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38


It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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]]

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This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or

[Bioc-devel] Account activation problems

2020-02-27 Thread Antti Honkela 

Dear Bioc-devel,

I am the maintainer of 'tigre', and tried to activate my account for 
BiocCredentials. For some reason, the system claims that my email 
(antti.honk...@helsinki.fi) is not associated with any package, although 
it is specified in the DESCRIPTION.


How can I activate my account?


Best regards,

Antti

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[Bioc-devel] RcppAnnoy changed in CRAN from 0.0.14 to 0.0.15, and might have broken some packages

2020-02-27 Thread Leonardo Collado Torres 
Hi,

When installing BiocNeighbors (1.4.1, latest release from Bioconductor
version 3.10) from source on linux I noticed the issue as a few hours
ago it all worked fine but now it doesn't. Locally, I noticed that I
had to update from RcppAnnoy 0.0.14 to 0.0.15, and while at my macOS I
can install the BiocNeighbors 1.4.1 binary, I did the actual tests at
https://github.com/LTLA/BiocNeighbors/issues/10 and noticed that
RcppAnnoy's change lead to this. I have no idea how RcppAnnoy works,
but well, maybe if you use it in your package you do.

Now I need to google how to set on my DESCRIPTION to use the CRAN
archived version of RcppAnnoy 0.0.14 that you can install with

packageurl <- 
"https://cran.r-project.org/src/contrib/Archive/RcppAnnoy/RcppAnnoy_0.0.14.tar.gz;
install.packages(packageurl, repos=NULL, type="source")
## From 
https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages

Best,
Leo

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Re: [Bioc-devel] List of Deprecated Packages Bioc 3.11

2020-02-27 Thread Ludwig Geistlinger 
Why will org.At.tair.db be deprecated and by what will it be replaced? It's the 
org package for Arabidopsis and thus central for gene ID mapping when working 
with Arabidopsis data ...

Thanks,
Ludwig

--
Dr. Ludwig Geistlinger
Department of Epidemiology and Biostatistics
CUNY School of Public Health
New York, NY 10027


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, February 27, 2020 12:32 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] List of Deprecated Packages Bioc 3.11

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. The current list of 
deprecated packages for Bioc 3.11 is as follows:

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw

Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)



Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
RCAS
bgafun
lol
M3D
MergeMaid


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 3.11 
but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38


It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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]]

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[Bioc-devel] List of Deprecated Packages Bioc 3.11

2020-02-27 Thread Shepherd, Lori 
The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly. The current list of 
deprecated packages for Bioc 3.11 is as follows:

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw

Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)



Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
RCAS
bgafun
lol
M3D
MergeMaid


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 3.11 
but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38


It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending emails out to packages that have been broken across all 
platforms for an extended period of time as those are packages that are up for 
immediate deprecation if not corrected in a timely fashion.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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]]

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[Bioc-devel] Fwd: Changing the maintanor of IMMAN package

2020-02-27 Thread Turaga, Nitesh 
Hi Minoo,

I'm adding this chain to the bioc-devel thread for follow up.

I've checked your Git credentials on your account with Bioconductor. Everything 
is fine on our end. You need to actually push to the remote repository once you 
have your "remotes" set up correctly.

http://bioconductor.org/developers/how-to/git/

I'm attaching the link to the documentation again. If you need more help please 
attach the error messages you are seeing. Also attach the outputs of the 
commands,

`git remote -v`


Best,

Nitesh

Begin forwarded message:

From: ni41435_ca 
mailto:nitesh.tur...@roswellpark.org>>
Subject: Re: [Bioc-devel] Changing the maintanor of IMMAN package
Date: February 20, 2020 at 8:34:46 AM EST
To: minoo ashtiani mailto:ashtiani.mi...@gmail.com>>

I see that the GitHub username has been changed by you already to the new one.

You just have to get your remote set up correctly by following the directions 
in the documentation.

Best,

Nitesh

On Feb 20, 2020, at 6:59 AM, minoo ashtiani 
mailto:ashtiani.mi...@gmail.com>> wrote:

Thanks a lot, Nitesh.

I will check them out. My old GitHub account was  
https://github.com/Minoo-Ashtiani  and the new one is 
https://github.com/Minoo-ASTY.

Thanks a lot for your assistance.

Minoo

On Wed, Feb 19, 2020 at 5:23 PM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi,

The remote is wrong.

You need to have to do something similar to #6 
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/.

Your remote should look like this, (but instead of BiocGenerics , it should be 
your package name) and (instead of  it should be your GitHub 
username).

git remote -v

origin  g...@github.com:/BiocGenerics.git 
(fetch)
origin  g...@github.com:/BiocGenerics.git 
(push)
upstream
g...@git.bioconductor.org:packages/BiocGenerics.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/BiocGenerics.git
 (push)

Please also take a look at the documentation we have here 
http://bioconductor.org/developers/how-to/git/.

It is very helpful. Can you give me your old GitHub account and new GitHub 
account links?

Best,

Nitesh

On Feb 19, 2020, at 10:06 AM, minoo ashtiani 
mailto:ashtiani.mi...@gmail.com>> wrote:

Hi Nitesh,

Thanks for your reply. The problem is my previous github account which was 
linked with my package repository is blocked. I tried to change my username and 
email address in BioCredential but its still not working as my last log in date 
is not changing anymore. I think as my whole account is changed maybe 
bioconductor team should changed it, I guess.
In the another hand, this is the result of step 2 try on my system:
$ git remote -v
origin  LINK (fetch)
origin  LINK (push)


I would be very grateful if you help me with this problem.

