Re: [Bioc-devel] Bioconductor package IMMAN

[minoo ashtiani]

Dear Lori,

Thanks for your help. I went according to your advice but I permanently get
error in the upstream mode, here is the output:

mintty screen dump

Minoo@DESKTOP-PGH7233 MINGW64 ~/Desktop/IMMAN (master)
 $ git push origin master
  git Enumerating objects: 9, done.
   Counting objects: 100% (9/9), done.
Delta compression using up to 4
threads Compressing objects:
100% (4/4), done.  Writing
objects: 100% (5/5), 417 bytes | 139.00 KiB/s, done.
 Total 5 (delta 3), reused 0 (delta 0)
  To git.bioconductor.org:packages/IMMAN.git
  01a56eb..57f5adc  master -> master

 Minoo@DESKTOP-PGH7233 MINGW64
~/Desktop/IMMAN (master)  $ git push upstream
master  To
https://github.com/Minoo-ASTY/IMMAN.git
   ! [rejected]master -> master (non-fast-forward)
   error: failed to push some refs to
'https://github.com/Minoo-ASTY/IMMAN.git'hint: Updates were
rejected because the tip of your current branch is behindhint: its
remote counterpart. Integrate the remote changes (e.g.
hint: 'git pull ...') before pushing again.
 hint: See the 'Note about fast-forwards' in 'git push --help'
for details.


and this is the output of pull command:
mintty screen dump

$ git pull upstream master
 From https://github.com/Minoo-ASTY/IMMAN
   * branchmaster -> FETCH_HEAD
   First, rewinding head to replay your work
on top of it...   Applying: Fix Version number in
IMMAN pre-release   Using index info to
reconstruct a base tree...  M
DESCRIPTION
 Falling back to patching base and 3-way merge...
  Auto-merging DESCRIPTION
   CONFLICT (content): Merge conflict in DESCRIPTION
error: Failed to merge in the changes.
 hint: Use 'git am
--show-current-patch' to see the failed patch Patch
failed at 0001 Fix Version number in IMMAN pre-release
   Resolve all conflicts manually, mark them as resolved with
"git add/rm ", then run "git rebase --continue".
   You can instead skip this commit: run "git rebase --skip".
To abort and get back to the state before "git rebase",
run "git rebase --abort".

  Minoo@DESKTOP-PGH7233
MINGW64 ~/Desktop/IMMAN (master|REBASE 1/11)  $ git am
--show-current-patch
commit 02b172ed888e9b4f6f827a791d4bd5ca8f3ed0f6
 Author: Nitesh Turaga  Date:
 Wed May 1 15:19:21 2019 -0400

   Fix Version number in IMMAN pre-release

 1.3.02 to 1.3.2

   diff --git
a/DESCRIPTION b/DESCRIPTION
index ece16fe..a2bfc10 100644
 --- a/DESCRIPTION
  +++ b/DESCRIPTION
   @@ -1,6 +1,6 @@
 Package: IMMAN
  Title: Interlog protein
network reconstruction by Mapping and Mining ANalysis  -Version:
1.3.02
+Version: 1.3.2
  Description: Reconstructing Interlog Protein Network (IPN)
integrated from several
   Protein protein Interaction
Networks (PPINs). Using this package,   overlaying
different PPINs to mine conserved common networks between diverse


I am unable to fix it. I tried everything. I don't know what else should I
do. Any help would be appreciated.

Thanks a lot,
Minoo

On Mon, Mar 23, 2020 at 1:30 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> I would do a
>
> git fetch --all   # get all branches
> git pull upstream master   # pulls changes from Bioconductor git server
>
> # resolve any merge conflicts that arise.
>
> It is good practice to always pull from origin and upstream before making
> any changes to code to make sure the code base is updated.
>
> Let us know if you have any further trouble.
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* minoo ashtiani 
> *Sent:* Monday, March 23, 2020 6:26 AM
> *To:* Shepherd, Lori ;
> bioc-devel@r-project.org 
> *Subject:* Re: Bioconductor package IMMAN
>
> Hi Lori,
>
> Thanks for the update. I edited the vignette in which the platform error
> comes from that. I

Re: [Bioc-devel] Bioconductor package IMMAN

[minoo ashtiani]

Hi Lori,

Thanks for the update. I edited the vignette in which the platform error
comes from that. I updated the by using

   1.

git push origin master

   2.

command and it was OK, however when I wanted to run the second command line

   1.

   git push upstream master

   2.

I faced error and I have no idea how to fix it. Here is a summary of the
output of the two commands line:

$ git push origin master
Enumerating objects: 9, done.
Counting objects: 100% (9/9), done.
Delta compression using up to 4 threads
Compressing objects: 100% (4/4), done.
Writing objects: 100% (5/5), 409 bytes | 136.00 KiB/s, done.
Total 5 (delta 3), reused 0 (delta 0)
To git.bioconductor.org:packages/IMMAN.git
   05b59cb..01a56eb  master -> master

$ git push upstream master
To https://github.com/Minoo-ASTY/IMMAN.git
 ! [rejected]master -> master (non-fast-forward)
error: failed to push some refs to 'https://github.com/Minoo-ASTY/IMMAN.git'
hint: Updates were rejected because the tip of your current branch is behind
hint: its remote counterpart. Integrate the remote changes (e.g.
hint: 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Is there any problem with or getting the output of "git push original
master" is enough?

