from:"Obenchain, Valerie"

Developers,

We are experiencing much longer runtimes for the Bioconductor 3.9 
(devel) builds which are running R 3.6. We are looking into a possible 
regression in R 3.6 or other causes.

Because of the long run times, the sub-builds are overlapping which can 
saturate the machines and further magnify the problem. Until this is 
sorted out, the Bioc 3.9 builds will not necessarily post everyday and 
the workflow, data-experiment and long-test builds may be infrequent.

We'll do our best to keep as current as possible, especially with the 
software builds.

Thanks for your patience.
Valerie


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Hi Jianhong,

Ghostscript is already installed on the builders.

On the Nov 1 build report for Bioc 3.9, motifStack is clean on tokay2 
(Windows) but failed on malbec2 (Linux). There were other packages that 
depended on grImports with similar errors on Linux - dagLogo and 
motifbreakR.

I went on the Linux builder to investigate and was able to build and 
check motifStack with no problem. I also saw the build results for today 
(Nov 2) and motifStack is clean so I'm not sure what happened in the 
previous day's builds.

The build report for today, Nov 2, should post within the next hour and 
motifStack should be green.

Valerie

On 11/2/18 6:05 AM, Jianhong Ou, Ph.D. wrote:
> My package motifStack import grImport which is depend on ghostscript.
> 
> Jianhong.
> 
> From: Kasper Daniel Hansen 
> Date: Friday, November 2, 2018 at 8:55 AM
> To: "Jianhong Ou, Ph.D." 
> Cc: bioc-devel 
> Subject: Re: [Bioc-devel] Ask help to install gs tokay2 build/check
> 
> Perhaps explain why
> 
> On Fri, Nov 2, 2018 at 8:19 AM Jianhong Ou, Ph.D. 
> mailto:jianhong...@duke.edu>> wrote:
> Hi,
> 
> Is it possible to install ghostscript in tokay2 for development package build?
> 
> Yours Sincerely,
> 
> Jianhong Ou
> 
> Email: 
> jianhong...@duke.edu>
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
> 
> Confidentiality Notice:
> This e-mail message, including any attachments, is for the sole use of the 
> intended recipient(s) and may contain confidential, proprietary and 
> privileged information. Any unauthorized review, use, disclosure or 
> distribution is prohibited. If you are not the intended recipient, please 
> contact the sender immediately and destroy or permanently delete all copies 
> of the original message.
> 
>  [[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
> 

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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] GenomicFeatures

Historically we used to flush the repos before a release. At some point 
we stopped and I could not remember why. The situation you describe 
below is probably it.

When preparing for 3.8, we ran into the case where we had quite a few 
stale packages in the repos. Their 'staleness' was due to being renamed, 
deprecated, etc. These left around old landing pages and appeared in 
biocViews inappropriately. At the time it seemed like a good idea to 
flush the repo (release only) for a clean start. This would result in no 
products (landing page, tarball, ...) for packages that did not build in 
the new release. (We also had a hiccup with generating landing pages 
with stale links that we're working on. Should be fixed soon.)

While no landing page / nonavailability is motivation for maintainers to 
fix broken packages it's also an inconvenience for users and this is not 
good. For the next release we'll probably do some combination of the two 
- flush only packages not in the manifest.

Sorry for this inconvenience - my fault entirely.

Valerie

PS/BTW I've fixed GenomicFeatures and if it doesn't have an internet 
burp during the builds it should be available tomorrow.

On 11/2/18 8:36 AM, Kasper Daniel Hansen wrote:
> Lates BiocManager
> 
> It is not flagging GenomicFeatures as out of date, presumably because it
> doesn't exists in the repos. So in some sense it is all internally
> consistent.  I was just surprised to not see it flagged as being out of
> date.
> 
> I guess I am also confused about what happens at release.  Is the repos
> wiped?  Because at some time pre-release GenomicFeatures existed in the
> Bioc 3.8 repos, and (usually) that would mean it would fall back to this
> previous version (seemingly 1.33.6 based on
>https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
> yet this package does not seem to exists (despite the URL)).
> 
> Ok, this is all a rather unfortunate and special case which I am not sure
> how should be handled. I was just surprised at what I am seeing, but I am
> also quite confident that when the package is fixed, it'll all work fine.
> 
> Best,
> Kasper
> 
> 
> On Fri, Nov 2, 2018 at 10:05 AM Martin Morgan 
> wrote:
> 
>> For which BiocManager::version() is this? BiocManager::valid() checks
>> within versions, and if there's no GenomicFeatures to reference, then there
>> is no way to flag it as out-of-date, sort of like a package you'd installed
>> that was in neither CRAN nor Bioconductor.
>>
>> Though of course we'd like GenomicFeatures to be available in 3.8
>>
>> Martin
>>
>> On 11/2/18, 1:05 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" <
>> bioc-devel-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com>
>> wrote:
>>
>>  Seem broken in release.
>>
>>  And btw., because it is broken, when I run
>>BiocManager::valid()
>>  it doesn't report GenomicFeatures as out of date, despite the fact
>> that I
>>  have version 1.33.2 installed, and there are newer versions in the
>> 1.33.x
>>  hierarchy and the "right" (but broken) version in Bioc 3.8 is 1.34.0.
>>
>>  Best,
>>  Kasper
>>
>>  [[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
> 

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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] GenomicFeatures

Thanks Kasper. I'm looking into the error in GenomicFeatures.

Martin or Marcel may have more to add but I think BiocManager::install() 
can only report what versions are in the repo. GenomicFeatures 1.34.0 
has not built so doesn't yet exist in the repo.

We archive all versions in release but not in devel. The older 1.33.x 
versions don't exist in "released" Bioconductor 3.8.

Valerie

On 11/2/18 6:05 AM, Kasper Daniel Hansen wrote:
> Seem broken in release.
> 
> And btw., because it is broken, when I run
>BiocManager::valid()
> it doesn't report GenomicFeatures as out of date, despite the fact that I
> have version 1.33.2 installed, and there are newer versions in the 1.33.x
> hierarchy and the "right" (but broken) version in Bioc 3.8 is 1.34.0.
> 
> Best,
> Kasper
> 
>   [[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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

2018-11-01 Thread Obenchain, Valerie

Yep, my mistake. I was confusing this with another error I was looking into.

Valerie




On 11/1/18 11:02 AM, Pages, Herve wrote:
> Just to clarify we see these warnings on Mac only:
> 
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/NormalyzerDE/merida2-checksrc.html
> 
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/M3C/merida2-checksrc.html
> 
> They seem to indicate problems with CRAN packages xts, ggplot2, and ape.
> For some unclear reason, we only see this problem on the Mac builder.
> Other CRAN packages (rgl, igraph, biglm, network, strucchange, etc..)
> are actually causing the same type of warnings on the BioC 3.9 build
> report. 359 Bioconductor software packages are affected.
> 
> We'll need to investigate. Safe to ignore for now.
> 
> Cheers,
> 
> H.
> 
> On 11/1/18 05:05, Obenchain, Valerie wrote:
>> Hi,
>>
>> I noticed this before the release - many packages are affected with a
>> similar error. Something this pervasive is likely due to a change (bug?)
>> in base R and not something you need to fix. It may also be fixed in a
>> later version of R version than what's on the build machines.
>>
>> Now that the release is over we'll start focusing on the Bioc 3.9 builds
>> and we'll look into this.
>>
>> Thanks.
>> Valerie
>>
>>
>>
>> On 11/1/18 2:56 AM, Christopher John wrote:
>>> Hi
>>>
>>> I also have a warning after the upgrade, just for the development version
>>> (I have not changed).
>>>
>>> I am not sure why this happened as I can't find the ape in the namespace
>>> and previously had no warning before upgrade.
>>>
>>> Thanks.
>>>
>>> * checking whether package ‘M3C’ can be installed ... WARNING
>>> Found the following significant warnings:
>>>  Warning: S3 method ‘ape::as.phylo.dendrogram’ was declared in
>>> NAMESPACE but not found
>>> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3C.Rcheck/00install.out’ for 
>>> details.
>>>
>>>
>>> On Thu, 1 Nov 2018 at 08:09, Jakob Willforss 
>>> wrote:
>>>
>>>> Hi! Getting closer to release, exciting!
>>>>
>>>> Today I saw that the build for my package NormalyzerDE gave a warning
>>>> after the release version bumps,
>>>> but only on the Windows build machine. No code has been changed from
>>>> previously succeeding builds.
>>>>
>>>> It seems to be unable to find certain functions in the libraries xts and
>>>> ggplot2 (see warning below). It seems to build fine on the Ubuntu and Mac
>>>> machines.
>>>>
>>>> Do you think this is something to worry about, or is it likely to be
>>>> something temporary to the build machines? I wonder in particular as my
>>>> work environment (and debugging environment of choice) is Linux, where the
>>>> problem don't seem to be reproduced.
>>>>
>>>> Best wishes,
>>>> Jakob
>>>>
>>>> The warning:
>>>>
>>>> * checking whether package ‘NormalyzerDE’ can be installed ... WARNING
>>>> Found the following significant warnings:
>>>>  Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE
>>>> but not found
>>>>  Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ 
>>>> were
>>>> declared in NAMESPACE but not found
>>>> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck/00install.out’
>>>> for details.
>>>>
>>>>[[alternative HTML version deleted]]
>>>>
>>>> ___
>>>> Bioc-devel@r-project.org mailing list
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=zbRfJqGI0IrvvjNQYWzYZ1IZI3KlU4K3SAfArdCEFJI=NFc2ZKQEuLA6u4oI3K6GZ9TGwHOUkR9XqlgMRfRZOHw=
>>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=zbRfJqGI0IrvvjNQYWzYZ1IZI3KlU4K3SAfArdCEFJI=NFc2ZKQEuLA6u4oI3K6GZ9TGwHOUkR9XqlgMRfRZOHw=
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential 
>> inform

Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

2018-11-01 Thread Obenchain, Valerie

Hi,

I noticed this before the release - many packages are affected with a 
similar error. Something this pervasive is likely due to a change (bug?) 
in base R and not something you need to fix. It may also be fixed in a 
later version of R version than what's on the build machines.

Now that the release is over we'll start focusing on the Bioc 3.9 builds 
and we'll look into this.

Thanks.
Valerie

On 11/1/18 2:56 AM, Christopher John wrote:
> Hi
> 
> I also have a warning after the upgrade, just for the development version
> (I have not changed).
> 
> I am not sure why this happened as I can't find the ape in the namespace
> and previously had no warning before upgrade.
> 
> Thanks.
> 
> * checking whether package ‘M3C’ can be installed ... WARNING
> Found the following significant warnings:
>Warning: S3 method ‘ape::as.phylo.dendrogram’ was declared in
> NAMESPACE but not found
> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3C.Rcheck/00install.out’ for details.
> 
> 
> On Thu, 1 Nov 2018 at 08:09, Jakob Willforss 
> wrote:
> 
>> Hi! Getting closer to release, exciting!
>>
>> Today I saw that the build for my package NormalyzerDE gave a warning
>> after the release version bumps,
>> but only on the Windows build machine. No code has been changed from
>> previously succeeding builds.
>>
>> It seems to be unable to find certain functions in the libraries xts and
>> ggplot2 (see warning below). It seems to build fine on the Ubuntu and Mac
>> machines.
>>
>> Do you think this is something to worry about, or is it likely to be
>> something temporary to the build machines? I wonder in particular as my
>> work environment (and debugging environment of choice) is Linux, where the
>> problem don't seem to be reproduced.
>>
>> Best wishes,
>> Jakob
>>
>> The warning:
>>
>> * checking whether package ‘NormalyzerDE’ can be installed ... WARNING
>> Found the following significant warnings:
>>Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE
>> but not found
>>Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were
>> declared in NAMESPACE but not found
>> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck/00install.out’
>> for details.
>>
>>  [[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
> 

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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.8 is released

2018-10-31 Thread Obenchain, Valerie

Thank you developers for contributing to the project!

Please see the full release announcement here:

   https://www.bioconductor.org/news/bioc_3_8_release/

The Bioconductor Team


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.8 branch created

2018-10-30 Thread Obenchain, Valerie

The 3.8 branch has been created and commits can resume to 
git.bioconductor.org. If all goes as planned over the next 24 hours 
we'll announce the release tomorrow.

You have access to 2 versions of your package in git: "release" and 
"devel". Release is for bug fixes and documentation improvements only 
and devel is where regular development should happen.