Bests,
Minoo

On Tue, Feb 18, 2020 at 3:24 PM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi,

The error you are showing in your feed is currently saying, you are NOT in a 
repository which is hosted by github.

Also, your remotes should be the set to look like Step #2 
(http://bioconductor.org/developers/how-to/git/push-to-github-bioc/). If that 
is set up, your GitHub name should have NO effect on pushing to Bioconductor.

If you'd like to change your Github username, you can log into the 
BiocCredentials application, and change your Github username on your account.

Best,

Nitesh

On Feb 18, 2020, at 8:51 AM, minoo ashtiani 
mailto:ashtiani.mi...@gmail.com>> wrote:

Hi to all,

This is Minoo Ashtiani the maintainer of "IMMAN" software package. My
git-hub account is changed from "Minoo-Ashtiani" to "Minoo-ASTY". Now I
want to update the package using my new account however I cant. When I want
push to the origin I faced this errors:

git push origin master
  fatal: 'LINK' does not appear to be a git repository
   fatal: Could not read from remote repository.


What should I do? Any help would be appreciated.
P.S. I am the only maintainer of this package.
--
Minoo Ashtiani,

Research Assistant @ Russell Lab, Heidelberg University
+491605667176 Germany
minoo.ashti...@bioquant.uni-heidelberg.de

for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEJ=en

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Re: [Bioc-devel] Change citation reference

2020-02-27 Thread Stian Lågstad 
Hi Federico,

I believe you need to update the package version (in the DESCRIPTION file)
to trigger a new build for those changes to be visible. If you update the
version and push that change then a new build will be triggered.

I see from http://bioconductor.org/checkResults/3.10/bioc-LATEST/ (search
for "vulcan" there) that your package was last built:
> Last Commit: b5638d5
> Last Changed Date: 2019-10-29 13:10:48 -0500

On Thu, Feb 27, 2020 at 3:19 PM Federico Giorgi 
wrote:

> Dear all,
>
> I would like to change the citation in the vulcan package.
>
> https://bioconductor.org/packages/release/bioc/html/vulcan.html
>
> I have changed the reference in the inst/CITATION file within the package a
> few weeks ago, but the old citation remains, even in the development
> version:
> https://bioconductor.org/packages/devel/bioc/html/vulcan.html
>
> Should I wait or is there another way to update the citation reference?
>
> Thanks,
>
> Federico
>
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>
> ___
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>


-- 
Stian Lågstad
+47 41 80 80 25

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Re: [Bioc-devel] Change citation reference

2020-02-27 Thread Shepherd, Lori 
Thank you for letting us know.  We will investigate on our end.


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 Federico 
Giorgi 
Sent: Thursday, February 27, 2020 9:18 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Change citation reference

Dear all,

I would like to change the citation in the vulcan package.

https://bioconductor.org/packages/release/bioc/html/vulcan.html

I have changed the reference in the inst/CITATION file within the package a
few weeks ago, but the old citation remains, even in the development
version:
https://bioconductor.org/packages/devel/bioc/html/vulcan.html

Should I wait or is there another way to update the citation reference?

Thanks,

Federico

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[Bioc-devel] Change citation reference

2020-02-27 Thread Federico Giorgi 
Dear all,

I would like to change the citation in the vulcan package.

https://bioconductor.org/packages/release/bioc/html/vulcan.html

I have changed the reference in the inst/CITATION file within the package a
few weeks ago, but the old citation remains, even in the development
version:
https://bioconductor.org/packages/devel/bioc/html/vulcan.html

Should I wait or is there another way to update the citation reference?

Thanks,

Federico

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Re: [Bioc-devel] update package

2020-02-27 Thread Shepherd, Lori 
Did you follow the advice Nitesh posted?

https://stat.ethz.ch/pipermail/bioc-devel/2020-February/016228.html


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 minoo ashtiani 

Sent: Thursday, February 27, 2020 6:37 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] update package

Dear Bioconductor team,

This is Minoo Ashtiani, maintainer of the IMMAN package. Recently, I had
problems updating my package and I asked you a few questions about it. I
was wondering if now I could update it successfully or not. I would be
truly grateful if you let me know.

Best regards,
--
Minoo Ashtiani,

Research Assistant @ Russell Lab, Heidelberg University
+491605667176 Germany
minoo.ashti...@bioquant.uni-heidelberg.de

for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEJ=en

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[Bioc-devel] update package

2020-02-27 Thread minoo ashtiani 
Dear Bioconductor team,

This is Minoo Ashtiani, maintainer of the IMMAN package. Recently, I had
problems updating my package and I asked you a few questions about it. I
was wondering if now I could update it successfully or not. I would be
truly grateful if you let me know.

Best regards,
-- 
Minoo Ashtiani,

Research Assistant @ Russell Lab, Heidelberg University
+491605667176 Germany
minoo.ashti...@bioquant.uni-heidelberg.de

for accessing papers:
https://scholar.google.com/citations?user=nnCwxpEJ=en

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