[Bioc-devel] ExperimentHub with AWS

[Spiro Stilianoudakis]

Hi all,

I am maintaining a newly added package on Bioconductor (preciseTAD). I am
interested in having an accompanying experiment data package where I will
be storing approximately ~5gb worth of rds (or Rda) objects. They are
currently being stored on a google drive but I would prefer them to be
accessed via AWS. I have been reading the tutorial for how to accomplish
this via experimenthub using

https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html#overview

Under section 2.1 of the above tutorial it mentions that this requires
assistance from a Bioconductor team member. I am new to this, so I just
want to make sure I am going about this correctly. I would greatly
appreciate any input/advice from someone more experienced in the matter.
Also, is it correct that I need to have the experiment package created
before the data is added to the hub?

Thank you ahead of time for any help you can provide!

Best,

Spiro Stilianoudakis
PhD Candidate | Department of Biostatistics
Virginia Commonwealth University

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Re: [Bioc-devel] Git pack file greater than 5MB

[McGrath, Max]

Hi all,

Thank you all for taking the time to discuss this issue. While the package does 
have a fairly long history with multiple authors, I am currently the only 
active developer on the project. So, if it preferable from Bioconductor’s 
perspective, I will rewrite the repository's history.

I do have one remaining question regarding the extent of the rewrite. Currently 
the package (not including the pack file) sits at ~1.6MB. After a test run of 
the rewrite I was able to reduce the pack file to ~4MB. So, the total package 
is still over 5MB, but each individual file is under the threshold. Is this 
acceptable? Or will I need to delete more from the history? I ask because I 
imagine it is preferable to limit the extent of the rewrite to a minimal 
acceptable standard.

Thanks,
Max

From: Bioc-devel  on behalf of Martin Morgan 

Sent: Thursday, October 1, 2020 10:32 AM
To: Henrik Bengtsson ; Nitesh Turaga 

Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Git pack file greater than 5MB

yes Hervé has made this point too -- mucking with the history of the package, 
potentially breaking historical checkouts (when large files are deleted from 
the history, too).

It's relevant because when a package is added to our repository we do a full 
clone of the master branch; an alternative would be to do a --depth 1 clone of 
the master branch, but to me this doesn't seem ideal at all -- from the 
Bioconductor perspective the git.bioconductor.org package is definitive, and 
all we would have would be 'and then a miracle occurred' for early package 
development. I'm also nervous about side-effects associated with maintaining 
the Bioconductor and non-Bioconductor repositories that have different 
historical starts.

My own feel is that most of these cases are packages that are still 'new' and 
seldom have clones / forks.

One could take a hybrid approach, where if a maintainer insists on the 
integrity of their git repository (or even automatically, if they do have large 
files in their history we automatically change strategy) then we do a --depth 1 
clone.

Martin

On 10/1/20, 12:17 PM, "Bioc-devel on behalf of Henrik Bengtsson" 
 
wrote:

I understood that it's a submission. Just wanted to make sure that it's
clear there might be side effects, e.g. people clone and collaborate also
before submitting to Bioc and a rewrite might surprise existing
collaborators etc.

/H

On Thu, Oct 1, 2020, 09:04 Nitesh Turaga  wrote:

> This package isn’t yet a Bioconductor package Henrik. It will break other
> forks most likely. This package hasn’t been submitted to the Contributions
> either to be reviewed. So this is the time to break what needs to be 
broken
> before it’s submitted to Bioconductor and gets into the Bioconductor git
> repository.
>
> Nitesh
>
> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson 
> wrote:
>
> Doesn't a git rewrite break all existing clones, forks out there? I'm
> happy to be corrected, if this is not the case.
>
> /Henrik
>
> On Thu, Oct 1, 2020, 08:16 Nitesh Turaga  wrote:
>
>> Hi,
>>
>> The BiocCheck will complain on the build system about the > 5MB package
>> size.
>>
>> The rewrite of the history with BFG cleaner (
>> https://rtyley.github.io/bfg-repo-cleaner/ <
>> https://rtyley.github.io/bfg-repo-cleaner/>) is not as severe as you
>> think it is to be honest. It is just removing these pack files which 
don’t
>> have a place in the tree structure. These are more often than not, orphan
>> files.
>>
>> If you are suspect of this solution, I would suggest you make a backup
>> clone of your repo and try it on that first before you touch the main 
repo.
>> Check the history (git log) to see if anything important is missing.
>>
>> But usually a software package has to be below 5MB. If you have some data
>> in there which is needed for the package, consider Experiment Hub.
>>
>> Best,
>>
>> Nitesh
>>
>> > On Sep 30, 2020, at 12:46 PM, McGrath, Max 
>> wrote:
>> >
>> > Hi all,
>> >
>> > We have a package that is ready for submission, but when running
>> BiocCheck a warning is generated noting that "The following files are 
over
>> 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and
>> run git gc which reduced the file size from 5.2 to 5.1MB, but I have been
>> unable to reduce it further.
>> >
>> > I'm reaching out to determine if this is an issue, and if so to ask for
>> recommendations for solving it. Currently, the only solution I've come up
>> with is to rewrite the repository's history using a tool like
>> "git-filter-repo", but this is a more drastic action than I would prefer 
to
>> take. I would greatly appreciate any advice on the matter.
>> >
>> > Thank you,
>> > Max McGrat

Re: [Bioc-devel] Updating to Python 3: Problem with Importlib library

[Martin Morgan]

The script is currently in the root directory of the package

~/b/git$ ls seq2pathway/scripts/
Function_PeakMutationAnnotation_GENCODE_05182015.py
Function_PeakMutationAnnotation_GENCODE_08182020.py

but needs to be in inst/scripts folder like the earlier version

~/b/git$ ls seq2pathway/inst/scripts/
Function_PeakMutationAnnotation_GENCODE_05182015.py

This is because the code in the package is evaluated after it has been 
installed, and top-level files other than DESCRIPTION, etc., are not copied to 
the install location.

Do you check your package before pushing changes, 

  R CMD build seq2pathway
  R CMD check seq2pathway_.tar.gz

?

Martin Morgan

On 10/1/20, 12:27 PM, "Bioc-devel on behalf of Yuxi Sun" 
 wrote:

Hi,

I am writing on behalf of the development team for the package seq2pathway.
After updating to python 3 and replacing the deprecated imp library with
importlib library, we encountered the following problem.

Our python code is included in the
file Function_PeakMutationAnnotation_GENCODE_08182020 in the same folder.
When I try to call the file by the following lines:

sink(file.path(tempdir(),name,fsep = .Platform$file.sep))
cat("from importlib.machinery import SourceFileLoader", sep="\n")
cat("SourceFileLoader('Function_PeakMutationAnnotation_GENCODE_08182020',")
cat("'", path, "').load_module()",sep="")

it failed and reported the following error message:

FileNotFoundError: [Errno 2] No such file or directory:

'/private/var/folders/7d/jtfhkky940n_83bv32nyv_bmgn/T/RtmpZS8eqz/Rinst4fbc14010ad1/seq2pathway//scripts/Function_PeakMutationAnnotation_GENCODE_08182020.py'


Would you please kindly instruct me how to fix this error?


Thanks and regards,

Jennifer

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Re: [Bioc-devel] Git pack file greater than 5MB

[Martin Morgan]

yes Hervé has made this point too -- mucking with the history of the package, 
potentially breaking historical checkouts (when large files are deleted from 
the history, too).

It's relevant because when a package is added to our repository we do a full 
clone of the master branch; an alternative would be to do a --depth 1 clone of 
the master branch, but to me this doesn't seem ideal at all -- from the 
Bioconductor perspective the git.bioconductor.org package is definitive, and 
all we would have would be 'and then a miracle occurred' for early package 
development. I'm also nervous about side-effects associated with maintaining 
the Bioconductor and non-Bioconductor repositories that have different 
historical starts.

My own feel is that most of these cases are packages that are still 'new' and 
seldom have clones / forks.

One could take a hybrid approach, where if a maintainer insists on the 
integrity of their git repository (or even automatically, if they do have large 
files in their history we automatically change strategy) then we do a --depth 1 
clone.