Release:
Bioconductor version 3.8
Git branch RELEASE_3_8
R version 3.5.*

Devel:
Bioconductor version 3.9
Git branch master
R version 3.6.*

To continue using your existing clone be sure to pull the version bump 
and branch creation changes from Bioconductor.

Instructions for syncing:

https://bioconductor.org/developers/how-to/git/pull-upstream-changes/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

Instructions for working with the branches:

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

If you have questions, please reply to this thread or post to the 
bioc-devel list at .

Thanks.
The Bioconductor team


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioconductor 3.8 branching today

2018-10-30 Thread Obenchain, Valerie

Bioc developers,

Today we'll be creating the Bioconductor 3.8 branch starting at 11am 
EST. All commits to git.bioconductor.org will be blocked for about 2.5 
hours. We'll post back when push access is restored and you can resume 
commits.

Thanks.
The Bioconductor team


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Creating Bioconductor 3.8 branch on Oct 30

2018-10-29 Thread Obenchain, Valerie

Developers,

Tomorrow we'll create the Bioc 3.8 branch starting at 11am EST. The 
process will take ~2.5 hours, maybe less.

An email will go out about an hour before we branch asking that all 
commits stop during the branch process. We often see a delay in messages 
posting to bioc-devel so I wanted to give a heads up today vs tomorrow's 
message not making it through in time.

Thanks!
Valerie


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.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioc 3.8 feature freeze

2018-10-24 Thread Obenchain, Valerie

Developers,

The release of Bioconductor 3.8 is one week out. Today marks the 'feature 
freeze' of 3.8 where we ask that all commits are limited to bug fixes and 
documentation (no more API changes).

Thanks.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Failing GenVisR package

2018-10-23 Thread Obenchain, Valerie

Hi Zach,

You should not have to add skip_on_bioc().

Confirming system dependencies, the vdiffr package requires FreeType >= 2.6.0 
and the Bioconductor 3.8 builder has version 2.6.1. Do you know which font 
libraries are used?

Did you start seeing these failures around the time of this commit or was that 
a separate issue?

commit 77866fb2b8d137ce38ea0d47b327fc379c4416e9 (HEAD -> master, origin/master, 
origin/HEAD)
Author: Zach Skidmore 

Date:   Thu Oct 11 16:37:33 2018 -0500

fixed failing test case in lolliplot caused by interpro domains changing


Valerie

On 10/22/18 9:51 AM, Skidmore, Zach wrote:

Hi All,

I'm looking for some advice, I maintain the GenVisR package, it is currently 
failing on malbec1-devel. I use the vdiffr package to perform visual test 
cases, essentially the package compares the SVG output to a predefined 
expectation and fails if an anomaly is detected. This worked perfectly until 
perhaps a month ago, given that the visual test-case fails only on malbec1 I 
suspect the issue is something small, perhaps malbec1 uses a different font 
library causing the SVG's to be significantly different.

At any rate I'm looking for any advice on how to:

1) determine what the difference is, normally I would run 
vdiffr::manage_cases() but obviously that is not possible with the automated 
build system. Is there a docker image available that corresponds exactly to 
malbec1?

2) Again I suspect that this is a minor issue given that everything is fine on 
the other two OS, but I'm trying to figure out the proper course of action to 
resolve this. I could add a skip_on_bioc() flag for all visual test-cases. I 
would rather not do that if there is a way to avoid it though.

Thanks for any advice!
Zach


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Need update access agaisnt package 'banocc'

2018-10-17 Thread Obenchain, Valerie

Hi George,

Thanks for letting us know - you should now have access.

Valerie


On 10/17/18 10:50 AM, George Weingart wrote:

Hello,

The package banocc has a build error - I was given the task to fix it and
update the "Maintainer" information to include me and the head of our Lab,
Prof. Curtis Huttenhower.

The package was developed originally by Emma Schwager who has left our Lab.

I cloned the package, made the necessary changes, ran a successful BUILD ,
CHECK, BiocCheck and committed the changes and am ready to push the
changes,  but I am getting a "permission denied" message - and indeed, I
see in my profile I can update only ccrepe.

I need update access against 'banocc"

Thanks!

George Weingart PhD

Huttenhower Lab

Harvard School of Public Health

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioc 3.8 packages: if/while condition

2018-10-15 Thread Obenchain, Valerie

Sorry for the formatting mess. Trying again.

biovizBase,1.29.2
cbaf,1.3.5
CONFESS,1.9.0
DaMiRseq,1.5.2
fabia,2.27.0
flowViz,1.45.0
gaia,2.25.3
GateFinder,1.1.0
GenVisR,1.13.2
Guitar,1.19.0
hapFabia,1.23.0
KEGGlincs,1.7.3
Linnorm,2.5.0
MassArray,1.33.0
methylPipe,1.15.0
NOISeq,2.25.0
pathview,1.21.2
phyloseq,1.25.3
rHVDM,1.47.0
SEPA,1.11.0
seq2pathway,1.13.2
SPLINTER,1.7.2
SVAPLSseq,1.7.0
TFEA.ChIP,1.1.1
twilight,1.57.0






On 10/15/18 5:37 AM, Obenchain, Valerie wrote:

Developers,

The packages below execute an if() or while() statement on a condition with 
length greater than 1. This is currently a warning in R but will soon become an 
error.

Thanks to Tomas Kalibera for identifying packages that contain this error. If 
you maintain one of these please have a look at the output Tomas provides and 
check in a fix.

https://github.com/kalibera/rifcond/
https://github.com/kalibera/rifcond/tree/master/outputs_38

BIOC 3.8 packages:

biovizBase,1.29.2 cbaf,1.3.5 CONFESS,1.9.0 DaMiRseq,1.5.2 fabia,2.27.0 
flowViz,1.45.0 gaia,2.25.3 GateFinder,1.1.0 GenVisR,1.13.2 Guitar,1.19.0 
hapFabia,1.23.0 KEGGlincs,1.7.3 Linnorm,2.5.0 MassArray,1.33.0 
methylPipe,1.15.0 NOISeq,2.25.0 pathview,1.21.2 phyloseq,1.25.3 rHVDM,1.47.0 
SEPA,1.11.0 seq2pathway,1.13.2 SPLINTER,1.7.2 SVAPLSseq,1.7.0 TFEA.ChIP,1.1.1 
twilight,1.57.0 Thanks. Valerie



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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Last build of Bioconductor 3.7

2018-10-15 Thread Obenchain, Valerie

Developers,

Tonight is the last build of Bioconductor 3.7. After the report posts tomorrow 
we'll stop the 3.7 builds and the branch will be frozen.

Any commits made today before 4:45pm EST will be included in the builds. Please 
run `R CMD build` and `R CMD check` before committing!

Thanks.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Bioc 3.8 packages: if/while condition

2018-10-15 Thread Obenchain, Valerie

Developers,

The packages below execute an if() or while() statement on a condition with 
length greater than 1. This is currently a warning in R but will soon become an 
error.

Thanks to Tomas Kalibera for identifying packages that contain this error. If 
you maintain one of these please have a look at the output Tomas provides and 
check in a fix.

https://github.com/kalibera/rifcond/
https://github.com/kalibera/rifcond/tree/master/outputs_38

BIOC 3.8 packages:

biovizBase,1.29.2 cbaf,1.3.5 CONFESS,1.9.0 DaMiRseq,1.5.2 fabia,2.27.0 
flowViz,1.45.0 gaia,2.25.3 GateFinder,1.1.0 GenVisR,1.13.2 Guitar,1.19.0 
hapFabia,1.23.0 KEGGlincs,1.7.3 Linnorm,2.5.0 MassArray,1.33.0 
methylPipe,1.15.0 NOISeq,2.25.0 pathview,1.21.2 phyloseq,1.25.3 rHVDM,1.47.0 
SEPA,1.11.0 seq2pathway,1.13.2 SPLINTER,1.7.2 SVAPLSseq,1.7.0 TFEA.ChIP,1.1.1 
twilight,1.57.0 Thanks. Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Package simulatorZ timeout under Windows on the release but not the devel branch

2018-10-11 Thread Obenchain, Valerie

Looks like this has cleared up in the Oct 10 report:

  https://www.bioconductor.org/checkResults/release/bioc-LATEST/

We send notifications about failures in release twice a week (Monday and 
Thursday). This could have been a transient problem but happened to occur on a 
day we send notifications. Unless this becomes consistent you can ignore it.

Thanks.
Valerie

On 10/9/18 3:00 PM, Yuqing Zhang wrote:

Hi all,

I received an email saying that my package, simulatorZ, is timing out. In
the current report, it is timing out under Windows in the release branch.
But it passes all builds and checks in the devel branch on all platforms
(on Windows it passes the check in about 5 minutes). I haven't changed
anything in the package, so I'm confused how I got this timeout issue...

Could anyone please advise what I need to do about this?

Thanks,
Yuqing






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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Invalid Parameter - /figure-html

2018-10-10 Thread Obenchain, Valerie

Hi,

It looks like vignette in TCGAWorkflow hasn't changed except for updating to 
use BiocManager. This often points to a breaking change in an upstream 
dependency (244 in your case) or it could be a problem on the builder.

The code chunk causing problems in devel is the call to ELMER::get.TFs().

TF <- get.TFs(data = mae,
  group.col = group.col,
  group1 = group1,
  group2 =  group2,
  mode = "supervised",
  enriched.motif = enriched.motif,
  dir.out = dir.out,
  cores = cores,
  diff.dir = direction,
  label = direction)

On Windows, this either hangs and crashes the R session or produces this error 
with what looks like a bad file name:

Quitting from lines 2387-2394 (TCGAWorkflow.Rmd)
Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
unable to open 
C:/Users/biocbuild/bbs-3.8-workflows/tmpdir/RtmpuGXyPJ/.heatmap_body_DNA 
methylation level_1_2348149424d.png

It looks like you were the last one to touch ELMER:

commit fbf589501eb035138d28d69640041547f54c38a4 (HEAD -> master, origin/master, 
origin/HEAD)
Author: tiagochst 
Date:   Thu Sep 20 15:39:46 2018 -0300

fix heatmap plot

R/GetNearbyGenes.R
R/Scatter.plot.R
R/TCGA_pipe.R
R/plots.R

commit 207f80398996bef2a593e67b9e7c12f3ae10a768
Merge: 17b72e7 b8721cb
Author: Tiago Chedraoui Silva 
Date:   Thu Sep 20 11:34:34 2018 -0700

Merge branch 'master' of https://github.com/tiagochst/ELMER

commit 17b72e79b42ad19ead302bbab17272575af352e2
Author: Tiago Chedraoui Silva 
Date:   Thu Sep 20 11:34:26 2018 -0700

Fixing the cluster within groups for heatmap

R/plots.R
man/heatmapPairs.Rd

Maybe the name of the file in the error message is familiar to you or you could 
revisit recent changes to ELMER that impacted get.TFs().

Along those lines, how about setting save=FALSE when calling get.TFs()? It 
takes a significant amount of time to write out all 20+ pdf files and AFAIK 
only the file with TF ranking is used in plotting. This ranking file could be 
saved in TCGAWorkflow/data and loaded for plotting. You can point out to the 
user that save=TRUE is an option they may want but for the purpose of the 
vignette it doesn't seem necessary.

Thanks.
Valerie


On 9/27/18 7:43 AM, Tiago Chedraoui Silva wrote:

Hello,

The workflow I'm maintaining is giving this message "Invalid Parameter -
/figure-html"  in the devel and release windows environment.

http://bioconductor.org/checkResults/devel/workflows-LATEST/TCGAWorkflow/tokay1-buildsrc.html

It seems other users had the same problem before:
https://stackoverflow.com/questions/48747959/biocstyle-vignettes-invalid-parameter-figure-html?rq=1

Please, someone knows how that could be fixed?

Best regards,
Tiago Chedraoui Silva

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Invalid Parameter - /figure-html

2018-10-09 Thread Obenchain, Valerie

Hi Tiago,

I'm looking into this.

Valerie


On 9/27/18 7:43 AM, Tiago Chedraoui Silva wrote:

Hello,

The workflow I'm maintaining is giving this message "Invalid Parameter -
/figure-html"  in the devel and release windows environment.

http://bioconductor.org/checkResults/devel/workflows-LATEST/TCGAWorkflow/tokay1-buildsrc.html

It seems other users had the same problem before:
https://stackoverflow.com/questions/48747959/biocstyle-vignettes-invalid-parameter-figure-html?rq=1

Please, someone knows how that could be fixed?

Best regards,
Tiago Chedraoui Silva

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-09 Thread Obenchain, Valerie

I'm not sure what you mean by flipping the script ...?