All the bests,
Minoo

On Mon, Mar 16, 2020 at 2:50 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Dear package maintainer,
>
> Please be aware your package continues to fail on Bioconductor devel
> 3.11.   Bioconductor release is scheduled for Tuesday April 28th. We
> appreciate
> your quick response in this matter. If your package remains broken we will
> begin
> the deprecation process to remove the package from Bioconductor.
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/IMMAN/
>
>
>
>
> 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.



-- 
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

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

[minoo ashtiani]

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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[Bioc-devel] Fwd: update bioconductor package

[minoo ashtiani]

Thank you very much Nitesh.

I would be really grateful if you give me the access right.

Bests,
Minoo

On Fri, Feb 8, 2019 at 8:58 PM Turaga, Nitesh 
wrote:

> Hi Minoo,
>
> There is access to just one username with the IMMAN package “jafarilab”.
> You cannot gain access through “Minoo-Ashtiani” as it checks for the SSH
> key and knows there is one user already registered with that key.
>
> I would suggest everyone in the lab, submit changes to
> https://github.com/jafarilab/IMMAN. And then, sync the GitHub repo with
> git.bioconductor.org:packages/IMMAN using the “jafarilab” account. This
> way, there credential management is handled entirely from your end.
>
> Otherwise, I’d have to give you access rights and you’d have to set up new
> SSH keys again.
>
> Best,
>
> Nitesh
>
>
>
> > On Feb 8, 2019, at 4:01 AM, minoo ashtiani 
> wrote:
> >
> >
> > Dear Nitesh,
> >
> > Thanks for your help. I used
> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/ to
> maintain my package. However, when I write this line
> >
> >  $ git clone g...@git.bioconductor.org:packages/IMMAN
> > Cloning into 'IMMAN'...
> > g...@git.bioconductor.org: Permission denied (publickey).
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> > and the repository exists.
> >
> > I got this error and I don't know how to fix it.
> >
> > PS: I am using another GitHub profile for maintenance. The first one was
> "jafarilab" that I published the package with that and now I am using
> "Minoo-Ashtiani" for updating. However, I have added the package SSH key to
> the "Minoo-AShtiani" profile.
> > Would please help get through this? I have no idea how to fix.
> >
> > All the best,
> > Minoo
> >
> >
> >
> >   Sender notified by
> > Mailtrack 02/08/19, 12:29:23 PM
> >
> > On Sun, Jan 27, 2019 at 7:07 PM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
> > You need to have access to your repository at git.bioconductor.org.
> >
> > http://bioconductor.org/developers/how-to/git/
> >
> > You should find all of your documentation in that link.
> >
> > Nitesh
> >
> >
> >
> > > On Jan 27, 2019, at 2:50 AM, minoo ashtiani 
> wrote:
> > >
> > > Hello everyone,
> > >
> > > I would like to update my Bioconductor package named "IMMAN". I made
> some
> > > changes and I wanted to update the package on the Bioconductor
> repository
> > > too, but I don't know how can I do it. Any idea?
> > >
> > >
> > > Bests,
> > > Minoo
> > >
> > >
> > > [image: Mailtrack]
> > > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > > Sender
> > > notified by
> > > Mailtrack
> > > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > > 01/27/19,
> > > 11:18:05 AM
> > >
> > >   [[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.
>
>
>
> 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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> received this message in error, please notify the sender immediately by
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[Bioc-devel] Fwd: update bioconductor package

[minoo ashtiani]

Dear Nitesh,

Thanks for your help. I used
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/ to
maintain my package. However, when I write this line

 $ git clone g...@git.bioconductor.org:packages/IMMAN
Cloning into 'IMMAN'...
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

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

I got this error and I don't know how to fix it.

PS: I am using another GitHub profile for maintenance. The first one was
"jafarilab" that I published the package with that and now I am using
"Minoo-Ashtiani" for updating. However, I have added the package SSH key to
the "Minoo-AShtiani" profile.
Would please help get through this? I have no idea how to fix.

All the best,
Minoo



[image: Mailtrack]
<https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;>
Sender
notified by
Mailtrack
<https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;>
02/08/19,
12:29:23 PM

On Sun, Jan 27, 2019 at 7:07 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> You need to have access to your repository at git.bioconductor.org.
>
> http://bioconductor.org/developers/how-to/git/
>
> You should find all of your documentation in that link.
>
> Nitesh
>
>
>
> > On Jan 27, 2019, at 2:50 AM, minoo ashtiani 
> wrote:
> >
> > Hello everyone,
> >
> > I would like to update my Bioconductor package named "IMMAN". I made some
> > changes and I wanted to update the package on the Bioconductor repository
> > too, but I don't know how can I do it. Any idea?
> >
> >
> > Bests,
> > Minoo
> >
> >
> > [image: Mailtrack]
> > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > Sender
> > notified by
> > Mailtrack
> > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > 01/27/19,
> > 11:18:05 AM
> >
> >   [[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] update bioconductor package

[minoo ashtiani]

Dear Nitesh,

Thanks for your help. I used
http://bioconductor.org/developers/how-to/git/maintain-bioc-only/ to
maintain my package. However, when I write this line

 $ git clone g...@git.bioconductor.org:packages/IMMAN
Cloning into 'IMMAN'...
g...@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

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

I got this error and I don't know how to fix it.

