date:20170911

Hi Nima,

The build machines are NOT trying to use version 1.0.0 of the
biotmleData package. They are using the version that is currently
publicly available here:

https://bioconductor.org/packages/3.6/data/experiment/html/biotmleData.html

It's version 1.1.0. The build machines installed it with just
biocLite("biotmleData"), like any user would. FWIW you can see all
the packages that are installed on the build machines by clicking
on the numbers in the "Installed pkgs" columns in the little table
at the top of the build report:

  https://bioconductor.org/checkResults/3.6/bioc-LATEST/

The problem is that this version of biotmleData does not have the
rnaseqtmleOut dataset. This is easy to verify:

> library(BiocInstaller)
Bioconductor version 3.6 (BiocInstaller 1.27.4), ?biocLite for help

> biocLite("biotmleData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.4), R 3.4.0 Patched (2017-04-26
  r72630).
Installing package(s) 'biotmleData'
trying URL 
'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/biotmleData_1.1.0.tar.gz'

Content type 'application/x-gzip' length 30240432 bytes (28.8 MB)
==
downloaded 28.8 MB

* installing *source* package 'biotmleData' ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (biotmleData)

The downloaded source packages are in
'/tmp/Rtmp6y3T4h/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

> library(biotmleData)

> data(rnaseqtmleOut)
Warning message:
In data(rnaseqtmleOut) : data set 'rnaseqtmleOut' not found

Even though the dataset is now included in the *git source* of the
package, which is also at version 1.1.0, it seems that at the
time biotmleData 1.1.0 propagated to our public repo, it didn't
have it.

So all you need to do is bump biotmleData's version to 1.1.1.

Travis's Ubuntu, Appveyor, and your local machine (macOS) probably
use the git version of biotmleData so that's why biotmle builds there.

Having different versions of a package around that have the same version
number is always a source of *a lot* of confusion!

Hope this helps,
H.

On 09/10/2017 08:30 PM, Nima Hejazi wrote:

Hi Hervé,

Thanks for your note. I do indeed believe that the error was initially
due to the build trying to use an older version of the data package
biotmleData (1.0.0, as you stated). After the update of biotmleData (to
1.1.0; aside: I realize this is rather bad practice, but I don't intend
to update the data package frequently at all -- hopefully never after
the next release), the package biotmle ought to be building properly. In
fact, as far as I can tell there might some kind of issue related to
caching in the Bioconductor build because

1) biocLite is installing v.1.1.0 of biotmleData, which is the version
required to properly build biotmle
2) independent builds are passing on all systems: Travis's Ubuntu,
Appveyor, and my local machine (macOS)
3) I bumped the version of biotmle last week but even the most recent
build (as of 09 September) is still failing, due to trying to use
v.1.0.0 of biotmleData

Is there something more I should be doing to fix the build? Thanks in
advance for your help.

Warm Regards,
— Nima Hejazi

--
Nima Hejazi
Doctoral Student
Division of Biostatistics
University of California, Berkeley
van der Laan Group

| Hubbard Group

http://www.stat.berkeley.edu/~nhejazi

http://nimahejazi.org

 |
Nima's blog

On Wed, Sep 6, 2017 at 9:15 AM, Hervé Pagès > wrote:

Hi Nima,

Normally you have to allow 24 hours

Re: [Bioc-devel] Package DMCHMM is not installed

2017-09-11 Thread Leonardo Collado Torres

It's only available on bioc-devel, not bioc-release. See
http://bioconductor.org/packages/devel/bioc/html/DMCHMM.html and
http://bioconductor.org/developers/how-to/useDevel/

On Mon, Sep 11, 2017 at 7:17 PM, Farhad Shokoohi  wrote:
> Hello,
>
> I tried to install my package on a machine and it gives the following warning 
> which does not make sense.
>
>> source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
>> biocLite("DMCHMM")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
> Installing package(s) ‘DMCHMM’
> Old packages: 'limma'
> Update all/some/none? [a/s/n]:
> n
> Warning message:
> package ‘DMCHMM’ is not available (for R version 3.4.1)
>>
>
>
> ———
> Farhad Shokoohi
> Assistant Professor
> Department of Mathematics & Statistics
> Concordia University
> S-LB 915-1, J.W. McConnell Building,
> 1455 De Maisonneuve W.,
> Montreal, Quebec, Canada, H3G 1M8
> Office: (514) 848-2424 ext. 4017
> Fax: (514) 848-2831
> shoko...@icloud.com
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Duplicate commit error on and off

2017-09-11 Thread Thomas Girke

The following allowed me to eliminate the duplicated commits in one step
via git merge --squash and then successfully push back to the bioc-git
server. After this I was able to switch to the swap branch approach to
avoid similar problems in the future.