Looks like I was out of date with my advice on the .BBSoptions. A few months 
ago the BBS was modified to install all packages so the

ForceInstall: True

is no longer needed. You can remove the .BBSoptions file - sorry for the 
confusion.

Lori will be updating the docs 
(https://github.com/Bioconductor/Contributions#submitting-related-packages) 
with more detail on handling packages with mutual (circular) dependencies. I 
see your package was assigned to Herve - if you are still having problems with 
the build you can ask @lshep or @hpages for help on the issue.

Thanks for the pull request, it's been merged.

Val


On 10/8/18 7:23 AM, Tim Triche, Jr. wrote:
D'oh.  Does this mean that I should flip the script a second time?

I went ahead and added the .BBSoptions file as suggested and flushed out some 
additional irritants; it seemed that having the main package Suggest: the Data 
package went more smoothly (no cycles) so I had updated the ticket to reflect 
this. I also updated the support site question to reflect that suggestion. But 
now I am not sure if that's right.

It is a bit confusing. I'd send a PR except I'm not really qualified to patch 
it. However, there was a reference to Subversion that stuck in my head after 
submission, and I did track that down; see 
https://github.com/Bioconductor/Contributions/pull/916 for details ;-)

Thank you,



--t


On Mon, Oct 8, 2018 at 8:44 AM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Hello,


The Single Package builder (SPB) does check the .BBSOptions but only for 
UnsupportedPlatforms.  This is because the single package builder automatically 
installs each package before the build and check stage as part of the process.  
Each package that goes through the single package builder for new submits 
temporarily gets its own directory to use for installing and referencing 
dependencies -  This is why we document that packages with additional or 
supporting packages should be built under the same issue as then they will be 
able to find each other.  The submission process where the data package that 
"suggests" the software package is submitted first, followed by the software 
package that "depends" on the data package is correct.


Its a little confusing at first but the following will/should happen on the SPB:


  1.   The data package will be submitted and fail because the software package 
is not available (but it will be installed in the Rlibs directory for the issue)
  2.  The software package is submitted and fails because the data package 
can't be found (but also installs)
  3.  The maintainer should do an arbitrary version bump on the data package to 
kick off a new build that should now pass as it will find the software package
  4.  Do any additional debugging on the data package to ensure the data 
package has a clean build and check.
  5.  The maintainer should do an arbitrary version bump on the software 
package, only after the data package is building and checking cleanly, to 
rebuild the software package
  6.  Review process continues and packages are accepted

The same failure scheme will happen on the main builders once the package is 
accepted, the only difference is the maintainer will not have to version bump 
for the new builds since the daily builds builds and checks all packages 
automatically (daily for software and  Sun/Tue/Thru for data packages)- The 
ERRORS will clean up on there own after 3-5 days depending on when it is 
accepted and added to the main builders in reference to the schedule of the 
building of data packages (Sun/Tue/Thur).  Once the packages are both installed 
once, the circular dependency issue will be resolved.

Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Obenchain, Valerie 
<mailto:valerie.obench...@roswellpark.org>
Sent: Sunday, October 7, 2018 11:54:46 AM
To: Michael Lawrence; Tim Triche, Jr.
Cc: packa...@bioconductor.org<mailto:packa...@bioconductor.org>; bioc-devel
Subject: Re: [Bioc-devel] avoiding circular dependencies between a Data package 
and a Software package

I forgot to add the .BBSoptions file should be located at the 'top' level of 
the package, e.g., MTseekerData/.BBSoptions. You might as well add that now 
instead of waiting until the packages are approved. I think the SPB was 
modified to be aware of the .BBSoptions file so it may require it too (Lori 
would know). If the SPB does require .BBSoptions we should document that in

https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md

Valerie

On 10/7/18 8:39 AM, Obenchain, Valerie wrote:

Hi Tim,

As Michael said, the usual case is the data package 'Suggests'

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-07 Thread Obenchain, Valerie

I forgot to add the .BBSoptions file should be located at the 'top' level of 
the package, e.g., MTseekerData/.BBSoptions. You might as well add that now 
instead of waiting until the packages are approved. I think the SPB was 
modified to be aware of the .BBSoptions file so it may require it too (Lori 
would know). If the SPB does require .BBSoptions we should document that in

https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md

Valerie

On 10/7/18 8:39 AM, Obenchain, Valerie wrote:

Hi Tim,

As Michael said, the usual case is the data package 'Suggests' the software and 
the software 'Depends' or 'Imports' the data but this dependency could be 
reversed.

When submitting a combo of packages to the SPB for review, the package that 
'Suggests' is submitted first followed by the package that 'Depends'. More on 
that here:

https://github.com/Bioconductor/Contributions#submitting-related-packages

One additional step taken to transition the packages to the build system after 
approval is to add a .BBSoptions file in the package that 'Suggests'. In this 
example, the .BBSoptions would be in the data package and have this one line:

ForceInstall: TRUE

Valerie


On 10/6/18 11:06 AM, Michael Lawrence wrote:

I think you're doing the right thing, suggesting the data package from the
software package. This might require some manual intervention on the build
system side to ensure that the software package is installed before passing
full check, so that the data package can be installed/checked and finally
the software package checked. I guess a note about this could be added to
the page at the cited URL.

Michael

On Sat, Oct 6, 2018 at 10:42 AM Tim Triche, Jr. 
<mailto:tim.tri...@gmail.com>
wrote:



Last night I submitted MTseeker and its companion package MTseekerData,
both festooned with examples that run smoothly and pass BiocCheck.

HOWEVER! Breaking up the data into a Data package inadvertently seems to
have created a circular dependency between the Software and Data packages.
I haven't had to deal with this in the past, and mostly sidestepped it by
skipping a Depends: entry in Data.

(cf. https://support.bioconductor.org/p/113711 , which I will update with
answers from here to try and avoid having other people with the same
problem bug youse plural)

The issue seems to be that, since the MTseeker-defined MVRanges and
MAlignments classes (which, as you might imagine, subclass the VRanges and
GAlignments classes) hold the data stored in MTseekerData, the examples in
MTseekerData call the `show` method (and others) on the objects and this
create issues.  The most bizarre of these complained at installation about
(sp?) .lazyLoadCacheManager() (I'm having trouble reproducing this exact
error but it was memorable).  Does this ring a bell for anyone? Is there an
elegant workaround?

I can't imagine I'm the first person to have this issue.  I know there are
also various automagic hooks in BioC to load a package upon discovering a
data structure that belongs to it (and not before) -- should I be using
attachNamespace() somehow to side-step this problem?  (Eventually I do want
to submit BAM files to ExperimentHub for an end-to-end example and unit
tests, but the more pressing issue here was BiocCheck).

Any feedback is much appreciated. It's kind of a drag when all the examples
and vignettes pass and build, but only with a side-stepping of
dependencies. That can't possibly be the correct solution, yet I'm at a
loss to find documentation (which I'm sure exists somewhere) that explains
how to avoid this (and/or implement the hooks).

Thank you,

--t

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-07 Thread Obenchain, Valerie

Hi Tim,

As Michael said, the usual case is the data package 'Suggests' the software and 
the software 'Depends' or 'Imports' the data but this dependency could be 
reversed.

When submitting a combo of packages to the SPB for review, the package that 
'Suggests' is submitted first followed by the package that 'Depends'. More on 
that here:

https://github.com/Bioconductor/Contributions#submitting-related-packages

One additional step taken to transition the packages to the build system after 
approval is to add a .BBSoptions file in the package that 'Suggests'. In this 
example, the .BBSoptions would be in the data package and have this one line:

ForceInstall: TRUE

Valerie


On 10/6/18 11:06 AM, Michael Lawrence wrote:

I think you're doing the right thing, suggesting the data package from the
software package. This might require some manual intervention on the build
system side to ensure that the software package is installed before passing
full check, so that the data package can be installed/checked and finally
the software package checked. I guess a note about this could be added to
the page at the cited URL.

Michael

On Sat, Oct 6, 2018 at 10:42 AM Tim Triche, Jr. 

wrote:



Last night I submitted MTseeker and its companion package MTseekerData,
both festooned with examples that run smoothly and pass BiocCheck.

HOWEVER! Breaking up the data into a Data package inadvertently seems to
have created a circular dependency between the Software and Data packages.
I haven't had to deal with this in the past, and mostly sidestepped it by
skipping a Depends: entry in Data.

(cf. https://support.bioconductor.org/p/113711 , which I will update with
answers from here to try and avoid having other people with the same
problem bug youse plural)

The issue seems to be that, since the MTseeker-defined MVRanges and
MAlignments classes (which, as you might imagine, subclass the VRanges and
GAlignments classes) hold the data stored in MTseekerData, the examples in
MTseekerData call the `show` method (and others) on the objects and this
create issues.  The most bizarre of these complained at installation about
(sp?) .lazyLoadCacheManager() (I'm having trouble reproducing this exact
error but it was memorable).  Does this ring a bell for anyone? Is there an
elegant workaround?

I can't imagine I'm the first person to have this issue.  I know there are
also various automagic hooks in BioC to load a package upon discovering a
data structure that belongs to it (and not before) -- should I be using
attachNamespace() somehow to side-step this problem?  (Eventually I do want
to submit BAM files to ExperimentHub for an end-to-end example and unit
tests, but the more pressing issue here was BiocCheck).

Any feedback is much appreciated. It's kind of a drag when all the examples
and vignettes pass and build, but only with a side-stepping of
dependencies. That can't possibly be the correct solution, yet I'm at a
loss to find documentation (which I'm sure exists somewhere) that explains
how to avoid this (and/or implement the hooks).

Thank you,

--t

[[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





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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Packages with 'Bad DESCRIPTION' on build report

2018-09-27 Thread Obenchain, Valerie

In the past, packages with a malformed DESCRIPTION file were skipped in the 
nightly builds and not posted on the build report. This was a little confusing 
for both the maintainer (what happened to my package?) and maintainers of 
packages that depended on it.

These packages are now reported as "ERROR (Bad DESCRIPTION file)" and are 
filtered on by checking the ERROR glyph check box at the top of the report.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] BioC 3.8 release schedule

2018-09-24 Thread Obenchain, Valerie

Hi all,

The release of Bioconductor 3.8 will be on October 31:

  https://www.bioconductor.org/developers/release-schedule/

Over the next weeks we'll announce key dates on the on 
bioc-devel@r-project.org mailing list. Thanks 
in advance for cleaning up packages and getting those last minute fixes in.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] push upstream master denied

2018-09-23 Thread Obenchain, Valerie

Hi Eric,

Thanks for the descriptive error report. The e.kort is your username from svn 
days. When slinky was added instead of linking the package to your existing 
username we accidentally linked it to your github id. This bug has since been 
fixed.

Ultimately it doesn't matter what the username is (svn or github) it's just 
used behind the scenes and we need one per user.

I've fixed the username on slinky and you should now have access.

Valerie



On 09/21/2018 08:29 AM, Kort, Eric wrote:

I am attempting my first push of updates to my recently accepted package, 
slinky, which is in the development branch of BioConductor.

When I try to push to the remote I get:

FATAL: W any packages/slinky e.kort DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

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

My remotes are setup like this:



git remote -v


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

I have submitted my ssh key to bioconductor, and confirmed that I have access 
with



ssh -T g...@git.bioconductor.org


hello e.kort, this is git@ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on 
git 2.18.0

Two things strike me as not quite right:
1. I am not sure where the username e.kort is coming from.  Does it matter?
2. When I login to  https://git.bioconductor.org/BiocCredentials/, the only 
package that it shows I have access to is dualKS, not my new package slinky.

Can someone spot what I am doing wrong?

Thank you!
-Eric

___
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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Fw: permission denied

2018-09-20 Thread Obenchain, Valerie

Minoo,

You can manage your credentials for the Bioconductor git server here:

https://git.bioconductor.org/BiocCredentials/

Activate your account with your email and you'll be logged in. Once in, you can 
see what SSH keys we have on file for you. If you still have problems, the docs 
at

https://www.bioconductor.org/developers/how-to/git/

might be helpful.

Valerie




On 09/20/2018 12:27 AM, Minoo Ashtiani wrote:





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?



[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Access permissions for DMRcate

Sorry I missed that one. You should have access now.

Valerie


On 09/13/2018 11:11 PM, Tim Peters wrote:

Sorry Valerie one more thing: looks like I have access to the data package, but 
not DMRcate itself - could you sync it as well please?

