date:20210714

Re: [Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

2021-07-14 Thread Paul Shannon

Thanks, Martin.   Your hunch was right, the problem was in our sever.  We had 
some expired ssl certificates on the nginx server which dispatched to Flask.

The irregular behavior we saw - where readVcf worked in some settings, and 
failed in others - is apparently due to different ssl stringencies in different 
operating systems, including across different versions of linux.

I should have known better than to pin this on VariantAnnotation and Rsamtools.

 - Paul



> On Jul 13, 2021, at 3:33 AM, Martin Morgan  wrote:
> 
> This 'worked for me' on my macOS and on the Bioconductor docker image after 
> BiocManager::install("VariantAnnotation")
> 
> The relevant packages are Rsamtools and Rhtslib, but these have gone through 
> very little change.
> 
> The shortest way to get to the call is through Rsamtools
> 
>  url = "https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz;
>  b = open(BcfFile(url))
> 
> This goes immediately into C code and (the quite old now) htslib. I looked at 
> the C code briefly, and there is no easy way to extract more information 
> about the reason for failure.
> 
> I don't really have any great insight to offer here; superficially it sounds 
> like the server is sometimes rejecting connections, and these have happened 
> to line up with OS.
> 
> Martin Morgan
> 
> On 7/12/21, 8:46 PM, "Bioc-devel on behalf of Paul Shannon" 
>  paul.thurmond.shan...@gmail.com> wrote:
> 
>The problem is described in full here, with 4 lines of code to reproduce.
> 
> https://support.bioconductor.org/p/9138262/ 
> 
> 
>James MacDonald pointed out that my initial analysis is wrong. (Thank you, 
> Jim!)  I claimed this works on macOS, fails on linux, and he shows in the 
> support thread that readVcf(remoteFile) worked find for him on linux.
> 
>So maybe, as Jim suggests, there is a problem with the latest version of 
> VariantAnnotation or packages it depends upon:?
> 
>Jim’s linux run, and my MacOD run, both used VariantAnnotation_1.38.0, 
>My docker (Docker devel) has VariantAnnotation_1.39.0.
> 
>However, I installed  1.38.0 on the docker image, and the problem 
> persisted.  Leading me to think that the problem may be one of the packages 
> (zlib, httr?) which VariantAnnotation uses?
> 
>One strategy we could employ is to expand the error message to tell us 
> more.  It currently reports
> 
>*[E::hts_open_format] Failed to open file
> https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz
>Error in open.BcfFile(BcfFile(file, character(0), ...)) :
>  ‘open'  VCF/BCF failed
>  filename: 
> https://igv-data.systemsbiology.net/static/ampad/test/chr2.vcf.gz*
> 
>Maybe  more information is available at the point of failure which, if 
> reported, might clarify the problem?
> 
> - Paul
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Updating stable release

2021-07-14 Thread Nitesh Turaga

Hi Margaret,

Please follow the documentation on the website, 
http://bioconductor.org/developers/how-to/git/. 