Example here for master branch:

git checkout master
git pull upstream master # just in case
git reset --hard  # Reset the current branch to the commit
right before dups started
git merge --squash HEAD@{1} # Squashes duplicated commits from chosen
 to HEAD@{1} (state right before previous reset step)
git commit -am "some_message" # Commit squashed changes
git push upstream master # Push to bioc-git server

I am not sure if the above is the best solution but I thought I report it
here in case others experience similar problems. BTW: in my case the
duplicates were all generated in the upstream merge (step 6) of the
instructions here: https://goo.gl/wWVEeT. None of the parent branches (on
github or bioc) used in this merge step contained duplicated commits at
least as far as I have checked so far. Perhaps some of this relates back to
the git svn/rebase steps we used under the old git mirror?

Just in case, the following command is very helpful to identify duplicate
commits based on patch-id. Commits with identical patch-ids are very likely
to have identical content.

git rev-list master | xargs -r -L1 git diff-tree -m -p | git patch-id
| sort | uniq -w40 -D | cut -c42-80  | xargs -r git log --no-walk
--pretty=format:"%h %ad %an (%cn) %s" --date-order --date=iso

After duplicated commit pairs have been identified, one can check with diff
or vimdiff whether their content is identical:

git --no-pager show  > zzz1
git --no-pager show  > zzz2
vimdiff zzz1 zzz2

Thomas

On Fri, Sep 8, 2017 at 9:16 PM Thomas Girke  wrote:

Since our duplicate commits slipped through to Bioc (probably during
> pre-receive hook downtime), the only option I see, to actually get to the
> actual swap branch step, is to first fix the current duplicate problem in
> the upstream Bioc remote by resetting the affected branches back to the
> commit right before the duplicates occurred. Manual fixes seem unrealistic
> given the number of instances. However, when following (see below) the
> reset instructions here (https://goo.gl/SeNCPk) I am getting a “hook
> declined” error. Not sure how to get beyond this? Or are there alternative
> solutions I should try?
>
> Interestingly, according to the instructions on the top of the Bioc
> instructions of this very topic (https://goo.gl/SeNCPk) I am supposedly
> now someone who "went nuclear". Wasn't this term introduced (or perhaps
> just abused) by the last presidential campaign? How can it get anymore
> frustrating than being affiliated with this outcome :).
>
> Thomas
>
> git reset --hard e3a8d2122a65305c478276e538faace277ea9ed6
> git push -f origin master
> git push -f upstream master
>
> Total 0 (delta 0), reused 0 (delta 0)
> remote: FATAL: + refs/heads/master packages/ChemmineR t.girke DENIED by 
> fallthru
> remote: error: hook declined to update refs/heads/master
> To g...@git.bioconductor.org:packages/ChemmineR.git
>  ! [remote rejected] master -> master (hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/ChemmineR.git'
>
> 
>
> On Fri, Sep 8, 2017 at 12:21 PM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
>
>> Hi Thomas,
>>
>> Thanks for understanding. Swapping branches is the best solution I could
>> come up with, and would advice you to go ahead with that.
>>
>> The catching of false positives was a couple of bugs in our pre-receive
>> hooks code, which we have since fixed. I’m glad to have made the shift to
>> Git, and hope the community enjoys it.
>>
>> Best Regards,
>>
>> Nitesh
>>
>>
>> > On Sep 8, 2017, at 2:59 PM, Thomas Girke  wrote:
>> >
>> > Dear Martin and Nitesh,
>> >
>> > If swapping branches is the recommended solution then I will do so. The
>> on/off situation with the duplicate commit error misled me to believe it is
>> a temporary problem on the Bioc end. I am sorry for the extra noise my
>> message may have caused.
>> >
>> > As a group that maintains GitHub versions of all our Bioc packages, we
>> are extremely excited about the recent git transition. Thanks Nitesh (and
>> your colleagues) for doing all of this. It must have been a massive effort
>> for so many packages.
>> >
>> > Best,
>> >
>> > Thomas
>> >
>> >
>> > On Fri, Sep 8, 2017 at 7:11 AM Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>> > On 09/08/2017 09:34 AM, Turaga, Nitesh wrote:
>> > > Hi Thomas,
>> > >
>> > > So, you do actually have a “duplicate” commit and you should NOT be
>> pushing this to the bioc-git server. Notice that the body of both those
>> commits is the same.
>> > >
>> > > If you want to check the rest of your commit history, please try `git
>> log - -oneline` . And you will see that you will have multiple duplicate
>> commits. This

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Kasper Daniel Hansen

I see how an eSet maps to a SummarizedExperiment; one can look at the
assays in the object.  I agree with Levi/Herve that this is the natural
(correct) choice.  It is less clear how you get the ranges for a
RangedSummarizedExperiment without making assumptions.