't.pet...@garvan.org.au<mailto:t.pet...@garvan.org.au>' has access to the 
following packages:
DMRcatedata
consensus




Cheers,

Tim


On 14/09/18 15:38, Tim Peters wrote:

Thanks Valerie, much obliged.

Cheers,
Tim

On 14/09/18 06:06, Obenchain, Valerie wrote:
Hi Tim,

We had 2 accounts for you, one under 
tim.pet...@csiro.au<mailto:tim.pet...@csiro.au><mailto:tim.pet...@csiro.au><mailto:tim.pet...@csiro.au>
 and one under 
t.pet...@garvan.org.au<mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au>.
 I've removed the @csiro.au account and your information (i.e., package 
permissions) should by synced up.

Valerie






On 09/11/2018 08:14 PM, Tim Peters wrote:

Hi BioC,

I'm attempting to sync the my repo https://github.com/timpeters82/DMRcate-devel 
with Bioconductor using the process here: 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.

However I'm encountering the following error at Step 9:

timpet@goodnow-lab:~/Documents/DMRcate$ git push upstream master
FATAL: W any packages/DMRcate timpeters82 DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

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

Here are my remotes:

timpet@goodnow-lab:~/Documents/DMRcate$ git remote -v
originhttps://github.com/timpeters82/DMRcate-devel/ (fetch)
originhttps://github.com/timpeters82/DMRcate-devel/ (push)
upstream
g...@git.bioconductor.org:packages/DMRcate.git<mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git>
 (fetch)
upstream
g...@git.bioconductor.org:packages/DMRcate.git<mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git><mailto:g...@git.bioconductor.org:packages/DMRcate.git>
 (push)


Possibly related, I noticed that my Bioconductor Git Credentials page 
https://git.bioconductor.org/BiocCredentials/permissions_by_user/ only gives me 
access to my newer package "consensus", but not "DMRcate". Can I add DMRcate 
myself through some process, or alternatively can I get an admin to do so 
please?

Best,

Tim

--

===

Tim Peters, PhD

Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

E: 
t.pet...@garvan.org.au<mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au><mailto:t.pet...@garvan.org.au>
 | W: http://www.garvan.org.au | P: +612 9295 8325


NOTICE
Please consider the environment before printing this email. This message and 
any attachments are intended for the addressee named and may contain legally 
privileged/confidential/copyright information. If you are not the intended 
recipient, you should not read, use, disclose, copy or distribute this 
communication. If you have received this message in error please notify us at 
once by return email and then delete both messages. We accept no liability for 
the distribution of viruses or similar in electronic communications. This 
notice should not be removed.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org><mailto: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 yo

Re: [Bioc-devel] Problems accessing BiocCredentials

Hi Jakob,

This was a bug on our end. It's been resolved and your account has been added.

Please try again to activate at

  https://git.bioconductor.org/BiocCredentials/

Once you're in you should see the SSH keys automatically added from your github 
account.

Valerie




On 09/14/2018 12:52 AM, Jakob Willforss wrote:

Dear Bioconductor,


I am the author of a new package 'NormalyzerDE' which got accepted into 
Bioconductor earlier this week. The package has been added to the development 
branch, and I am able to install it locally through Bioconductor, but its 
version hasn't been bumped to 1.0.0 and no landing page created yet despite 
showing build success at the 'checkResults' page.


I am able to clone the repository through its https path 
(https://git.bioconductor.org/packages/NormalyzerDE.git), but not through its 
ssh path 
(g...@git.bioconductor.org:packages/NormalyzerDE.git)
 leading me to think that I haven't managed to set up SSH-keys successfully. My 
account at GitHub has associated public keys.


In response to this I tried following the procedure to add SSH-keys manually at 
the BiocCredentials page. When trying to activate my email I get the response 
that my email 
(jakob.willfo...@immun.lth.se) isn't 
associated with a maintainer of a Bioconductor package.


Any input on how to proceed? I might have missed something obvious here, but 
can't seem to figure it out.


Best wishes,

Jakob

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] iClusterPlus/iChip/iSeq packages

Hi Quincy,

Your email has been updated. Please visit

  https://git.bioconductor.org/BiocCredentials

and activate your account with the 
qianxing...@moffitt.org address. Once activated 
you can login and see the SSH keys we have on file for you.

Valerie





On 09/13/2018 11:47 AM, Mo, Qianxing wrote:

Dear Sir/Madam,

My name is Qianxing Mo, the maintainer of iClusterPlus, iSeq and iChip packages.
Previously, I worked at Baylor College of Medicine and my email address was 
q...@bcm.edu.
However, my email address 
q...@bcm.edu is 
no longer valid because I have left Baylor.  Therefore, I could not reset my 
password and update my packages.

Now, I am working at H. Lee Moffitt Cancer Center and my email is 
qianxing...@moffitt.org.
  Could you change my former email 
q...@bcm.edu to 
my current email 
qianxing...@moffitt.org
 so that I could receive email from Bioconductor to update my packages?

Thank you very much!

Best,

Quincy


Qianxing Mo, Ph.D.
Associate Member
Department of Biostatistics & Bioinformatics
H. Lee Moffitt Cancer Center & Research Institute
12902 Magnolia Drive, Tampa, FL 33612

Phone: 813-745-2252
Email: qianxing...@moffitt.org



Please consider the environment before printing this email.

This transmission may be confidential or protected from disclosure and is only 
for review and use by the intended recipient. Access by anyone else is 
unauthorized. Any unauthorized reader is hereby notified that any review, use, 
dissemination, disclosure or copying of this information, or any act or 
omission taken in reliance on it, is prohibited and may be unlawful. If you 
received this transmission in error, please notify the sender immediately. 
Thank you.

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor Git Credentials

Hi John,

Your account was associated with email 
'john.gag...@gmail.com'. Assuming this was an old 
email, I've updated to 
'john.gagnon...@gmail.com'.

You should now be able to activate your account with this current email.

Valerie




On 09/12/2018 04:54 PM, John Gagnon wrote:

Hello,

I recently had a package accepted but am unable to sign in to submit your SSH 
public key or github id to Bioconductor. I�m not sure if this is necessary to 
do since I submitted my app through GitHub in the first place but when I go to 
log in or create an account, I get the error message:

"john.gagnon...@gmail.com is not associated 
with a maintainer of a Bioconductor package. Please check the spelling or 
contact bioc-devel@r-project.org for help.�

Any help would be greatly appreciated!

Thanks,
John
___
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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Access permissions for DMRcate

2018-09-13 Thread Obenchain, Valerie

Hi Tim,

We had 2 accounts for you, one under 
tim.pet...@csiro.au and one under 
t.pet...@garvan.org.au. I've removed the 
@csiro.au account and your information (i.e., package permissions) should by 
synced up.

Valerie






On 09/11/2018 08:14 PM, Tim Peters wrote:

Hi BioC,

I'm attempting to sync the my repo https://github.com/timpeters82/DMRcate-devel 
with Bioconductor using the process here: 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.

However I'm encountering the following error at Step 9:

timpet@goodnow-lab:~/Documents/DMRcate$ git push upstream master
FATAL: W any packages/DMRcate timpeters82 DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

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

Here are my remotes:

timpet@goodnow-lab:~/Documents/DMRcate$ git remote -v
originhttps://github.com/timpeters82/DMRcate-devel/ (fetch)
originhttps://github.com/timpeters82/DMRcate-devel/ (push)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (fetch)
upstream
g...@git.bioconductor.org:packages/DMRcate.git
 (push)


Possibly related, I noticed that my Bioconductor Git Credentials page 
https://git.bioconductor.org/BiocCredentials/permissions_by_user/ only gives me 
access to my newer package "consensus", but not "DMRcate". Can I add DMRcate 
myself through some process, or alternatively can I get an admin to do so 
please?

Best,

Tim

--

===

Tim Peters, PhD

Bioinformatics Research Officer | Immunogenomics Laboratory | Immunology 
Division

Garvan Institute of Medical Research

384 Victoria St., Darlinghurst, NSW, Australia 2010

E: 
t.pet...@garvan.org.au
 | W: http://www.garvan.org.au | P: +612 9295 8325


NOTICE
Please consider the environment before printing this email. This message and 
any attachments are intended for the addressee named and may contain legally 
privileged/confidential/copyright information. If you are not the intended 
recipient, you should not read, use, disclose, copy or distribute this 
communication. If you have received this message in error please notify us at 
once by return email and then delete both messages. We accept no liability for 
the distribution of viruses or similar in electronic communications. This 
notice should not be removed.

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Activation failure

2018-09-13 Thread Obenchain, Valerie

Hi Lang,

Thanks for letting us know. There was a bug in the code that checked the github 
username against other usernames (confirming "uniqueness"). This has been fixed 
and I've added your account.

One SSH key was added automatically from your langholee github account. Please 
try again to activate your account, then log in and you can see the key we have 
on file for you.

Valerie




On 09/12/2018 07:35 AM, Lang Ho Lee wrote:

Dear Mr. or Ms.

I am trying to submit my SSH key, since my package, XINA was accepted to
Bioconductor.  However, I couldn't activate my ID and got the following
message.

langho...@gmail.com is not associated with a 
maintainer of a Bioconductor
package. Please check the spelling or contact 
bioc-devel@r-project.org for
help.

My package description for the maintainer is below.

Authors@R: c(person("Lang Ho", "Lee", email = 
"langho...@gmail.com",  role
= c("aut", "cre")), person("Sasha", "Singh", email = "
sasi...@bwh.harvard.edu",  role = c("aut")))

Maintainer: Lang Ho Lee  and 
Sasha A. Singh <
sasi...@bwh.harvard.edu>

Could you help me to activate my account?

Thanks,
Lang

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Activating Account failed

2018-09-12 Thread Obenchain, Valerie

Hi,

There was a bug in the code that added new accounts. The bug was fixed and your 
account has been added. Please try again to activate and log in. I see that 2 
SSH keys were automatically from your ipumin github account. Once you login 
you'll be able to see these.

Valerie



On 09/12/2018 06:44 AM, $BM{IaL1(B wrote:

Hi,
ipu...@163.com is associated with a maintainer of the 
primirTSS which has been 
accepted(https://github.com/Bioconductor/Contributions/issues/817). But I can 
not activate ipu...@163.com in 
https://git.bioconductor.org/BiocCredentials/account_activation/, and "ssh -T 
g...@git.bioconductor.org" shows 
"g...@git.bioconductor.org: Permission denied 
(publickey)."
How can I solve this problem? Than you for any suggestions.
[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Request the change of the email of the maintainer

2018-09-10 Thread Obenchain, Valerie

Hi Sohrab,

If you still have access to the old email you can change this yourself. 
Activate your account here with the old email:

  https://git.bioconductor.org/BiocCredentials

Once activated you can login. Then got to --> user profile --> update email.

If you don't have access to sohrab.sar...@utu.fi I 
can change this for you.

Valerie



On 09/10/2018 04:09 AM, Sohrab Saraei wrote:

Hello,

I am writing to request to change the maintainer email of phosphonormalizer 
package. The information needed is included  below:

Current maintainer email: sohrab.saraei at utu.fi
New maintainer email: sohrab.saraei at helsinki.fi

Kind regards,

Sohrab Saraei




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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] proteoQC

2018-09-07 Thread Obenchain, Valerie

Bo,

It looks like you have access to proteoQC, customproDB and PGA.

Git credentials are managed through the new app here

https://git.bioconductor.org/BiocCredentials/

We have an account for both wenbos...@gmail.com and 
we...@genomics.cn.

1) Is we...@genomics.cn the 'old' email you no longer 
have access to? If yes, I will delete this account. There are no SSH keys 
associated with this account.

2) The wenbos...@gmail.com account is activated. 
This means someone has visited the app and activated the account ... I'm 
assuming this was you?

There are no keys associated with the 
wenbos...@gmail.com account. When logged in, you'll 
see instructions for adding keys via your github account (scraped 2x/day) or 
manually through the app.

Valerie

On 09/07/2018 10:47 AM, Herv� Pag�s wrote:

Care to provide some details? What you have tried? Error you got?

A must-read document that extensively covers the topic of maintaining
a Bioconductor package via git/GitHub is:

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

See in particular question 3. in the FAQ.

Hope this helps,
H.

On 09/07/2018 10:25 AM, Bo Wen wrote:

Yes.
Bo

On Fri, Sep 7, 2018 at 12:24 PM Herv� Pag�s 
mailto:hpa...@fredhutch.org>
> wrote:

Hi Bo,

Are you saying you cannot push changes to your package?

H.