Martin

On 10/1/20, 12:17 PM, "Bioc-devel on behalf of Henrik Bengtsson" 
 
wrote:

I understood that it's a submission. Just wanted to make sure that it's
clear there might be side effects, e.g. people clone and collaborate also
before submitting to Bioc and a rewrite might surprise existing
collaborators etc.

/H

On Thu, Oct 1, 2020, 09:04 Nitesh Turaga  wrote:

> This package isn’t yet a Bioconductor package Henrik. It will break other
> forks most likely. This package hasn’t been submitted to the Contributions
> either to be reviewed. So this is the time to break what needs to be 
broken
> before it’s submitted to Bioconductor and gets into the Bioconductor git
> repository.
>
> Nitesh
>
> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson 
> wrote:
>
> Doesn't a git rewrite break all existing clones, forks out there? I'm
> happy to be corrected, if this is not the case.
>
> /Henrik
>
> On Thu, Oct 1, 2020, 08:16 Nitesh Turaga  wrote:
>
>> Hi,
>>
>> The BiocCheck will complain on the build system about the > 5MB package
>> size.
>>
>> The rewrite of the history with BFG cleaner (
>> https://rtyley.github.io/bfg-repo-cleaner/ <
>> https://rtyley.github.io/bfg-repo-cleaner/>) is not as severe as you
>> think it is to be honest. It is just removing these pack files which 
don’t
>> have a place in the tree structure. These are more often than not, orphan
>> files.
>>
>> If you are suspect of this solution, I would suggest you make a backup
>> clone of your repo and try it on that first before you touch the main 
repo.
>> Check the history (git log) to see if anything important is missing.
>>
>> But usually a software package has to be below 5MB. If you have some data
>> in there which is needed for the package, consider Experiment Hub.
>>
>> Best,
>>
>> Nitesh
>>
>> > On Sep 30, 2020, at 12:46 PM, McGrath, Max 
>> wrote:
>> >
>> > Hi all,
>> >
>> > We have a package that is ready for submission, but when running
>> BiocCheck a warning is generated noting that "The following files are 
over
>> 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and
>> run git gc which reduced the file size from 5.2 to 5.1MB, but I have been
>> unable to reduce it further.
>> >
>> > I'm reaching out to determine if this is an issue, and if so to ask for
>> recommendations for solving it. Currently, the only solution I've come up
>> with is to rewrite the repository's history using a tool like
>> "git-filter-repo", but this is a more drastic action than I would prefer 
to
>> take. I would greatly appreciate any advice on the matter.
>> >
>> > Thank you,
>> > Max McGrath
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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[Bioc-devel] Updating to Python 3: Problem with Importlib library

[Yuxi Sun]

Hi,

I am writing on behalf of the development team for the package seq2pathway.
After updating to python 3 and replacing the deprecated imp library with
importlib library, we encountered the following problem.

Our python code is included in the
file Function_PeakMutationAnnotation_GENCODE_08182020 in the same folder.
When I try to call the file by the following lines:

sink(file.path(tempdir(),name,fsep = .Platform$file.sep))
cat("from importlib.machinery import SourceFileLoader", sep="\n")
cat("SourceFileLoader('Function_PeakMutationAnnotation_GENCODE_08182020',")
cat("'", path, "').load_module()",sep="")

it failed and reported the following error message:

FileNotFoundError: [Errno 2] No such file or directory:
'/private/var/folders/7d/jtfhkky940n_83bv32nyv_bmgn/T/RtmpZS8eqz/Rinst4fbc14010ad1/seq2pathway//scripts/Function_PeakMutationAnnotation_GENCODE_08182020.py'


Would you please kindly instruct me how to fix this error?


Thanks and regards,

Jennifer

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Re: [Bioc-devel] Git pack file greater than 5MB

[Henrik Bengtsson]

I understood that it's a submission. Just wanted to make sure that it's
clear there might be side effects, e.g. people clone and collaborate also
before submitting to Bioc and a rewrite might surprise existing
collaborators etc.

