[Bioc-devel] Help: git push complains non-existing files being too big

[Zhu, Lihua (Julie)]

Martin,

A while ago, Jim suggested to replace two big data files with two smaller ones, 
which I did.

Oddly, when I tried to import the package GUIDEseq to github today, it still 
mentions these two files being too big, although I do not see these two files 
in my local repository, checked out from the Bioconductor repository.

JulieZhuMac2017:GUIDEseq ZHUJ$ git rm -r inst/extdata/HEK293_site4All.bed
fatal: pathspec 'inst/extdata/HEK293_site4All.bed' did not match any files

Could you please help? Thanks!

Best regards,

Julie


FYI, I am following the steps outlined at 
https://bioconductor.org/developers/how-to/git/maintain-github-bioc/

JulieZhuMac2017:GUIDEseq ZHUJ$  git push origin master
Counting objects: 515, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (180/180), done.
Writing objects: 100% (515/515), 107.80 MiB | 18.38 MiB/s, done.
Total 515 (delta 344), reused 483 (delta 320)
remote: Resolving deltas: 100% (344/344), done.
remote: warning: File inst/extdata/HEK293_site4All.bam is 87.88 MB; this is 
larger than GitHub's recommended maximum file size of 50.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File 
Storage - https://git-lfs.github.com.
remote: error: Trace: faafca1a45d562b62039862ac0dfbf85
remote: error: See http://git.io/iEPt8g for more information.
remote: error: File inst/extdata/HEK293_site4All.bed is 124.11 MB; this exceeds 
GitHub's file size limit of 100.00 MB
To https://github.com/LihuaJulieZhu/GUIDEseq.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 
'https://github.com/LihuaJulieZhu/GUIDEseq.git'

From: "Zhu, Lihua (Julie)" 
Date: Monday, October 19, 2015 at 1:32 PM
To: Michael Lawrence , Jim Hester 

Subject: Re: Data files in GUIDEseq

Jim, FYI, I have removed the two large datasets with much smaller replacements. 
Thanks for your feedback!

Michael, please feel free to check out the new dataset in the following commit. 
Thanks!

Best regards,

Julie



Julie-Zhus-MacBook-Pro-Intel-Core-i7:GUIDEseq zhuj$ svn ci -m "changed to 
smaller test datasets"
SendingDESCRIPTION
Deleting   inst/extdata/HEK293_site4All.bam
Deleting   inst/extdata/HEK293_site4All.bed
Adding  (bin)  inst/extdata/bowtie2.HEK293_site4_chr13.sort.bam
Adding inst/extdata/bowtie2.HEK293_site4_chr13.sort.bed
Transmitting file data ...
Committed revision 109732.

From: Lihua Julie Zhu >
Date: Thursday, October 15, 2015 2:16 PM
To: Michael Lawrence 
>, Jim Hester 
>
Subject: Re: Data files in GUIDEseq

Yes, we need to fetch a few enriched regions.


From: Michael Lawrence 
>
Date: Thursday, October 15, 2015 2:13 PM
To: Jim Hester 
>
Cc: Michael Lawrence 
>, Lihua Julie Zhu 
>
Subject: Re: Data files in GUIDEseq

Since this is peak calling, we probably want to keep all the reads within a 
smaller region.

On Thu, Oct 15, 2015 at 11:12 AM, Jim Hester 
> wrote:
FWIW the hard limit that was causing the error with the git mirrors is 100
Mb, but I would try and shoot for a file around 20 Mb or so at max.

An easy way if you just want uniform sampling is using samtools (where -s
is the fraction of reads you want to keep).

samtools view  HEK293_site4All.bam -s .1 -b -o HEK293_site4All2.bam

Thanks,

Jim
​

On Thu, Oct 15, 2015 at 2:07 PM, Michael Lawrence 

> wrote:

> Probably best to come up with smaller files, because we want them in the
> package for demonstration purposes, right? Just need to filter them,
> somehow. Actually, all we need is the BAM file...
>
> On Thu, Oct 15, 2015 at 10:43 AM, Zhu, Lihua (Julie) <
> julie@umassmed.edu> wrote:
>
>> Thanks, Jim!
>>
>> These files were included for Michael to test functions he is developing


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Re: [Bioc-devel] Update data in data package, pcxnData

[Turaga, Nitesh]

Hi Sokratis,

Your key(s) on file is 

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf

ssh-rsa 
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

Are you sure you are using a private key which corresponds to any of these 
public keys? I’d start with that. 

Best 

Nitesh 


> On Mar 23, 2018, at 8:20 AM, Sokratis Kariotis  
> wrote:
> 
> Hey Lori,
> 
> While under the RELEASE_3_6 branch and using git fetch upstream or git push
> upstream/RELEASE_3_6:
> 
> 
> 
> 
> 
> 
> *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 rightsand the
> repository exists.*
> 
> 
> git remove -v results to:
> 
> 
> 
> 
> 
> 
> *origin  https://github.com/hidelab/pcxn.git
>  (fetch)origin
> https://github.com/hidelab/pcxn.git 
> (push)upstreamg...@git.bioconductor.org:packages/pcxn.git
> (fetch)upstreamg...@git.bioconductor.org:packages/pcxn.git (push)*
> The ssh command also gives:
> 
> 
> 
> 
> *Warning: Permanently added 'git.bioconductor.org
> ,34.192.48.227' (ECDSA) to the list of known
> hosts.Permission denied (publickey).*
> 
> *Cheers,*
> 
> *Sokratis*
> 
> 
> On 23 March 2018 at 11:35, Shepherd, Lori 
> wrote:
> 
>> Where you able to update master?  Or are you having access trouble
>> for both branches?  Please use reply all so that other members on the team
>> can answer when appropriate and the responses go to the mailing list.
>> 
>> Your package is in the git repository and has access with the ID s.kariotis.
>> Can you please copy the commands with the output you are receiving that
>> make you think that you do not have access?
>> 
>> Please also include the output of
>> 
>> git remote -v
>> 
>> and
>> 
>> ssh -T g...@git.bioconductor.org
>> (you should see RW access next to your package)
>> 
>> 
>> Please
>> 
>> 
>> 
>> 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
>> Shepherd, Lori 
>> *Sent:* Friday, November 24, 2017 10:13 AM
>> *To:* Sokratis Kariotis; bioc-devel
>> *Subject:* Re: [Bioc-devel] Update data in data package, pcxnData
>> 
>> You should make changes and push to the master branch of your package at
>> g...@git.bioconductor.org:packages/pcxnData.git  .  This will update the
>> devel version of your package.
>> 
>> As long as the package builds correctly, It will be available for download
>> immediately with Bioc devel 3.7.
>> 
>> 
>> We don't encourage updating release unless it is a bug correction or
>> justifiable updates, but if you push changes to the RELEASE_3_6 branch they
>> will also be available in Bioc 3.6
>> 
>> 
>> Instructions for pushing data to our git repository can be found here:
>> 