PS: I am using another GitHub profile for maintenance. The first one was
"jafarilab" that I published the package with that and now I am using
"Minoo-Ashtiani" for updating. However, I have added the package SSH key to
the "Minoo-AShtiani" profile.
Would please help get through this? I have no idea how to fix.

All the best,
Minoo



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Sender
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Mailtrack
<https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;>
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On Sun, Jan 27, 2019 at 7:07 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> You need to have access to your repository at git.bioconductor.org.
>
> http://bioconductor.org/developers/how-to/git/
>
> You should find all of your documentation in that link.
>
> Nitesh
>
>
>
> > On Jan 27, 2019, at 2:50 AM, minoo ashtiani 
> wrote:
> >
> > Hello everyone,
> >
> > I would like to update my Bioconductor package named "IMMAN". I made some
> > changes and I wanted to update the package on the Bioconductor repository
> > too, but I don't know how can I do it. Any idea?
> >
> >
> > Bests,
> > Minoo
> >
> >
> > [image: Mailtrack]
> > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > Sender
> > notified by
> > Mailtrack
> > <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> > 01/27/19,
> > 11:18:05 AM
> >
> >   [[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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[Bioc-devel] update bioconductor package

[minoo ashtiani]

Hello everyone,

I would like to update my Bioconductor package named "IMMAN". I made some
changes and I wanted to update the package on the Bioconductor repository
too, but I don't know how can I do it. Any idea?


Bests,
Minoo


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[Bioc-devel] change my email address

[Minoo Ashtiani]

Hi to all,


How can I change my email address to my gmail address 
"ashtiani.mi...@gmail.com"?


All the best,

Minoo

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Re: [Bioc-devel] 'IMMAN' Bioconductor package

[Minoo Ashtiani]

Hi to all,


Thanks a lot for your all efforts.


My package "IMMAN" has ERRORS in  Multiple platform build/check report for BioC 
3.7 :

https://bioconductor.org/checkResults/3.7/bioc-LATEST/IMMAN/tokay2-buildsrc.html

But the error is related to the connection lost and is not for the package. How 
can I fix it?


Besides, It seems that there is no error on the devel version and it is just 
happening in the release version.


Bests,

Minoo




From: Morrell, Kayla 
Sent: Thursday, September 27, 2018 7:01:22 PM
To: Minoo Ashtiani
Cc: Shepherd, Lori
Subject: 'IMMAN' Bioconductor package


The next Bioconductor release 3.8 is scheduled for October 31st. The current 
Bioc 3.7 release brach will be frozen October 15th and the last day to commit 
to the devel branch is October 29th.


We like to make an effort to have all Bioconductor packages building and 
checking without ERROR or TIMEOUT in all release and devel versions. It seems 
your package is having an ERROR across the three platforms on the release 
version of Bioconductor. There is also an ERROR on the Linux platform on the 
devel version of Bioconductor. Could you please investigate this as soon as 
possible.


release version - https://bioconductor.org/checkResults/3.7/bioc-LATEST/IMMAN/


devel version - https://bioconductor.org/checkResults/3.8/bioc-LATEST/IMMAN/


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

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[Bioc-devel] Fw: permission denied

[Minoo Ashtiani]

From: Minoo Ashtiani
Sent: Wednesday, September 19, 2018 4:51 PM
To: bioc-devel-boun...@r-project.org
Subject: Fw: permission denied


Please if you have any idea to fix the mentioned problem, let me know.


Bests,

Minoo



From: Minoo Ashtiani
Sent: Tuesday, September 18, 2018 2:30 PM
To: bioc-devel-boun...@r-project.org
Subject: permission denied


Hi,


I would like to fix the problem that is happened when building IMMAN package in 
new version of Bioconductor updates, however, when I try to commit I faced this 
error:


$ git fetch --all
Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

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

Any idea about it?



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[Bioc-devel] update schedule of packages

[Minoo Ashtiani]

Hi there,


Thanks for publishing my package on Bioconductor. Just one more question, is 
the updating schedule of Bioconductor only each year on April?


We are planing to submit the paper of the package on a journal. We wanted to 
know if we can make some editions in the package according to the journal 
reviewers comments in the future before next April or not?


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[Bioc-devel] package is not available (for R version 3.4.4)

[Minoo Ashtiani]

Hi there,

I installed the "IMMAN" package which was built on Bioconductor 3.7 (devel) 
recently. I tried to install it but I faced this

package �IMMAN� is not available (for R version 3.4.4)

Why does it happen and how can i fix it?

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