On Mon, Sep 11, 2017 at 8:09 PM, Hervé Pagès  wrote:

> I don't know the reasons behind this choice, I didn't implement
> these methods. It would make sense to have these coercions defined
> for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
> signatures if they only access the eSet part of the object.
> I'll look into this.
>
> H.
>
> On 09/11/2017 04:50 PM, Levi Waldron wrote:
>
>> Thanks Ludwig and Kasper. This old presentation from Martin also helped me
>> a lot:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bio
>> conductor.org_packages_devel_bioc_vignettes_Biobase_inst_
>> doc_BiobaseDevelopment.pdf=DwIGaQ=eRAMFD45gAfqt84VtBcfh
>> Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s44znXbg9V
>> OxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=C-oKupgUQZm6PA2e1IWSKKQq
>> PsQIy4uTGUg_CSvBeq4=
>>
>> But I still wonder, why provide the coercion for ExpressionSet, if
>> providing it for eSet would work not only for ExpressionSet but for
>> everything else derived from eSet? The coercion function seems to work
>> fine
>> on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from)
>> )
>>   seems to work regardless of the storage mode}:
>>
>> library(Biobase)> library(SummarizedExperiment)>
>>> example("NChannelSet-class", echo=FALSE)> class(obj)[1] "NChannelSet"
>>>
>> attr(,"package")
>> [1] "Biobase"> is(obj, "eSet")[1] TRUE
>>
>> storageMode(obj)[1] "lockedEnvironment"
>>>
>>
>> makeSummarizedExperimentFromExpressionSet(obj) class:
>>>
>> RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData
>> annotation
>> protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
>> colnames(3): A B C colData names(3): ChannelRData ChannelGData
>> ChannelRAndG
>>
>> as(obj, "RangedSummarizedExperiment")
>>>
>>
>> Error in as(obj, "RangedSummarizedExperiment") :
>>no method or default for coercing “NChannelSet” to
>> “RangedSummarizedExperiment”
>>
>>
>>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt
>> 84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s4
>> 4znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=qKI2hqP0ltgK5_
>> LBtVFG6Va-8XAUuGwbXp9eKUfulXs=
>>
>>
> --
> Hervé Pagès
>
> 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
>

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment


I don't know the reasons behind this choice, I didn't implement
these methods. It would make sense to have these coercions defined
for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
signatures if they only access the eSet part of the object.
I'll look into this.

H.

On 09/11/2017 04:50 PM, Levi Waldron wrote:

Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_devel_bioc_vignettes_Biobase_inst_doc_BiobaseDevelopment.pdf=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=s44znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg=C-oKupgUQZm6PA2e1IWSKKQqPsQIy4uTGUg_CSvBeq4=

But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for ExpressionSet but for
everything else derived from eSet? The coercion function seems to work fine
on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
  seems to work regardless of the storage mode}:


library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", 
echo=FALSE)> class(obj)[1] "NChannelSet"

attr(,"package")
[1] "Biobase"> is(obj, "eSet")[1] TRUE


storageMode(obj)[1] "lockedEnvironment"



makeSummarizedExperimentFromExpressionSet(obj) class:

RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG


as(obj, "RangedSummarizedExperiment")


Error in as(obj, "RangedSummarizedExperiment") :
   no method or default for coercing “NChannelSet” to
“RangedSummarizedExperiment”





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--
Hervé Pagès

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

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf

But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for ExpressionSet but for
everything else derived from eSet? The coercion function seems to work fine
on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
 seems to work regardless of the storage mode}:

> library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", 
> echo=FALSE)> class(obj)[1] "NChannelSet"
attr(,"package")
[1] "Biobase"> is(obj, "eSet")[1] TRUE

> storageMode(obj)[1] "lockedEnvironment"

> makeSummarizedExperimentFromExpressionSet(obj) class:
RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG

> as(obj, "RangedSummarizedExperiment")

Error in as(obj, "RangedSummarizedExperiment") :
  no method or default for coercing “NChannelSet” to
“RangedSummarizedExperiment”

>

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[Bioc-devel] Package DMCHMM is not installed

2017-09-11 Thread Farhad Shokoohi

Hello,

I tried to install my package on a machine and it gives the following warning 
which does not make sense. 

> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite("DMCHMM")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘DMCHMM’
Old packages: 'limma'
Update all/some/none? [a/s/n]: 
n
Warning message:
package ‘DMCHMM’ is not available (for R version 3.4.1) 
> 


———
Farhad Shokoohi
Assistant Professor 
Department of Mathematics & Statistics 
Concordia University
S-LB 915-1, J.W. McConnell Building,
1455 De Maisonneuve W.,
Montreal, Quebec, Canada, H3G 1M8
Office: (514) 848-2424 ext. 4017
Fax: (514) 848-2831
shoko...@icloud.com


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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Kasper Daniel Hansen

An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay.
That makes no sense for example for methylation where we have (say)
Green/Red assays or Meth/Unmeth assays (or transformations of these).