http://bioconductor.org/developers/how-to/version-numbering/ 

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 14, 2021, at 4:01 PM, James W. MacDonald  wrote:
> 
> The release version of your package is 1.8.0, and the devel is on increment 
> ahead (e.g., 1.9.x). You cannot increment the middle version number of your 
> release package because that makes it a devel package, hence the pre-release 
> hook denying your changes.
> 
> You should change the version to 1.8.1 for the release version.
> 
> Jim
> 
> 
> -Original Message-
> From: Bioc-devel  On Behalf Of margaret 
> linan
> Sent: Wednesday, July 14, 2021 12:56 PM
> To: bioc-devel 
> Subject: Re: [Bioc-devel] Updating stable release
> 
> Hi -
> 
> I successfully updated my devel PoTRA package recently, now I am trying to 
> push these same changes to the stable PoTRA package. I am encountering the 
> following issue (see highlight below).
> Note - in the github PoTRA repo, I have pulled and merged from head --> 
> RELEASE_3_13. Also the devel commit never had a problem with my version bump.
> 
> 
> git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
> 
> git checkout RELEASE_3_13
> Switched to branch 'RELEASE_3_13'
> Your branch is up to date with 'origin/RELEASE_3_13'.
> 
> git push upstream RELEASE_3_13
> Enumerating objects: 1, done.
> Counting objects: 100% (1/1), done.
> Writing objects: 100% (1/1), 641 bytes | 641.00 KiB/s, done.
> Total 1 (delta 0), reused 0 (delta 0), pack-reused 0
> remote: Error: Illegal version bump from '1.8.0' to '1.9.1'.
> remote:
> remote: Check http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details.
> remote:
> To git.bioconductor.org:packages/PoTRA.git
> ! [remote rejected] RELEASE_3_13 -> RELEASE_3_13 (pre-receive hook
> declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/PoTRA.git'
> 
> Thanks,
> Margaret
> 
> 
> 
> 
> On Wed, Jul 14, 2021 at 9:01 AM Kern, Lori 
> wrote:
> 
>> In your steps you were good when you checked out RELEASE_3_13
>> 
>> So after git checkout RELEASE_3_13
>> 
>> apply the changes you did to fix master.  You can do this manually or 
>> you investigate how to use git cherry-pick
>> 
>> When you have changed the files remember to do a git commit that 
>> includes the version bump in the DESCRIPTION
>> 
>> You should push those changes with a git push upstream RELEASE_3_13
>> 
>> Please ask further questions on bioc-devel so other members of the 
>> team can also assist.
>> 
>> Cheers,
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> --
>> *From:* margaret linan 
>> *Sent:* Wednesday, July 14, 2021 11:55 AM
>> *To:* Kern, Lori 
>> *Subject:* Re: [Bioc-devel] Updating stable release
>> 
>> Hi Lori,
>> 
>> I followed the instructions, but it seems that everything is 
>> up-to-date already, I also didn't see anything pushed to RELEASE_3_13. 
>> Here are my steps.
>> 
>> git fetch --all
>> Fetching origin
>> Fetching upstream
>> 
>> git checkout RELEASE_3_13
>> Switched to a new branch 'RELEASE_3_13'
>> Branch 'RELEASE_3_13' set up to track remote branch 'RELEASE_3_13' 
>> from 'upstream'.
>> 
>> git merge upstream/RELEASE_3_13
>> Already up to date.
>> 
>> git merge origin/RELEASE_3_13
>> merge: origin/RELEASE_3_13 - not something we can merge
>> 
>> git checkout master
>> Switched to branch 'master'
>> Your branch is up to date with 'origin/master'.
>> 
>> git checkout -b RELEASE_3_13 upstream/RELEASE_3_13
>> fatal: A branch named 'RELEASE_3_13' already exists.
>> 
>> git checkout master
>> Already on 'master'
>> Your branch is up to date with 'origin/master'.
>> 
>> git push upstream RELEASE_3_13
>> Everything up-to-date
>> 
>> git push origin RELEASE_3_13
>> Total 0 (delta 0), reused 0 (delta 0), pack-reused 0
>> remote:
>> remote: Create a pull request for 'RELEASE_3_13' on GitHub by visiting:
>> remote:  https://github.com/PoTRA-Package/PoTRA/pull/new/RELEASE_3_13
>> > dQZXjtu2Ye_OFvo9Gt_SINdBynMZM_YiIsc25aGOnlsZlZ3JToY54VUPz4-nfYIJjjV_rQ
>> adro327xvnfCleDCAGOngTyw2B46GkscVAiv5mtmvx1pgxaIF4dJMQiU7jfMDGy-yVU3Gh
>> fXxjw2CzEpo9_ifAXV4zor7AUdJNhDovKaGRwy1Pze3n3vK24R-h8sK2D9emGrY79mD9qK
>> HcmWyqL9KoxNcDddh_xCirS3DXCG6TkfRBuBXDuwYT-emKtz7EII4HhQluBIIQzoPGueOP
>> -/https%3A%2F%2Fgithub.com%2FPoTRA-Package%2FPoTRA%2Fpull%2Fnew%2FRELE
>> ASE_3_13>
>> remote:
>> To https://github.com/PoTRA-Package/PoTRA.git
>>

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread James W. MacDonald

The release version of your package is 1.8.0, and the devel is on increment 
ahead (e.g., 1.9.x). You cannot increment the middle version number of your 
release package because that makes it a devel package, hence the pre-release 
hook denying your changes.

You should change the version to 1.8.1 for the release version.