/H

On Thu, Oct 1, 2020, 09:04 Nitesh Turaga  wrote:

> This package isn’t yet a Bioconductor package Henrik. It will break other
> forks most likely. This package hasn’t been submitted to the Contributions
> either to be reviewed. So this is the time to break what needs to be broken
> before it’s submitted to Bioconductor and gets into the Bioconductor git
> repository.
>
> Nitesh
>
> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson 
> wrote:
>
> Doesn't a git rewrite break all existing clones, forks out there? I'm
> happy to be corrected, if this is not the case.
>
> /Henrik
>
> On Thu, Oct 1, 2020, 08:16 Nitesh Turaga  wrote:
>
>> Hi,
>>
>> The BiocCheck will complain on the build system about the > 5MB package
>> size.
>>
>> The rewrite of the history with BFG cleaner (
>> https://rtyley.github.io/bfg-repo-cleaner/ <
>> https://rtyley.github.io/bfg-repo-cleaner/>) is not as severe as you
>> think it is to be honest. It is just removing these pack files which don’t
>> have a place in the tree structure. These are more often than not, orphan
>> files.
>>
>> If you are suspect of this solution, I would suggest you make a backup
>> clone of your repo and try it on that first before you touch the main repo.
>> Check the history (git log) to see if anything important is missing.
>>
>> But usually a software package has to be below 5MB. If you have some data
>> in there which is needed for the package, consider Experiment Hub.
>>
>> Best,
>>
>> Nitesh
>>
>> > On Sep 30, 2020, at 12:46 PM, McGrath, Max 
>> wrote:
>> >
>> > Hi all,
>> >
>> > We have a package that is ready for submission, but when running
>> BiocCheck a warning is generated noting that "The following files are over
>> 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and
>> run git gc which reduced the file size from 5.2 to 5.1MB, but I have been
>> unable to reduce it further.
>> >
>> > I'm reaching out to determine if this is an issue, and if so to ask for
>> recommendations for solving it. Currently, the only solution I've come up
>> with is to rewrite the repository's history using a tool like
>> "git-filter-repo", but this is a more drastic action than I would prefer to
>> take. I would greatly appreciate any advice on the matter.
>> >
>> > Thank you,
>> > Max McGrath
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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Re: [Bioc-devel] Git pack file greater than 5MB

[Nitesh Turaga]

This package isn’t yet a Bioconductor package Henrik. It will break other forks 
most likely. This package hasn’t been submitted to the Contributions either to 
be reviewed. So this is the time to break what needs to be broken before it’s 
submitted to Bioconductor and gets into the Bioconductor git repository.

Nitesh 

> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson  
> wrote:
> 
> Doesn't a git rewrite break all existing clones, forks out there? I'm happy 
> to be corrected, if this is not the case.
> 
> /Henrik
> 
> On Thu, Oct 1, 2020, 08:16 Nitesh Turaga  > wrote:
> Hi,
> 
> The BiocCheck will complain on the build system about the > 5MB package size. 
> 
> The rewrite of the history with BFG cleaner 
> (https://rtyley.github.io/bfg-repo-cleaner/ 
>  
>  >) is not as severe as you think 
> it is to be honest. It is just removing these pack files which don’t have a 
> place in the tree structure. These are more often than not, orphan files.
> 
> If you are suspect of this solution, I would suggest you make a backup clone 
> of your repo and try it on that first before you touch the main repo. Check 
> the history (git log) to see if anything important is missing. 
> 
> But usually a software package has to be below 5MB. If you have some data in 
> there which is needed for the package, consider Experiment Hub. 
> 
> Best,
> 
> Nitesh 
> 
> > On Sep 30, 2020, at 12:46 PM, McGrath, Max  > > wrote:
> > 
> > Hi all,
> > 
> > We have a package that is ready for submission, but when running BiocCheck 
> > a warning is generated noting that "The following files are over 5MB in 
> > size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and run git 
> > gc which reduced the file size from 5.2 to 5.1MB, but I have been unable to 
> > reduce it further.
> > 
> > I'm reaching out to determine if this is an issue, and if so to ask for 
> > recommendations for solving it. Currently, the only solution I've come up 
> > with is to rewrite the repository's history using a tool like 
> > "git-filter-repo", but this is a more drastic action than I would prefer to 
> > take. I would greatly appreciate any advice on the matter.
> > 
> > Thank you,
> > Max McGrath
> > 
> >   [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org  mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> > 
> 
> 
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> 
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> 


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Re: [Bioc-devel] Git pack file greater than 5MB

[Henrik Bengtsson]

Doesn't a git rewrite break all existing clones, forks out there? I'm happy
to be corrected, if this is not the case.