On 09/07/2018 09:55 AM, Bo Wen wrote:
 > Hi,
 > I'm the developer of proteoQC (
 >

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_bioc_html_proteoQC.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-qRky554yTDVN2u7XQ0xlXDcnNdMzg93wm5J1Z0dAd8=-VtwzQI55NcHpB3lD1tbE7rFlcgsdXxMK5gB0NJTCug=).
I
 > changed my job so my previous email is not valid. Can anyone help
me update
 > my email to wenbos...@gmail.com 
 in
the package?
 > Thanks.
 > Bo Wen
 >
 >   [[alternative HTML version deleted]]
 >
 > ___
 > Bioc-devel@r-project.org 

mailing list
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-qRky554yTDVN2u7XQ0xlXDcnNdMzg93wm5J1Z0dAd8=8KSj7P_s3AiHvIUqkGETwbJeuTqxb0ptt1zRCEzYMbE=
 >

--
Herv� Pag�s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org 

Phone:  (206) 667-5791
Fax:(206) 667-1319

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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] DMCHMM package new dev release

2018-09-04 Thread Obenchain, Valerie

The builds start ~5pm EST daily. Commits made before that time will be included 
in the nightly builds. The build report posts the following day (see time at 
top of page):

https://www.bioconductor.org/checkResults/release/bioc-LATEST/
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/

If you don't see the package version you expected it's likely you missed the 
cutoff or didn't push to the git.bioconductor.org server. See git documentation 
here:

https://www.bioconductor.org/developers/how-to/git/

Valerie


On 09/04/2018 07:58 AM, Farhad Shokoohi via Bioc-devel wrote:

Hello,

I have made some changes and updated my package DMCHMM and pushed it to GitHub.
When the new update appears on bioconductor?

Best,

���
Farhad Shokoohi,
Ph.D. in Statistics

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] No Mac builds Aug 29

2018-09-04 Thread Obenchain, Valerie

MacStadium has applied the "ARP" patch

  https://blog.macstadium.com/blog/osx-10-9-mavericks-bugs

to merida2 and network performance looks much better. Hopefully all goes well 
with the builds tonight and merida2 is back in the report tomorrow.

Valerie


On 08/31/2018 06:54 AM, Obenchain, Valerie wrote:
We've been having problems with the release Mac builder (merida2) after the 
migration. It may be in and (mostly) out of the build report until we can 
resolve this.

Valerie

On 08/29/2018 09:06 AM, Obenchain, Valerie wrote:
The migration is done. The Macs should be back in the build report tomorrow.

Valerie


On 08/24/2018 05:57 AM, Obenchain, Valerie wrote:

MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm 
EST. The downtime is during our software builds so the Macs (merida1, merida2) 
won't build that night and won't be in the Aug 29th report. They should be back 
in the report on the 30th.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] No Mac builds Aug 29

2018-08-31 Thread Obenchain, Valerie

We've been having problems with the release Mac builder (merida2) after the 
migration. It may be in and (mostly) out of the build report until we can 
resolve this.

Valerie

On 08/29/2018 09:06 AM, Obenchain, Valerie wrote:
The migration is done. The Macs should be back in the build report tomorrow.

Valerie


On 08/24/2018 05:57 AM, Obenchain, Valerie wrote:

MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm 
EST. The downtime is during our software builds so the Macs (merida1, merida2) 
won't build that night and won't be in the Aug 29th report. They should be back 
in the report on the 30th.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Logolas package broken for R (3.4) users

2018-08-29 Thread Obenchain, Valerie

Kasper is right, you can only update code in the current release (Bioc  3.7) or 
devel (Bioc 3.8). Sorry I didn't read your question carefully enough. You 
could, however, use the AMI suggested below to attempt to reproduce the 
reported error.

This is the last build report for Bioc 3.6 and Logolas is not broken:

  https://www.bioconductor.org/checkResults/3.6/bioc-20180412/

If you can reproduce the error (with the AMI) you probably did not have a 
comprehensive set of tests which is why the build report is green. If you can't 
reproduce the error, the people reporting problems may be using mismatched 
R/Bioconductor package versions. The output of their sessionInfo() should be 
informative.

Valerie



On 08/29/2018 09:45 AM, Kasper Daniel Hansen wrote:
I think the "correct" answer to this, is that it is impossible. Old releases 
are locked.

The way to discover such things is to have appropriate test functions which 
will signal an error if things break.

Best,
Kasper

On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>> 
wrote:
You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:

https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

Valerie


On 08/27/2018 11:48 AM, kushal kumar dey wrote:

Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal





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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] No Mac builds Aug 29

2018-08-29 Thread Obenchain, Valerie

The migration is done. The Macs should be back in the build report tomorrow.

Valerie


On 08/24/2018 05:57 AM, Obenchain, Valerie wrote:

MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm 
EST. The downtime is during our software builds so the Macs (merida1, merida2) 
won't build that night and won't be in the Aug 29th report. They should be back 
in the report on the 30th.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Logolas package broken for R (3.4) users

2018-08-28 Thread Obenchain, Valerie

You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:

https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

Valerie


On 08/27/2018 11:48 AM, kushal kumar dey wrote:

Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal





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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Don't have access to new package

2018-08-28 Thread Obenchain, Valerie

Hi John,

The error was on our end. I've cleaned this up and you should now have access 
to multiHiCcompare and HiCcompare.

Valerie


On 08/27/2018 11:13 PM, John Stansfield wrote:

I recently had a new package accepted to Bioconductor, however when I try
to push changes upstream I get the following error:

FATAL: W any packages/multiHiCcompare j.stansfield DENIED by fallthru
(or you mis-spelled the reponame)

I also checked on the bioconductor git credentials and under packages I
have access to, only my first Bioconductor package is listed. My new
package, multiHiCcompare, does not show up and when checking my read write
privileges I only have read access to multiHiCcompare. I added my SSH key
to my github account and I can push to my other package, it is only the new
package that I cannot access.

What do I need to do gain write access to my new package?

Thank you,
John Stansfield

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] No Mac builds Aug 29

2018-08-24 Thread Obenchain, Valerie

MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm 
EST. The downtime is during our software builds so the Macs (merida1, merida2) 
won't build that night and won't be in the Aug 29th report. They should be back 
in the report on the 30th.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Multiple Bioconductor Maintainers?

2018-08-22 Thread Obenchain, Valerie

Hi Charles,

We want just one person in the 'Maintainer' field in DESCRIPTION so there is a 
single point of contact.

You can give multiple people commit access to the package on the 
git.bioconductor.org server. To do this, write this list (bioc-devel) and 
provide the emails and github usernames of the persons to add. Alternatively 
you could add these other people as collaborators on your github account - this 
would allow multiple active developers but restrict one person pushing to the 
git.bioconductor.org server.

Valerie


On 08/21/2018 01:51 PM, Warden, Charles wrote:

Hi,

Somebody asked if they could be added as a maintainer for a Bioconductor 
package.  Is it possible to have more than one maintainer for a package?

My understanding was that packages were typically maintained by one person, but 
I wanted to double-check.  Otherwise, I see that I can add multiple authors 
(with e-mail addresses), which might be OK in this case.

Thanks,
Charles


-SECURITY/CONFIDENTIALITY WARNING-

This message and any attachments are intended solely for the individual or 
entity to which they are addressed. This communication may contain information 
that is privileged, confidential, or exempt from disclosure under applicable 
law (e.g., personal health information, research data, financial information). 
Because this e-mail has been sent without encryption, individuals other than 
the intended recipient may be able to view the information, forward it to 
others or tamper with the information without the knowledge or consent of the 
sender. If you are not the intended recipient, or the employee or person 
responsible for delivering the message to the intended recipient, any 
dissemination, distribution or copying of the communication is strictly 
prohibited. If you received the communication in error, please notify the 
sender immediately by replying to this message and deleting the message and any 
accompanying files from your system. If, due to the security risks, you do not 
wish to rec
 eive further communications via e-mail, please reply to this message and 
inform the sender that you do not wish to receive further e-mail from the 
sender. (LCP301)


[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] update AnnotationHub and ExperimentHub server

2018-08-17 Thread Obenchain, Valerie

The update is done and all hub-related services appear normal. Let us know on 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> if you notice any 
problems.

Thanks.
Valerie



On 08/16/2018 02:18 PM, Obenchain, Valerie wrote:
I ran in to a few snags when I tried this update last week. Just a heads up, 
I'm going to try again tomorrow, Friday Aug 17, from 9-noon EST.

Valerie




On 08/08/2018 02:51 PM, Obenchain, Valerie wrote:

Tomorrow (Thursday, August 7) we'll be doing some updates to the server that 
host AnnotationHub and ExperimentHub. The work will take place from 9-noon EST. 
We don't anticipate any noticeable downtime (if all goes well) so this is just 
an fyi.

Thanks.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] update AnnotationHub and ExperimentHub server

2018-08-16 Thread Obenchain, Valerie

I ran in to a few snags when I tried this update last week. Just a heads up, 
I'm going to try again tomorrow, Friday Aug 17, from 9-noon EST.

Valerie




On 08/08/2018 02:51 PM, Obenchain, Valerie wrote:

Tomorrow (Thursday, August 7) we'll be doing some updates to the server that 
host AnnotationHub and ExperimentHub. The work will take place from 9-noon EST. 
We don't anticipate any noticeable downtime (if all goes well) so this is just 
an fyi.

Thanks.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] tokay2 internet connectivity

2018-08-13 Thread Obenchain, Valerie

Just to close the loop on this - the conversation went off-line and was 
resolved. When the omabrowser server OS was changed from Ubuntu to CentOS the 
problems on the Windows builders went away.

Valerie



On 07/23/2018 08:14 AM, Obenchain, Valerie wrote:
Hi Klara,

Unfortunately I still don't have an solution for this. For some reason, 
Internet Explorer on our Windows build machines cannot access the 
https://omabrowser.org/ web site. The problem can be reproduced independent of 
your package simply by opening IE and trying to access the site - this returns 
a 'page cannot be displayed' error.

I've looked extensively into the settings for IE, cipher suites and any known 
security issues. None of these has led to a solution. I don't have a problem 
accessing other web sites from IE on the Windows builders. However, I also 
don't have a problem accessing omabrowser.org from other browsers or other 
combinations of Windows/IE. The problem appears to be unique to the combination 
of the omabrowser.org site and some setting in Windows Server 2012R/ IE 11 on 
the builders.

If anyone in the community has experienced a similar problem with IE I'd 
welcome help troubleshooting - feel free to contact me off-list at 
valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>.

I've contacted the OMA browser people to ask if anything has changed with their 
web interface in the recent months. For the time being please ignore the 
Windows error for OmaDB.

Thanks.
Valerie




On 07/06/2018 10:38 AM, Obenchain, Valerie wrote:

Thanks for your patience on this. I belive it's related to the Internet 
Explorer settings on the builders. Hope to have this resolved soon.

Valerie



On 07/05/2018 10:35 AM, Obenchain, Valerie wrote:
Thanks for the report. I'll look into it.

Valerie

On 07/02/2018 06:00 AM, Klara Kaleb wrote:

Hi Bioc team,

I am one of the maintainers for the OmaDB package, now in 3.7 release. The 
package is passing build and check on both mac and linux, however I am still 
experiencing an error on windows (tokay2) which I reported earlier and was 
suggested it might be due to connectivity problems by Martin. We have increased 
the robustness of the error handling in the package since (more useful error 
message, sending the request again 3 times at increasing intervals if it does 
fail etc) which has shown that the error is indeed due to transient internet 
connection of the server.

To alleviate this in the vignettes, instead of sending requests to the API I 
have included some lightweight example objects with the package. However, the 
error still occurs in tests and some function examples. As the package is an 
API wrapper and so internet connection dependant, I am not sure what is the 
best way to address this error. Would you kindly be able to provide some 
guidance on this?

Many thanks in advance,

Klara
___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org><mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: sessionInfo() breaks the 5000-character limit on support.bioconductor.org

2018-08-12 Thread Obenchain, Valerie

I see you've posted the ExpermentHub problem on the Support site. I'll take a 
look / respond there.

Valerie




On 08/12/2018 08:53 PM, Obenchain, Valerie wrote:
Tim,

Regarding the ExperimentHub problem, please post your issue here - code you 
tried, what error you saw. Last Thursday from ~9-noon EST I did some work on 
the server that hosts the hubs. I briefly had the new server live, saw some 
problem and reverted to the old server. I want to make sure the issue you're 
seeing isn't related to that switch but is a real, reproducible problem.

The character limit for the support site is a separate issue and is better 
addressed/explained by someone else (probably Lori).