Jim

-Original Message-
From: Bioc-devel  On Behalf Of margaret linan
Sent: Wednesday, July 14, 2021 12:56 PM
To: bioc-devel 
Subject: Re: [Bioc-devel] Updating stable release

Hi -

I successfully updated my devel PoTRA package recently, now I am trying to push 
these same changes to the stable PoTRA package. I am encountering the following 
issue (see highlight below).
Note - in the github PoTRA repo, I have pulled and merged from head --> 
RELEASE_3_13. Also the devel commit never had a problem with my version bump.

 git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

  git checkout RELEASE_3_13
Switched to branch 'RELEASE_3_13'
Your branch is up to date with 'origin/RELEASE_3_13'.

 git push upstream RELEASE_3_13
Enumerating objects: 1, done.
Counting objects: 100% (1/1), done.
Writing objects: 100% (1/1), 641 bytes | 641.00 KiB/s, done.
Total 1 (delta 0), reused 0 (delta 0), pack-reused 0
remote: Error: Illegal version bump from '1.8.0' to '1.9.1'.
remote:
remote: Check http://bioconductor.org/developers/how-to/version-numbering/
remote: for details.
remote:
To git.bioconductor.org:packages/PoTRA.git
 ! [remote rejected] RELEASE_3_13 -> RELEASE_3_13 (pre-receive hook
declined)
error: failed to push some refs to 'git.bioconductor.org:packages/PoTRA.git'

Thanks,
Margaret

On Wed, Jul 14, 2021 at 9:01 AM Kern, Lori 
wrote:

> In your steps you were good when you checked out RELEASE_3_13
>
> So after git checkout RELEASE_3_13
>
> apply the changes you did to fix master.  You can do this manually or 
> you investigate how to use git cherry-pick
>
> When you have changed the files remember to do a git commit that 
> includes the version bump in the DESCRIPTION
>
> You should push those changes with a git push upstream RELEASE_3_13
>
> Please ask further questions on bioc-devel so other members of the 
> team can also assist.
>
> Cheers,
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* margaret linan 
> *Sent:* Wednesday, July 14, 2021 11:55 AM
> *To:* Kern, Lori 
> *Subject:* Re: [Bioc-devel] Updating stable release
>
> Hi Lori,
>
> I followed the instructions, but it seems that everything is 
> up-to-date already, I also didn't see anything pushed to RELEASE_3_13. 
> Here are my steps.
>
>  git fetch --all
> Fetching origin
> Fetching upstream
>
>  git checkout RELEASE_3_13
> Switched to a new branch 'RELEASE_3_13'
> Branch 'RELEASE_3_13' set up to track remote branch 'RELEASE_3_13' 
> from 'upstream'.
>
>  git merge upstream/RELEASE_3_13
> Already up to date.
>
>  git merge origin/RELEASE_3_13
> merge: origin/RELEASE_3_13 - not something we can merge
>
>  git checkout master
> Switched to branch 'master'
> Your branch is up to date with 'origin/master'.
>
>  git checkout -b RELEASE_3_13 upstream/RELEASE_3_13
> fatal: A branch named 'RELEASE_3_13' already exists.
>
>  git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
>
>  git push upstream RELEASE_3_13
> Everything up-to-date
>
>  git push origin RELEASE_3_13
> Total 0 (delta 0), reused 0 (delta 0), pack-reused 0
> remote:
> remote: Create a pull request for 'RELEASE_3_13' on GitHub by visiting:
> remote:  https://github.com/PoTRA-Package/PoTRA/pull/new/RELEASE_3_13
>  dQZXjtu2Ye_OFvo9Gt_SINdBynMZM_YiIsc25aGOnlsZlZ3JToY54VUPz4-nfYIJjjV_rQ
> adro327xvnfCleDCAGOngTyw2B46GkscVAiv5mtmvx1pgxaIF4dJMQiU7jfMDGy-yVU3Gh
> fXxjw2CzEpo9_ifAXV4zor7AUdJNhDovKaGRwy1Pze3n3vK24R-h8sK2D9emGrY79mD9qK
> HcmWyqL9KoxNcDddh_xCirS3DXCG6TkfRBuBXDuwYT-emKtz7EII4HhQluBIIQzoPGueOP
> -/https%3A%2F%2Fgithub.com%2FPoTRA-Package%2FPoTRA%2Fpull%2Fnew%2FRELE
> ASE_3_13>
> remote:
> To https://github.com/PoTRA-Package/PoTRA.git
> 
>  * [new branch]  RELEASE_3_13 -> RELEASE_3_13
>
>  git checkout RELEASE_3_13
> Switched to branch 'RELEASE_3_13'
> Your branch is up to date with 'upstream/RELEASE_3_13'.
>
>  git push upstream RELEASE_3_13
> Everything up-to-date
>
>

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread margaret linan

Hi -

I successfully updated my devel PoTRA package recently, now I am trying to
push these same changes to the stable PoTRA package. I am encountering the
following issue (see highlight below).
Note - in the github PoTRA repo, I have pulled and merged from head -->
RELEASE_3_13. Also the devel commit never had a problem with my version
bump.

 git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

  git checkout RELEASE_3_13
Switched to branch 'RELEASE_3_13'
Your branch is up to date with 'origin/RELEASE_3_13'.