/Henrik

On Thu, Oct 1, 2020, 08:16 Nitesh Turaga  wrote:

> Hi,
>
> The BiocCheck will complain on the build system about the > 5MB package
> size.
>
> The rewrite of the history with BFG cleaner (
> https://rtyley.github.io/bfg-repo-cleaner/ <
> https://rtyley.github.io/bfg-repo-cleaner/>) is not as severe as you
> think it is to be honest. It is just removing these pack files which don’t
> have a place in the tree structure. These are more often than not, orphan
> files.
>
> If you are suspect of this solution, I would suggest you make a backup
> clone of your repo and try it on that first before you touch the main repo.
> Check the history (git log) to see if anything important is missing.
>
> But usually a software package has to be below 5MB. If you have some data
> in there which is needed for the package, consider Experiment Hub.
>
> Best,
>
> Nitesh
>
> > On Sep 30, 2020, at 12:46 PM, McGrath, Max 
> wrote:
> >
> > Hi all,
> >
> > We have a package that is ready for submission, but when running
> BiocCheck a warning is generated noting that "The following files are over
> 5MB in size: '.git/objects/pack/pack-xxx...". I've pruned, repacked, and
> run git gc which reduced the file size from 5.2 to 5.1MB, but I have been
> unable to reduce it further.
> >
> > I'm reaching out to determine if this is an issue, and if so to ask for
> recommendations for solving it. Currently, the only solution I've come up
> with is to rewrite the repository's history using a tool like
> "git-filter-repo", but this is a more drastic action than I would prefer to
> take. I would greatly appreciate any advice on the matter.
> >
> > Thank you,
> > Max McGrath
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] Git pack file greater than 5MB

[Nitesh Turaga]

Hi,

The BiocCheck will complain on the build system about the > 5MB package size. 

The rewrite of the history with BFG cleaner 
(https://rtyley.github.io/bfg-repo-cleaner/ 
) is not as severe as you think it 
is to be honest. It is just removing these pack files which don’t have a place 
in the tree structure. These are more often than not, orphan files.

If you are suspect of this solution, I would suggest you make a backup clone of 
your repo and try it on that first before you touch the main repo. Check the 
history (git log) to see if anything important is missing. 

But usually a software package has to be below 5MB. If you have some data in 
there which is needed for the package, consider Experiment Hub. 

Best,

Nitesh 

> On Sep 30, 2020, at 12:46 PM, McGrath, Max  wrote:
> 
> Hi all,
> 
> We have a package that is ready for submission, but when running BiocCheck a 
> warning is generated noting that "The following files are over 5MB in size: 
> '.git/objects/pack/pack-xxx...". I've pruned, repacked, and run git gc which 
> reduced the file size from 5.2 to 5.1MB, but I have been unable to reduce it 
> further.
> 
> I'm reaching out to determine if this is an issue, and if so to ask for 
> recommendations for solving it. Currently, the only solution I've come up 
> with is to rewrite the repository's history using a tool like 
> "git-filter-repo", but this is a more drastic action than I would prefer to 
> take. I would greatly appreciate any advice on the matter.
> 
> Thank you,
> Max McGrath
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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Re: [Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all

[Nitesh Turaga]

Most people don’t use passphrase for SSH keys on Bioconductor. But it seems 
like you do have one or your permissions for the SSH key pair you have are 
wrong. 

1. If you have a passphrase and forgot it, just make a new SSH key and add it 
to your BiocCredentials account.

2. If it’s a permissions issue with your SSH key pair, check #16 in the FAQ 
http://bioconductor.org/developers/how-to/git/faq/ 
. You can change 
permissions of your key and it should work. 