Valerie


On 08/12/2018 10:27 AM, Tim Triche, Jr. wrote:

This seems like a bug, since sessionInfo() is requested, but simply
cut-and-pasting my sessionInfo() output breaks the character limit for the
support site.

I suppose I can also post a support question about this... the original
motivation was to document a bizarre failure mode where
ExperimentHub-hosted data/experiment packages appear to break a working
install due to libcurl issues. That seems like a pretty severe flaw -- even
the worst issues with .db0 packages did not, to my recollection, render a
working installation unworkable. But this new  experimentHub "bug" (maybe
not correct term?) does.

--t

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: sessionInfo() breaks the 5000-character limit on support.bioconductor.org

2018-08-12 Thread Obenchain, Valerie

Tim,

Regarding the ExperimentHub problem, please post your issue here - code you 
tried, what error you saw. Last Thursday from ~9-noon EST I did some work on 
the server that hosts the hubs. I briefly had the new server live, saw some 
problem and reverted to the old server. I want to make sure the issue you're 
seeing isn't related to that switch but is a real, reproducible problem.

The character limit for the support site is a separate issue and is better 
addressed/explained by someone else (probably Lori).

Valerie


On 08/12/2018 10:27 AM, Tim Triche, Jr. wrote:

This seems like a bug, since sessionInfo() is requested, but simply
cut-and-pasting my sessionInfo() output breaks the character limit for the
support site.

I suppose I can also post a support question about this... the original
motivation was to document a bizarre failure mode where
ExperimentHub-hosted data/experiment packages appear to break a working
install due to libcurl issues. That seems like a pretty severe flaw -- even
the worst issues with .db0 packages did not, to my recollection, render a
working installation unworkable. But this new  experimentHub "bug" (maybe
not correct term?) does.

--t

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] [bcbmail] Re: EXTERNAL: Password Reset Help

2018-08-09 Thread Obenchain, Valerie

Let me know if you want to change the email associated with the account and we 
can do that.

Valerie


On 08/09/2018 09:31 AM, Augustin Luna wrote:

I do have access to the email, but I can no longer send emails from
the mskcc.org account. I just activated my account; I thought it was
the account from the SVN. I need to spend some time trying to figure
out if I can commit.

Thanks,
Augustin Luna

On Wed, Aug 8, 2018 at 8:57 AM, Obenchain, Valerie [Valerie.Obenchain
AT RoswellPark.org] <mailto:can...@gmail.com> wrote:


External Email - Use Caution

Hi Augustin,

Your account is under lu...@cbio.mskcc.org<mailto:lu...@cbio.mskcc.org> and it 
looks like this has not
been activated. Do you still have access to this email?

When I tried to enter a bogus email for a password reset at

  https://git.bioconductor.org/BiocCredentials/password_reset/

I did not get an informative error message. This must have been what
happened to you - you entered an email not associated with an account but
didn't get any indication that was the case. I'll add a better error
message.

Valerie




On 08/07/2018 05:29 PM, Augustin Luna wrote:

I requested a password reset from this site:

https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/

a couple of times and I haven't received it. Not sure what to do.

Thanks,
Augustin Luna

___
Bioc-devel@r-project.org<mailto: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, 
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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] update AnnotationHub and ExperimentHub server

2018-08-08 Thread Obenchain, Valerie

Tomorrow (Thursday, August 7) we'll be doing some updates to the server that 
host AnnotationHub and ExperimentHub. The work will take place from 9-noon EST. 
We don't anticipate any noticeable downtime (if all goes well) so this is just 
an fyi.

Thanks.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: Password Reset Help

2018-08-08 Thread Obenchain, Valerie

Hi Augustin,

Your account is under lu...@cbio.mskcc.org and it 
looks like this has not been activated. Do you still have access to this email?

When I tried to enter a bogus email for a password reset at

  https://git.bioconductor.org/BiocCredentials/password_reset/

I did not get an informative error message. This must have been what happened 
to you - you entered an email not associated with an account but didn't get any 
indication that was the case. I'll add a better error message.

Valerie




On 08/07/2018 05:29 PM, Augustin Luna wrote:

I requested a password reset from this site:

https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/

a couple of times and I haven't received it. Not sure what to do.

Thanks,
Augustin Luna

___
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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: RSA key format

2018-08-06 Thread Obenchain, Valerie

Hi,

On 08/06/2018 07:36 AM, j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl> wrote:
Dear Valerie,

Thanks for helping me out.

1) https://github.com/jellegoeman is my github account indeed but it has no 
public repositories so far so I guess you can�t see it for that reason?

Possibly. Follow instructions here to add globaltest to your github repo. If 
it's already there, please make it public.

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



2) All except can j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl> be removed.

How do I diagnose the "Permission denied (publickey)" problem? The ssh key I 
uploaded is the one in my ~/.ssh folder.

Log into the app at https://git.bioconductor.org/BiocCredentials and confirm 
the key you see there is the key you are using. Next, read #13-17 on the FAQ:

  https://bioconductor.org/developers/how-to/git/faq/

If you still have problems, please post the exact command you're trying and the 
error message.

Valerie




Best wishes, Jelle


From: Obenchain, Valerie [mailto:valerie.obench...@roswellpark.org]
Sent: maandag 6 augustus 2018 16:11
To: Goeman, J.J. (MSTAT); 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: EXTERNAL: [Bioc-devel] RSA key format

Hi Jelle,

1) To see the SSH keys we have on file for you go to this site and login with 
j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl>:

https://git.bioconductor.org/BiocCredentials/

It looks like you've activated your account and we have one key on file for 
you. The github username associated with this account is 'jellegoeman'. I don't 
see a github account for user 'jellegoeman'. Is this still active?

You can add keys through the app at 
https://git.bioconductor.org/GiocCredentials or by adding them to your github 
account. Twice daily we scrape keys from github.com/username.keys. In either 
case, invalid keys will be rejected.


2) While we're at it, let's clean up access to globaltest. Currently these 
people have access:

 j.oost...@lumc.nl<mailto:j.oost...@lumc.nl> 
j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl> l.finos a.solari j.goeman

j.goeman is your old SVN username which I can remove since you're now using 
j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl>. How about the others? Should 
j.oost...@lumc.nl<mailto:j.oost...@lumc.nl> and l.finao and a.solari still have 
access?

Valerie




On 08/06/2018 06:45 AM, j.j.goe...@lumc.nl<mailto:j.j.goe...@lumc.nl> wrote:

 Dear All,



It's been a long time that I haven't made any updates to globaltest, so I'm 
still not updated to the new git system (which I think is a very good idea). 
I'm having trouble connecting, however. When I use git fetch upstream I get 
"Permission denied (publickey)" I have uploaded my rsa key to the bioconductor 
git credentials page, but I'm guessing something went wrong there. I noticed 
that there are several formats for public keys (e.g. starting with "ssh-rsa" or 
with "-BEGIN RSA PUBLIC KEY-"). Which is the format I should use?



Best wishes, Jelle



___

Bioc-devel@r-project.org<mailto: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, 
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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: Updating SSH keys without previous email account

2018-08-05 Thread Obenchain, Valerie

Hi,

There is an account for email anth...@achiu.me with 
github username 'idno0001'.

Visit this page and activate (not login to) your account:

  https://git.bioconductor.org/BiocCredentials

Once you're in you can see the keys we have for you. We scrape keys every 12 
hours from https://github.com/username.keys, e.g.,

  https://github.com/idno0001.keys

I'm guessing those are current and you have access to them. If not, please 
update them. If 'idno0001' is not your github account please let me know.

Valerie


On 08/02/2018 02:58 AM, Anthony Chiu wrote:

Hello

I maintain the 'twoddpcr' package and I have left my previous institute. I
no longer have the SSH keys that I used to push to the Git repository. I
never activated my Git credentials account at [1] (I submitted my public
key using the Google form during the transition from SVN), and I no longer
have access to my old 
 
email either.

Please could someone help me get access to the Git repositories again?

Thanks
Anthony

[1]: https://git.bioconductor.org/BiocCredentials/account_activation/

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] tokay2 internet connectivity

2018-07-23 Thread Obenchain, Valerie

Hi Klara,

Unfortunately I still don't have an solution for this. For some reason, 
Internet Explorer on our Windows build machines cannot access the 
https://omabrowser.org/ web site. The problem can be reproduced independent of 
your package simply by opening IE and trying to access the site - this returns 
a 'page cannot be displayed' error.

I've looked extensively into the settings for IE, cipher suites and any known 
security issues. None of these has led to a solution. I don't have a problem 
accessing other web sites from IE on the Windows builders. However, I also 
don't have a problem accessing omabrowser.org from other browsers or other 
combinations of Windows/IE. The problem appears to be unique to the combination 
of the omabrowser.org site and some setting in Windows Server 2012R/ IE 11 on 
the builders.

If anyone in the community has experienced a similar problem with IE I'd 
welcome help troubleshooting - feel free to contact me off-list at 
valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>.

I've contacted the OMA browser people to ask if anything has changed with their 
web interface in the recent months. For the time being please ignore the 
Windows error for OmaDB.

Thanks.
Valerie




On 07/06/2018 10:38 AM, Obenchain, Valerie wrote:

Thanks for your patience on this. I belive it's related to the Internet 
Explorer settings on the builders. Hope to have this resolved soon.

Valerie



On 07/05/2018 10:35 AM, Obenchain, Valerie wrote:
Thanks for the report. I'll look into it.

Valerie

On 07/02/2018 06:00 AM, Klara Kaleb wrote:

Hi Bioc team,

I am one of the maintainers for the OmaDB package, now in 3.7 release. The 
package is passing build and check on both mac and linux, however I am still 
experiencing an error on windows (tokay2) which I reported earlier and was 
suggested it might be due to connectivity problems by Martin. We have increased 
the robustness of the error handling in the package since (more useful error 
message, sending the request again 3 times at increasing intervals if it does 
fail etc) which has shown that the error is indeed due to transient internet 
connection of the server.

To alleviate this in the vignettes, instead of sending requests to the API I 
have included some lightweight example objects with the package. However, the 
error still occurs in tests and some function examples. As the package is an 
API wrapper and so internet connection dependant, I am not sure what is the 
best way to address this error. Would you kindly be able to provide some 
guidance on this?

Many thanks in advance,

Klara
___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org><mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: Adding one more maintainer - Mergeomics package

2018-07-20 Thread Obenchain, Valerie

Hi,

I don't see a github account under the name of liuwenting ... is  this correct?

Valerie




On 07/20/2018 12:55 AM, Zeyneb Kurt wrote:

Dear Bioc team,

I am maintaining the �Mergeomics� package and would like to add one of my
colleagues as an *additional* maintainer. Her github username is liuwenting (am
cc�ing her here).

Best,
Zeyneb Kurt

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] EXTERNAL: MEDIPS

2018-07-19 Thread Obenchain, Valerie

Hi Lukas,

Your account was associated with 
cha...@molgen.mpg.de and I've changed this to 
lukascha...@ucsd.edu.

You'll first need to 'activate' your account (vs 'login') at

https://git.bioconductor.org/BiocCredentials/

Once you're in, you can add SSH keys or the name of a github account and we'll 
scrape keys from https://github.com/username.keys.

Let me know if you have problems.

Valerie




On 07/19/2018 04:46 PM, Chavez, Lukas wrote:

Hi,

I am the developer and maintainer of the MEDIPS package.

I was informed to  change my bioc-devel vignette and package code to support 
the use of `BiocManager`. While I was able to to svn check out and update my 
package, I cannot commit the changes anymore:



svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEDIPS 
--username l.chavez
svn update


Updating '.':
At revision 132278.


svn ci -m "BiocManager Update"


svn: E175013: Commit failed (details follow):
svn: E175013: Access to '/bioconductor/!svn/me� forbidden

I would think that I will have to (finally) move to git instead? Therefore, I 
just tried to set up an account at 
https://git.bioconductor.org/BiocCredentials/account_activation/ but somehow my 
emails are not associated with my package: �...is not associated with a 
maintainer of a Bioconductor package.�

I have recently moved to UC San Diego and would like to have my UCSD email 
associated with my Bioconductor package, if possible: 
lukascha...@ucsd.edu
 ?

Sincerely,

_
Lukas Chavez, Ph.D.
Assistant Professor, Department of Medicine
University of California, San Diego (UCSD)
Biomedical Research Facility 2 | Room 2A24
9500 Gilman Drive | MC 0765 | La Jolla, CA 92093
T: 858 246 1919 | Email: 
lukascha...@ucsd.edu
www.oncoepigenomics.org


[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Date for the next release

2018-07-10 Thread Obenchain, Valerie

Hi,

We don't have a date yet but it will probably be in October (not necessarily 
the 31st).