 git push upstream RELEASE_3_13
Enumerating objects: 1, done.
Counting objects: 100% (1/1), done.
Writing objects: 100% (1/1), 641 bytes | 641.00 KiB/s, done.
Total 1 (delta 0), reused 0 (delta 0), pack-reused 0
remote: Error: Illegal version bump from '1.8.0' to '1.9.1'.
remote:
remote: Check http://bioconductor.org/developers/how-to/version-numbering/
remote: for details.
remote:
To git.bioconductor.org:packages/PoTRA.git
 ! [remote rejected] RELEASE_3_13 -> RELEASE_3_13 (pre-receive hook
declined)
error: failed to push some refs to 'git.bioconductor.org:packages/PoTRA.git'

Thanks,
Margaret

On Wed, Jul 14, 2021 at 9:01 AM Kern, Lori 
wrote:

> In your steps you were good when you checked out RELEASE_3_13
>
> So after git checkout RELEASE_3_13
>
> apply the changes you did to fix master.  You can do this manually or you
> investigate how to use git cherry-pick
>
> When you have changed the files remember to do a git commit that includes
> the version bump in the DESCRIPTION
>
> You should push those changes with a git push upstream RELEASE_3_13
>
> Please ask further questions on bioc-devel so other members of the team
> can also assist.
>
> Cheers,
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* margaret linan 
> *Sent:* Wednesday, July 14, 2021 11:55 AM
> *To:* Kern, Lori 
> *Subject:* Re: [Bioc-devel] Updating stable release
>
> Hi Lori,
>
> I followed the instructions, but it seems that everything is up-to-date
> already, I also didn't see anything pushed to RELEASE_3_13. Here are my
> steps.
>
>  git fetch --all
> Fetching origin
> Fetching upstream
>
>  git checkout RELEASE_3_13
> Switched to a new branch 'RELEASE_3_13'
> Branch 'RELEASE_3_13' set up to track remote branch 'RELEASE_3_13' from
> 'upstream'.
>
>  git merge upstream/RELEASE_3_13
> Already up to date.
>
>  git merge origin/RELEASE_3_13
> merge: origin/RELEASE_3_13 - not something we can merge
>
>  git checkout master
> Switched to branch 'master'
> Your branch is up to date with 'origin/master'.
>
>  git checkout -b RELEASE_3_13 upstream/RELEASE_3_13
> fatal: A branch named 'RELEASE_3_13' already exists.
>
>  git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
>
>  git push upstream RELEASE_3_13
> Everything up-to-date
>
>  git push origin RELEASE_3_13
> Total 0 (delta 0), reused 0 (delta 0), pack-reused 0
> remote:
> remote: Create a pull request for 'RELEASE_3_13' on GitHub by visiting:
> remote:  https://github.com/PoTRA-Package/PoTRA/pull/new/RELEASE_3_13
> 
> remote:
> To https://github.com/PoTRA-Package/PoTRA.git
> 
>  * [new branch]  RELEASE_3_13 -> RELEASE_3_13
>
>  git checkout RELEASE_3_13
> Switched to branch 'RELEASE_3_13'
> Your branch is up to date with 'upstream/RELEASE_3_13'.
>
>  git push upstream RELEASE_3_13
> Everything up-to-date
>
>  git push origin RELEASE_3_13
> Everything up-to-date
>
> Thanks,
> Margaret
>
> On Wed, Jul 14, 2021 at 8:40 AM Kern, Lori 
> wrote:
>
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread Kern, Lori



Did you push your changes to the RELEASE_3_13 branch in addition to the master 
branch?




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 margaret linan 

Sent: Wednesday, July 14, 2021 11:32 AM
To: bioc-devel 
Subject: [Bioc-devel] Updating stable release

Hi Bioc,

I recently fixed the build errors for my devel version of PoTRA and the
build is succeeding. However, the stable release of PoTRA still displays
"build error". What can I do to fix this?

Thanks,
Margaret

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[Bioc-devel] Updating stable release

2021-07-14 Thread margaret linan

Hi Bioc,

I recently fixed the build errors for my devel version of PoTRA and the
build is succeeding. However, the stable release of PoTRA still displays
"build error". What can I do to fix this?

Thanks,
Margaret

[[alternative HTML version deleted]]

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Re: [Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

Re: [Bioc-devel] Updating stable release

Re: [Bioc-devel] Updating stable release

Re: [Bioc-devel] Updating stable release

Re: [Bioc-devel] Updating stable release

[Bioc-devel] Updating stable release

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