Best,

Nitesh 

> On Oct 1, 2020, at 7:38 AM, Krutik Patel (PGR)  
> wrote:
> 
> Hi Bioconductor,
> 
> Wanted to clarify a small issue before continuing with a package update.
> 
> I just added a new SSH key to biocredentials and my github account.
> It seems to have worked fine, but I got a warning when I tried to fetch. I 
> have copied the output from git remove -v and git fetch --all below.
> 
> Is there something else I need to do before continuing with merging the 
> upstream and master braches?
> 
> Best,
> 
> Krutik
> 
> $ git remote -v
> origin g...@github.com:Krutik6/TimiRGeN.git (fetch)
> origin g...@github.com:Krutik6/TimiRGeN.git (push)
> upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (fetch)
> upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (push)
> 
> $ git fetch --all
> Fetching origin
> Warning: Permanently added the RSA host key for IP address '140.82.121.4' to 
> the list of known hosts.
> Enter passphrase for key '/home/krutik/.ssh/id_rsa':
> Fetching upsteam
> 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.
> Enter passphrase for key '/home/krutik/.ssh/id_rsa':
> Connection to git.bioconductor.org closed by remote host.
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upsteam
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: Publickey permission denied

[Emilie Secherre]

Hello,
It was resolved, thank you! I fixed the error on first build report by
removing lines causing it.
Regards,
Émilie

Le jeu. 1 oct. 2020 à 14:37, Interdonato, Kayla <
kayla.morr...@roswellpark.org> a écrit :

> Hello,
>
> I am assigned as the reviewer for this package. I see a valid push on the
> issue and a build report was produced. Is it safe to assume this was
> resolved or are you still experiencing issues? If you want to comment on
> the issue directly I'd be happy to help you with any further problems you
> may have.
>
> Best,
> Kayla
>
> On 10/1/20, 5:11 AM, "Bioc-devel on behalf of Emilie Secherre" <
> bioc-devel-boun...@r-project.org on behalf of emiseche...@gmail.com>
> wrote:
>
> Hello,
> I submitted my package to Bioconductor yesterday. I had an error to
> fix,
> once fixed I wanted to push the updated package to
> g...@git.bioconductor.org:
> packages/famat.
>
> So i used these command lines (which both worked) :
> - git remote add upstream g...@git.bioconductor.org:packages/famat.git
> - git remote -v
> origin  https://github.com/emiliesecherre/famat (fetch)
>  origin
> https://github.com/emiliesecherre/famat (push)   upstream
> g...@git.bioconductor.org:packages/famat.git (fetch) upstream
> g...@git.bioconductor.org:packages/famat.git (push)
>
> Though, when i use git fetch --all i get this :
> Fetching 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/[fingerprint])?
> yes
> Warning: Permanently added 'git.bioconductor.org
> ,34.192.48.227'
> (ECDSA) to the list of known hosts.
> 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.
> error: Could not fetch upstream
>
> How can I access to this repository ?
> Thanks in advance for answers,
> Emilie
>
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>
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>
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Re: [Bioc-devel] EXTERNAL: Publickey permission denied

[Interdonato, Kayla]

Hello,

I am assigned as the reviewer for this package. I see a valid push on the issue 
and a build report was produced. Is it safe to assume this was resolved or are 
you still experiencing issues? If you want to comment on the issue directly I'd 
be happy to help you with any further problems you may have.

Best,
Kayla

On 10/1/20, 5:11 AM, "Bioc-devel on behalf of Emilie Secherre" 
 wrote:

Hello,
I submitted my package to Bioconductor yesterday. I had an error to fix,
once fixed I wanted to push the updated package to 
g...@git.bioconductor.org:
packages/famat.

So i used these command lines (which both worked) :
- git remote add upstream g...@git.bioconductor.org:packages/famat.git
- git remote -v
origin  https://github.com/emiliesecherre/famat (fetch)   origin
https://github.com/emiliesecherre/famat (push)   upstream
g...@git.bioconductor.org:packages/famat.git (fetch) upstream
g...@git.bioconductor.org:packages/famat.git (push)

Though, when i use git fetch --all i get this :
Fetching 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/[fingerprint])? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227'
(ECDSA) to the list of known hosts.
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.
error: Could not fetch upstream

How can I access to this repository ?
Thanks in advance for answers,
Emilie

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[Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all

[Krutik Patel (PGR)]

Hi Bioconductor,

Wanted to clarify a small issue before continuing with a package update.