Valerie


On 07/09/2018 11:34 PM, Samuel Wieczorek wrote:

Hi



I am the developer of the packages DAPAR and Prostar. I have to plan in
advance some work and I would like to synchronise this with the next
release of Bioconductor.

I know it is a bit early but do you know the date of the next release ?
Will it be the 31th of Octobre as last year ?



Thanks in advance



Sam

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] tokay2 internet connectivity

2018-07-05 Thread Obenchain, Valerie

Thanks for the report. I'll look into it.

Valerie

On 07/02/2018 06:00 AM, Klara Kaleb wrote:

Hi Bioc team,

I am one of the maintainers for the OmaDB package, now in 3.7 release. The 
package is passing build and check on both mac and linux, however I am still 
experiencing an error on windows (tokay2) which I reported earlier and was 
suggested it might be due to connectivity problems by Martin. We have increased 
the robustness of the error handling in the package since (more useful error 
message, sending the request again 3 times at increasing intervals if it does 
fail etc) which has shown that the error is indeed due to transient internet 
connection of the server.

To alleviate this in the vignettes, instead of sending requests to the API I 
have included some lightweight example objects with the package. However, the 
error still occurs in tests and some function examples. As the package is an 
API wrapper and so internet connection dependant, I am not sure what is the 
best way to address this error. Would you kindly be able to provide some 
guidance on this?

Many thanks in advance,

Klara
___
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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] updating maintainer

2018-07-05 Thread Obenchain, Valerie

Sorry - my email was out of sync and I didn't see your earlier response. I'll
take of this today.

Valerie

On 07/05/2018 06:57 AM, Obenchain, Valerie wrote:

Sam,

I haven't heard back from you. Do you still want to make this change?

Valerie

On 06/27/2018 05:24 AM, Obenchain, Valerie wrote:
Hi Sam,

As Kasper mentioned, you should update the maintainer field in the DESCRIPTION
file of your packages. We'll also need this information:

- What packages to you currently maintain
- What is your PI's github account and email
- List of Bioconductor packages you PI currently maintains, if any any

It's a good idea for the email in the DESCRIPTION file to match the email used
to make the account in the GitApp:

https://git.bioconductor.org/BiocCredentials

This is not strictly enforced but it make communication easier.

Thanks.
Valerie

On 06/27/2018 12:45 AM, Kasper Daniel Hansen wrote:

You update the maintainer field in devel. I don't know what to do about
release.

I don't understand the question about github. There is no "github email",
there is a github username. And that username does not have to be the same
as a maintainer email, because they really have nothing to do with each
other. In the DESCRIPTION field the github address is given as a URL not as
an email, like
URL: https://github.com/hansenlab/minfi
BugReports: https://github.com/hansenlab/minfi/issues

On Tue, Jun 26, 2018 at 4:18 PM, Samuel E Zimmerman <
sezim...@einstein.yu.edu<mailto:sezim...@einstein.yu.edu><mailto:sezim...@einstein.yu.edu><mailto:sezim...@einstein.yu.edu>>
wrote:

Dear bioc-devs,

I will no longer be working at my current university in about a week, and
the email address associated with the bioconductor packages I maintain will
be removed. How should I go about updating my email address to keep
maintaining the packages?

Also, my PI would like to have the github account, where the repos for the
bioconductor packages live, be under her email address instead of mine.
Would it be a problem if the maintainer's email address and the github
email address are different?

Thank you very much.

Best,
Sam

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org>
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org><mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] updating maintainer

2018-07-05 Thread Obenchain, Valerie

Sam,

I haven't heard back from you. Do you still want to make this change?

Valerie



On 06/27/2018 05:24 AM, Obenchain, Valerie wrote:
Hi Sam,

As Kasper mentioned, you should update the maintainer field in the DESCRIPTION 
file of your packages. We'll also need this information:

- What packages to you currently maintain
- What is your PI's github account and email
- List of Bioconductor packages you PI currently maintains, if any any

It's a good idea for the email in the DESCRIPTION file to match the email used 
to make the account in the GitApp:

  https://git.bioconductor.org/BiocCredentials

This is not strictly enforced but it make communication easier.

Thanks.
Valerie





On 06/27/2018 12:45 AM, Kasper Daniel Hansen wrote:

You update the maintainer field in devel.  I don't know what to do about
release.

I don't understand the question about github.  There is no "github email",
there is a github username. And that username does not have to be the same
as a maintainer email, because they really have nothing to do with each
other. In the DESCRIPTION field the github address is given as a URL not as
an email, like
  URL: https://github.com/hansenlab/minfi
  BugReports: https://github.com/hansenlab/minfi/issues



On Tue, Jun 26, 2018 at 4:18 PM, Samuel E Zimmerman <
sezim...@einstein.yu.edu<mailto:sezim...@einstein.yu.edu>> wrote:



Dear bioc-devs,

I will no longer be working at my current university in about a week, and
the email address associated with the bioconductor packages I maintain will
be removed. How should I go about updating my email address to keep
maintaining the packages?

Also, my PI would like to have the github account, where the repos for the
bioconductor packages live, be under her email address instead of mine.
Would it be a problem if the maintainer's email address and the github
email address are different?

Thank you very much.

Best,
Sam

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] updating maintainer

2018-06-27 Thread Obenchain, Valerie

Hi Sam,

As Kasper mentioned, you should update the maintainer field in the DESCRIPTION 
file of your packages. We'll also need this information:

- What packages to you currently maintain
- What is your PI's github account and email
- List of Bioconductor packages you PI currently maintains, if any any

It's a good idea for the email in the DESCRIPTION file to match the email used 
to make the account in the GitApp:

  https://git.bioconductor.org/BiocCredentials

This is not strictly enforced but it make communication easier.

Thanks.
Valerie





On 06/27/2018 12:45 AM, Kasper Daniel Hansen wrote:

You update the maintainer field in devel.  I don't know what to do about
release.

I don't understand the question about github.  There is no "github email",
there is a github username. And that username does not have to be the same
as a maintainer email, because they really have nothing to do with each
other. In the DESCRIPTION field the github address is given as a URL not as
an email, like
  URL: https://github.com/hansenlab/minfi
  BugReports: https://github.com/hansenlab/minfi/issues



On Tue, Jun 26, 2018 at 4:18 PM, Samuel E Zimmerman <
sezim...@einstein.yu.edu> wrote:



Dear bioc-devs,

I will no longer be working at my current university in about a week, and
the email address associated with the bioconductor packages I maintain will
be removed. How should I go about updating my email address to keep
maintaining the packages?

Also, my PI would like to have the github account, where the repos for the
bioconductor packages live, be under her email address instead of mine.
Would it be a problem if the maintainer's email address and the github
email address are different?

Thank you very much.

Best,
Sam

[[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





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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] New DESCRIPTION fields in build products

2018-06-20 Thread Obenchain, Valerie

This is an FYI on some changes made to the build products and VIEWS files.

The build system code was recently modified to add 5 new fields to the 
DESCRIPTION file of the build products. These fields only appear in the built 
tarball or binary (not source code) and are parsed into the VIEWS files. The 
data in VIEWS are used for building parts of the website such as landing pages, 
badges, etc.

The new fields:

git_url: The url for the source code on the git server.
git_branch: The git branch (master or RELEASE_3_7).
git_last_commit: Last git commit hash.
git_last_commit_date: Last git commit date.
Date/Publication: Date the built package was propagated to the repo and became 
available via biocLite().

The VIEWS files for devel:

https://bioconductor.org/packages/devel/bioc/VIEWS
https://bioconductor.org/packages/devel/workflows/VIEWS
https://bioconductor.org/packages/devel/data/experiment/VIEWS

The VIEWS file is only updated when a package is propagated (version bump). To 
make these fields available in the devel VIEWS, we force propagated all devel 
packages. We did not do the same for release because of consistency issues with 
'Date/Publication'. Because of this, the devel VIEWS has the fields for all 
packages but release VIEWS has them only for packages that had a version bump.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] rJava on Windows builders

2018-05-31 Thread Obenchain, Valerie

Just a heads up that the new version of rJava that came out 5/29/2018 failed to 
install on the Windows builders yesterday. Because of this we see an increased 
number of failures in both release and devel. Unfortunately I didn't notice 
this before the builds started today so we'll see the same errors tomorrow.

This should be cleared up for the report that posts on Saturday, June 2.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] onLoad failed for rJava in nigthly 'devel' build

2018-05-31 Thread Obenchain, Valerie

Hi Lulu,

Thanks for keeping an eye on the build report!

It looks like something went wrong when the new version of rJava was installed 
on the Windows builders yesterday. Unfortunately today's builds started before 
we realized this so your package will likely have the same error on tomorrow's 
report. We'll investigate and hopefully have this cleared up for the report 
that will post on Saturday.

Valerie


On 05/31/2018 11:43 AM, Lulu Chen wrote:

Dear Bioc Team,

My package "CAMTHC" has been accepted and  included in the nigthly 'devel'
build . However, build error appears in "Windows Server 2012 R2 Standard /
x64":

install for i386

* installing *source* package 'CAMTHC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: library.dynam("rJava", pkgname, libname)
  error: DLL 'rJava' not found: maybe not installed for this architecture?
ERROR: lazy loading failed for package 'CAMTHC'
* removing
'C:/Users/biocbuild/bbs-3.8-bioc/meat/CAMTHC.buildbin-libdir/CAMTHC'
In R CMD INSTALL
In R CMD INSTALL

I only met this problem in my own computer before I set java correctly. All
advice I find online is about how to set java in your own computer. I
passed the build check at the Bioconductor Contributions repository. So
now,  could anyone help me to fix this problem in  'devel' build? Thanks!

Best,
Lulu

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

2018-05-31 Thread Obenchain, Valerie

Hi Mike,
Is this still an issue or has it been resolved?
Val


On 05/22/2018 02:19 PM, Mike Smith wrote:

In trying to diagnose this issue at
https://support.bioconductor.org/p/108548/ I've found some weird behaviour
with Windows, normalizePath(), and non-ASCII characters.  Essentially, if I
run normalizePath() recursively on a path that contains  '�' (I haven't
tried other characters) something 'changes' in the string, but I can't work
out what, and it breaks a subsequent .Call() which uses the path.

The example below tries to demonstrate this in a fairly concise manner. It
works fine if normalizePath() is run once, but fails after it's run a
second time on itself.

However, change "�xample" for "example" and both instances work. Similarly,
both run fine on my Linux machine with the non-ASCII character inplace.

I'd be grateful if anyone else with a Windows machine could verify this
behaviour, or to shed any light on what might be the difference between path1
and path2 below.

Thank,
Mike

--

## setup some HDF5 components required later
flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC"))
fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CREATE", allowNULL = TRUE)
fapl <- rhdf5::H5Pcreate("H5P_FILE_ACCESS")

## create a folder with non-ASCII character
dir.create('�xample')
setwd("�xample")

## create two normalized paths recursively - these are 'identical'
path1 <- normalizePath('test.h5', mustWork = FALSE)
path2 <- normalizePath(path1, mustWork = FALSE)
identical(path1, path2)

## create an HDF5 file using path1 - this works
fid <- .Call("_H5Fcreate", path1, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
.Call("_H5Fclose", fid, PACKAGE = "rhdf5")
file.remove(path1)

## create an HDF5 file using path2 - this fails
fid <- .Call("_H5Fcreate", path2, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
if(exists('fid2')) {
  .Call("_H5Fclose", fid2, PACKAGE = "rhdf5")
  file.remove(path2)
}

## tidy up
rhdf5::h5closeAll()
setwd("../")

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] merge two maintainer accounts

2018-05-21 Thread Obenchain, Valerie

Hi Rhonda,

Thanks for letting us know. We can definitely merge maintainers and would 
prefer just one account per person.

I've removed the account for rbac...@ufl.edu. You now 
have the single account for 
rhonda.bac...@gmail.com which is tied to 
packages Trendy and SCnorm.

Valerie



On 05/20/2018 09:42 AM, Rhonda Bacher wrote:

Hi,

I seem to have two different Bioconductor credentials for two different
packages that I maintain. The package Trendy is using the email
rhonda.bac...@gmail.com and SCnorm is using 
rbac...@ufl.edu (but my access
to push upstream to Bioconductor is not not working for this one). Is it
possible for you to merge both packages under my gmail email (
rhonda.bac...@gmail.com) ?

Thanks!