Re: [Bioc-devel] hook declined or non-fast-forward problem

[Turaga, Nitesh]

Hi Yuande,

This is being blocked because you have completely unrelated histories from what 
you have on your Github to the Bioc-git repo. We deliberately don’t allow force 
pushing. 

Are you sure you want to merge the unrelated histories? This is important to 
consider, particularly because we’ve had this problem of packages having 
duplicate commits.Please make sure your Github Repo does not have any duplicate 
commits. (“git log --oneline”)

If you think the Github repo is at a state where it needs to synced to the 
Bioc-git repo, let me know and I’ll take a look at it and sync it for you.

Send me the link to your Github repo or just send me the output to “git remove 
-v”.

Best,

Nitesh 

> On Mar 25, 2018, at 11:55 AM, Yuande Tan  wrote:
> 
> Dear All,
> I tried to git push upstream master but I met problem:
> 
> To git.bioconductor.org:packages/MBttest.git
> 
> ! [rejected]master -> master (non-fast-forward)
> 
> error: failed to push some refs to 'g...@git.bioconductor.org:
> packages/MBttest.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.
> 
> 
> Actually fixed merge conflict by using git add . and git commit -m
> "Resolved merge conflict by incorporating both suggestions."
> 
> and git add ../README.md and git commit -m "add README.md file."
> 
> I used git pull --allow-unrelated-histories origin master
> 
> and I got
> 
> 
> From https://github.com/Yuande/MBttest
> 
> * branchmaster -> FETCH_HEAD
> 
> Already up to date.
> 
> I still did *~/.ssh*$ git push upstream master and I got the same error
> (non-fast-forward).
> 
> 
> When I used *~/.ssh*$ git push -f upstream master, I got "error: hook
> declined to update refs/heads/master"
> 
> 
> 
> So how do I address this "hook declined" error?
> 
> 
> Thanks
> 
> 
> Yuande Tan
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

[Ludwig Geistlinger]

Hi Lori,


I have worked through the ToPASeq package.


1. The package implements an extended range of operations for the 'Pathway' 
class (defined in the graphite package).

I am currently in contact with the author of the graphite package, Gabriele 
Sales, whether these operations are generally useful for the class and could be 
accordingly moved to the graphite package.


2. The implementations of the pathway enrichment methods SPIA, DEGraph, and 
TopologyGSA are redundant with existing functionality in Bioconductor and will 
be accordingly delegated to corresponding implementations in the graphite and 
EnrichmentBrowser package. The core of the package that I will maintain further 
are the implementations of the pathway enrichment methods PRS, PWEA and TAPPA, 
which seem to be unique to the package.


3. Parallel computation will be reworked to be based on BiocParallel, thereby 
resolving the package's current platform dependence (linux-only).


I have  required access rights, have set up a github repo under 
lgeistlinger/ToPASeq, and I am optimistic to have a working version ready in 
devel in agreement with the respective deadline of the release schedule (Wed, 
April 25,

Deadline for packages passing ��R CMD build�� and ��R CMD check�� without 
errors or warnings).


Best,

Ludwig


--
Dr. Ludwig Geistlinger
CUNY School of Public Health

From: Shepherd, Lori 
Sent: Monday, March 26, 2018 8:07 AM
To: Ludwig Geistlinger
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7


Hi Ludwig,


I just wanted to touch base and make sure you had the access rights to ToPASeq. 
 The release is scheduled

for next month 
http://bioconductor.org/developers/release-schedule/
  and I was curious as to your estimated time frame for looking at fixing the 
ERRORs in the package?


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Saturday, March 3, 2018 5:51:10 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7


Hi Lori,


Yes I would take over maintenance.

Anything particular that I need to take care of?


Otherwise I would just follow:


https://bioconductor.org/developers/how-to/git/maintain-github-bioc/


to accordingly set this up.


Thanks,

Ludwig


--
Dr. Ludwig Geistlinger
CUNY School of Public Health

From: Shepherd, Lori 
Sent: Saturday, March 3, 2018 5:14 PM
To: Ludwig Geistlinger; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7


Hi Ludwig,


Were you still interested in taking over maintainership of ToPaSeq?  We have 
switched permission and you should have access now.  If you are no longer 
interested please let us know.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Friday, December 15, 2017 1:05:16 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Lori,

I would be willing to take over maintenance of

ToPASeq

in case maintainers remain unresponsive.

Best,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Friday, December 15, 2017 9:29 AM
To: Martin Morgan
Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

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 is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010



Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq


Lori Shepherd

Bioconductor Core Team

Roswell Park