I just added a new SSH key to biocredentials and my github account.
It seems to have worked fine, but I got a warning when I tried to fetch. I have 
copied the output from git remove -v and git fetch --all below.

Is there something else I need to do before continuing with merging the 
upstream and master braches?

Best,

Krutik

$ git remote -v
origin g...@github.com:Krutik6/TimiRGeN.git (fetch)
origin g...@github.com:Krutik6/TimiRGeN.git (push)
upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (fetch)
upsteam g...@git.bioconductor.org:packages/TimiRGeN.git (push)

$ git fetch --all
Fetching origin
Warning: Permanently added the RSA host key for IP address '140.82.121.4' to 
the list of known hosts.
Enter passphrase for key '/home/krutik/.ssh/id_rsa':
Fetching upsteam
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.
Enter passphrase for key '/home/krutik/.ssh/id_rsa':
Connection to git.bioconductor.org closed by remote host.
fatal: Could not read from remote repository.

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








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Re: [Bioc-devel] SSL error on Ubuntu 20.04

[Mike Smith]

Hi Lara,

I've encountered this issue with biomaRt too.

I found I could get the connection to work with the following:

library(httr)
url <- "https://www.ensembl.org/";
httr_config <-  config(ssl_cipher_list = "DEFAULT@SECLEVEL=1")
res <- with_config(config = httr_config, GET(url))

I haven't quite decided the best way to integrate that into my package, for
now it uses the httr_config if it's running on any Linux, which seems quite
heavy handed. It may be that specifying a particular cipher or determining
the host capabilities would be preferable to "DEFAULT", but does seem to
work for now on Ubuntu 20.04 and hasn't thrown any problems for my tests on
16.04 and 18.04.

Best,
Mike

On Wed, 30 Sep 2020 at 21:02, Selles Vidal, Lara <
lara.selle...@imperial.ac.uk> wrote:

> Dear BioC community,
>
> We were recently informed that a multilayered bug due to an increased
> security level in Ubuntu 20.04, configuration issues on server side and a
> bug in OpenSSL 1.1.1 caused our packages to fail on Ubuntu 20.04 with the
> following error:
>
>error:14094410:SSL routines:ssl3_read_bytes:sslv3 alert handshake
> failure
>
> This affects the two packages I maintain, rfaRm and ncRNAtools. As a
> temporary fix, we were suggested to use HTTP instead of HTTPS. However,
> some of the web resources accessed with our packages do not seem to be
> accessible via HTTP. This is reflected in the latest build for rfaRm for
> example (http://bioconductor.org/checkResults/devel/bioc-LATEST/rfaRm/) ,
> which fails as a consequence of all the URLs being changed to the “http”
> version instead of “https”.
>
> The problem seems to have been discussed here
> https://github.com/Ensembl/ensembl-rest/issues/427 , with a temporary fix
> suggested here
> https://askubuntu.com/questions/1233186/ubuntu-20-04-how-to-set-lower-ssl-security-level
> . However, this seems to involve changing some openssl options through the
> openssl config file. We are unsure on whether this temporary fix could be
> implemented from within our package. We would greatly appreciate any
> guidance on how to implement it, or on any other alternative temporary
> workarounds.
>
> Thanks a lot in advance!
>
> Best wishes,
>
> Lara
>
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[Bioc-devel] Publickey permission denied

[Emilie Secherre]

Hello,
I submitted my package to Bioconductor yesterday. I had an error to fix,
once fixed I wanted to push the updated package to g...@git.bioconductor.org:
packages/famat.

So i used these command lines (which both worked) :
- git remote add upstream g...@git.bioconductor.org:packages/famat.git
- git remote -v
origin  https://github.com/emiliesecherre/famat (fetch)   origin
https://github.com/emiliesecherre/famat (push)   upstream
g...@git.bioconductor.org:packages/famat.git (fetch) upstream
g...@git.bioconductor.org:packages/famat.git (push)

Though, when i use git fetch --all i get this :
Fetching 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/[fingerprint])? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227'
(ECDSA) to the list of known hosts.
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.
error: Could not fetch upstream

How can I access to this repository ?
Thanks in advance for answers,
Emilie

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