Rhonda Bacher

[[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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] About MLSeq Package

2018-05-17 Thread Obenchain, Valerie

Hi Gokmen,

An account exits for you with email
"gokmenzarar...@erciyes.edu.tr". This was
the email associated with the svn user when the package was first accepted.

I have changed the email to
gokmenzarar...@hotmail.com and you should
now be able to activate the account.

Let me know if you have problems.

Valerie

On 05/16/2018 12:21 PM, G�kmen Zarars�z wrote:

Hello,

I am the maintainer of MLSeq package. As we read from Bioconductor Source
Control, SVN is not supported anymore and i want migrate to GitHub repository.
I have tried to activate my account and login through
https://git.bioconductor.org/BiocCredentials/account_activation/ in order to
manage developer account. However, it gives an error that my e-mail address is
not associated with the MLSeq package. If such an account is not created
before, how should i create it? We actually want to do followings:

(1) Create a developer account for MLSeq package.
(2) Change the maintainer to and associate
Bioconductor repositories with new maintainer's GitHub repository

Should the developer account (1) be created for current maintainer and then
transferred to new maintainer or is it possible to create this account for new
maintainer at once?

Could you please help us,

Best,

Gokmen Zararsiz,
Maintainer of MLSeq package.

Asst.Prof.Dr. Gokmen Zararsiz

Erciyes University,
Fac. of Medicine,
Dept. of Biostatistics,
38039, Melikgazi/KAYSERI
+90(352)-207 / ext:23480
http://bit.do/gokmenzararsiz
-
Turcosa Analytics,
Yeni Mah., Asik Veysel Blv.,
67B, Teknopark-5, No:80
38039, Melikgazi/KAYSERI
+90(352)-5030902
www.turcosa.com.tr
[https://docs.google.com/uc?export=download=0B_raor8m9qYzN1hwaFc5TGp1dGM=0B_raor8m9qYzZEtSZ1Zlb1kyZnA4b2tKY0QvcXJUOCtuN3F3PQ][https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcRg-2eZCQ8vdJT6tHaq_kyHWSeLY0dMSV9UJe3Fcgkt9eWGzMe9qQ]

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] rsvg on mac

2018-05-15 Thread Obenchain, Valerie

Yes, when a new version appears on CRAN it is automatically picked up by the
build machines.

Valerie

On 05/14/2018 05:04 AM, Kevin Horan wrote:

Valerie,

Sorry, I think my memory of what the actual problem was was wrong. I have
spoken to the rsvg author and he has now fixed the build of rsvg in CRAN for OS
X. So will that then just get automatically put on your machines, or else,
would it now be possible to manually put it on? Sorry for all the confusion,
and thanks for you help.

ChemmineR is green now because I removed the functions requiring rsvg to
get it through the release. They were new functions anyway.

Kevin

On 05/09/2018 03:25 PM, Obenchain, Valerie wrote:
Kevin,

I feel like we're not on the same page. We've had this discussion and both
Herve and I tried to explain the situation:

https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012812.html

We do not build CRAN packages from source on the Windows and Mac build
machines. If a CRAN binary is not available for one of your dependencies, e.g.,
rsvg, the best thing for you to do is contact the maintainer or post on the
r-sig-mac mailing list:

https://stat.ethz.ch/mailman/listinfo/r-sig-mac

However, ChemmineR is green on both release and devel build reports. I'm not
sure why you are asking us (again) to install the rsvg system dependency on the
Mac builders. Did I misunderstand what you wanted?

Valerie

On 05/09/2018 07:41 AM, Kevin Horan wrote:

Now that this past bioc release is done, and R 3.5 is stable, would it be
possible to install the "rsvg" package on your build machines? Thanks.

Kevin

On 02/19/2018 02:01 PM, Alexey Sergushichev wrote:
Valerie, thanks. Will try to ask there.

However, after looking through the mailing list it looks like R-devel builds
for OS X aren't trivial and aren't part of CRAN...

--
Alexey

On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>
wrote:
Hi,

There has been some discussion of the devel Mac binaries on the R-SIG-Mac
mailing list. That list would be the best place to ask this question.

https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html

Valerie

On 02/19/2018 08:32 AM, Alexey Sergushichev wrote:
Valerie,

Are there any estimates on how often CRAN OS X builds happen? There are still
no builds for rsvg and other packages...

Thanks,
Alexey

On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>
wrote:
Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see this on the
rsvg landing page:

https://cran.r-project.org/web/packages/rsvg/index.html

Nothing we can do until CRAN makes them available.

Valerie

On 02/07/2018 08:29 AM, Kevin Horan wrote:

The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html

Kevin

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>>
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org<mailto: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.

Re: [Bioc-devel] rsvg on mac

2018-05-09 Thread Obenchain, Valerie

Kevin,

I feel like we're not on the same page. We've had this discussion and both
Herve and I tried to explain the situation:

https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012812.html

https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Valerie

On 05/09/2018 07:41 AM, Kevin Horan wrote:

Now that this past bioc release is done, and R 3.5 is stable, would it be
possible to install the "rsvg" package on your build machines? Thanks.

Kevin

On 02/19/2018 02:01 PM, Alexey Sergushichev wrote:
Valerie, thanks. Will try to ask there.

However, after looking through the mailing list it looks like R-devel builds
for OS X aren't trivial and aren't part of CRAN...

--
Alexey

On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>
wrote:
Hi,

There has been some discussion of the devel Mac binaries on the R-SIG-Mac
mailing list. That list would be the best place to ask this question.

https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html

Valerie

On 02/19/2018 08:32 AM, Alexey Sergushichev wrote:
Valerie,

Are there any estimates on how often CRAN OS X builds happen? There are still
no builds for rsvg and other packages...

Thanks,
Alexey

On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>
wrote:
Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see this on the
rsvg landing page:

https://cran.r-project.org/web/packages/rsvg/index.html

Nothing we can do until CRAN makes them available.

Valerie

On 02/07/2018 08:29 AM, Kevin Horan wrote:

The ChemmineR build is failing on the mac due to a new dependency not
being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html

Kevin

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org>>
mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
Bioc-devel@r-project.org<mailto: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.

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Transition from Google Sheet to Web App

2018-05-07 Thread Obenchain, Valerie

Lluis,

A little follow up on this. When a new package is submitted, the email in 
DESCRIPTION is checked against the Support Site so those 2 fields are in sync 
for new packages ... at least for awhile. Right now we don't have plans to sync 
the App with DESCRIPTION and the Support Site but it may be considered in the 
future.

Valerie


On 04/19/2018 07:59 AM, Obenchain, Valerie wrote:
Hi Lluis,

We (or at least I) had not considered linking the profile in the credentials 
app with the profile in the Support Site and currently they are not aware of 
each other. The email in DESCRIPTION was used to get some emails for the 
credentials app but it is not the case that an email change in the app will 
propagate to DESCRIPTION.

We do require package maintainers to be registered on the Support Site in order 
to submit a package but I'm not sure if this email is checked against the 
DESCRIPTION.

I see what you mean by having this information in 3 places, DESCRIPTION file, 
credentials app and Support Site. I think the 'if' and 'how' of connecting 
these pieces needs some thought. I'll discuss with the group at our next 
meeting and will follow up here.

Thanks for bringing this up.

Valerie




On 04/19/2018 06:35 AM, Llu�s Revilla wrote:
Hi all,

I have a couple of doubts related to the new app.

I've seen that one can update mail, and github id, and add new keys (Nice!). 
However I couldn't find if this account will be somehow linked to the user 
profile in the support site. Are there any plans in this direction?
At the moment the email of the maintainer of a package should be registered in 
the support site, which is the same one used for the app. When someone updates 
the email in the app is it updated in other sites of Bioconductor? Will the 
email of the Description files of the packages  and the account in the support 
site be updated?

Many thanks,

Llu�s


On 18 April 2018 at 17:13, Obenchain, Valerie 
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> 
wrote:
The Web App for managing SSH keys is now available at

  https://git.bioconductor.org/BiocCredentials/

Accounts have been created for all package maintainers. Note the central 
identifier, i.e., how you login is your email. This email was taken from the 
DESCRIPTION of your package or the Google Sheet if you registered a key there.

When you first visit the App you'll need to activate your account. An 
activation link will be sent to your email. Once your account is activated you 
can login. Trying to login without activation will lead to an error.

Let us know if you have any questions or problems.



On 04/18/2018 05:56 AM, Obenchain, Valerie wrote:
This transition will start at 9am EST today. We'll post back when it's done.

Valerie


On 04/17/2018 10:27 AM, Obenchain, Valerie wrote:

Hi developers,

Tomorrow we are bringing a web app online to help with the management of SSH 
keys. The app will replace the Google Sheet currently used to add keys. Through 
the web interface you'll be able to add keys and change your email or github 
username. There is also an option to see what packages you have access to.

Using the app is not a requirement. It's intended to help package authors get 
setup with keys and access to their package in the Bioconductor git repository. 
Those of you already set up with keys and access may never need to use it.

Tomorrow, April 18, we'll have downtime from 9-11am EST while we take down the 
Google Sheet and bring up the app.

Thanks.

Valerie and Nitesh


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]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto:Bioc-devel@

Re: [Bioc-devel] Package download when using functions from affy and oligo

2018-05-04 Thread Obenchain, Valerie

Joris,

Sorry I don't have much to offer here. I've cc'd the authors of oligo and affy 
who may have some insight.

Valerie


On 05/02/2018 11:35 AM, Joris Meys wrote:

Dear,

I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downloading another
package and end with either R crashing or a warning that -after
installation succeeded- the package is not available. After which using
some functions of both packages still crash R.

The warning I get when trying oligo::read.celfiles() on a single CEL file
right after installing it about the pd.hugene.1.0.st.v1 package. The even
more annoying thing is that on my machine it insists on building from
source, whereas on another Windows machine without Rtools, it downloads a
binary.

Reason it frustrates the heck out of me, is that both affy and oligo
crashed the R session in different ways. During installation of a package,
during use of a function, and at different points when comparing my machine
with the one of our students. The culprit seems to be in one of the
underlying packages, but I wasn't even able to detect which package is the
culprit, let alone which function crashes everything.

Is there a way around this so I can ensure that at least I have the same
setup as they have and I can try to come up with a reproducible example to
report this critical bug?

Thank you in advance
Joris





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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] errors on Windows 3.7 builds

For reasons unknown, the stringi package took a long time to compile on tokay2 
yesterday or possibly it may have hung. We have a limit of 40 minutes for 
installation (to avoid infinite timeouts) after which the process gets killed. 
When the installation of stringi was killed, a lock file was left behind and 
the package was left in a broken state. stringi has been re-installed on tokay2 
and things look ok now.

There was a new source tarball for stringi on May 2 and this may be part of the 
problem.

Valerie



On 05/03/2018 10:21 AM, Obenchain, Valerie wrote:

Please ignore the errors on the3.7  Windows builds today. Something obviously 
went wrong as there are 933 build failures. We're looking into it.

Valerie


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]]

___
Bioc-devel@r-project.org<mailto: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.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] errors on Windows 3.7 builds

Please ignore the errors on the3.7  Windows builds today. Something obviously 
went wrong as there are 933 build failures. We're looking into it.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] no Mac in devel build report today

We had a reachability problem with the devel Mac builder yesterday. We're 
getting things sorted out and merida1 should be back in the builds tomorrow.

Valerie


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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Email no longer active

OK you should be good to go. Try activating your account with your new email 
and you should see the SSH key we have on file for you.

Valerie



On 05/03/2018 06:37 AM, Maria Keays wrote:
Hi Valerie,

Thanks very much. My GitHub username is mkeays and the email is 
maria.ke...@gmail.com<mailto:maria.ke...@gmail.com> .

Thanks!

Maria



On Thu, 3 May 2018 at 14:10, Obenchain, Valerie 
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> 
wrote:
Hi Maria,

I can help you with this. I need the email you want the account under and your 
github username.

Valerie




On 05/03/2018 04:20 AM, Maria Keays wrote:

Hello,

I�m not sure if this is the right place for this so apologies if not, but:
my Bioconductor developer account is associated with an email address which
is no longer active (mke...@ebi.ac.uk<mailto:mke...@ebi.ac.uk>), and what with 
one thing and another
I didn�t manage to change it before the account was deactivated. I�ve tried
to log in here:
https://git.bioconductor.org/BiocCredentials/account_activation/

  � but I
get a message saying that an email has been sent to the deactivated
address. Is it possible to switch the email address to this one instead?

Thanks,
Maria

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org<mailto: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, 
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]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Email no longer active