Best,
Kasper

On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

> Concerning 1) Why have some developers chosen to extend eSet instead of
> ExpressionSet:
>
> As far as I understand it, ExpressionSet was thought to exclusively
> represent a microarray experiment (MIAME = Minimum Information About a
> Microarray Experiment).
>
> Thus, back in the days when more and more people started using RNA-seq and
> there was no SummarizedExperiment, developers extended eSet with e.g.
> assayData slots called `counts` instead of `exprs` to represent RNA-seq
> data.
>
>
> > On Mon, Sep 11, 2017 at 2:02 PM, HervÃ© PagÃ¨s 
> > wrote:
> >
> >> Hi,
> >>
> >> I added coercion from ExpressionSet to SummarizedExperiment in
> >> SummarizedExperiment 1.7.6.
> >>
> >
> > Thank you HervÃ©!
> >
> >
> >> The current behavior of the SummarizedExperiment() constructor
> >> when called on a ExpressionSet object doesn't make much sense to
> >> me. I'd rather have it consistent with what the coercion does.
> >> Will fix it.
> >>
> >
> > Thank you, again.
> >
> > A couple more questions while I'm at it, that may expose the limitations
> > in
> > my understanding of inheritance and project history... 1) Why have some
> > developers chosen to extend eSet instead of ExpressionSet (definition
> >  536f137165ca08b3be22819e51e055b3e7afe86d/R/DataClasses.R#L166>),
> > and 2) why are these coercion methods developed for ExpressionSet rather
> > than eSet? Wouldn't an eSet coercion method be preferable because it
> would
> > cover ExpressionSet as well as all the classes that extend eSet?
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Dr. Ludwig Geistlinger
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Ludwig Geistlinger

Concerning 1) Why have some developers chosen to extend eSet instead of
ExpressionSet:

As far as I understand it, ExpressionSet was thought to exclusively
represent a microarray experiment (MIAME = Minimum Information About a
Microarray Experiment).

Thus, back in the days when more and more people started using RNA-seq and
there was no SummarizedExperiment, developers extended eSet with e.g.
assayData slots called `counts` instead of `exprs` to represent RNA-seq
data.


> On Mon, Sep 11, 2017 at 2:02 PM, HervÃ© PagÃ¨s 
> wrote:
>
>> Hi,
>>
>> I added coercion from ExpressionSet to SummarizedExperiment in
>> SummarizedExperiment 1.7.6.
>>
>
> Thank you HervÃ©!
>
>
>> The current behavior of the SummarizedExperiment() constructor
>> when called on a ExpressionSet object doesn't make much sense to
>> me. I'd rather have it consistent with what the coercion does.
>> Will fix it.
>>
>
> Thank you, again.
>
> A couple more questions while I'm at it, that may expose the limitations
> in
> my understanding of inheritance and project history... 1) Why have some
> developers chosen to extend eSet instead of ExpressionSet (definition
> ),
> and 2) why are these coercion methods developed for ExpressionSet rather
> than eSet? Wouldn't an eSet coercion method be preferable because it would
> cover ExpressionSet as well as all the classes that extend eSet?
>
>   [[alternative HTML version deleted]]
>
> ___
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-- 
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès  wrote:

> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>

Thank you Hervé!

> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make much sense to
> me. I'd rather have it consistent with what the coercion does.
> Will fix it.
>

Thank you, again.

A couple more questions while I'm at it, that may expose the limitations in
my understanding of inheritance and project history... 1) Why have some
developers chosen to extend eSet instead of ExpressionSet (definition
),
and 2) why are these coercion methods developed for ExpressionSet rather
than eSet? Wouldn't an eSet coercion method be preferable because it would
cover ExpressionSet as well as all the classes that extend eSet?

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Re: [Bioc-devel] updating Bioconductor package that is already on Github

2017-09-11 Thread Simina Boca

Thank you again Sean and Lori! I am now past that initial stage. I now have
to resolve merge conflicts, primarily in the DESCRIPTION file. When
following the instructions here http://bioconductor.org/
developers/how-to/git/resolve-conflicts/ however, I ended up getting the
error below:

~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB 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.

Thank you so much!

Best,
Simina


On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca  wrote:

> Thank you so much Sean and Lori! For some reason I thought the ssh key
> part was only relevant if the package was submitted via svn, which is why i
> had overlooked those instructions initially.
>
> Cheers,
> Simina
>
> On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>> Have you submitted your ssh key
>>
>>
>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
>> o4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>
>> 
>> git / svn transition: ssh keys
>> 
>> docs.google.com
>> Use this form to link your existing svn credentials with access
>> permissions to the new Bioconductor git repository. To do this, we need an
>> ssh public key. You might have added these to github, see
>> https://github.com/your-github-id.keys. Alternatively, you may provide
>> the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To
>> generate ssh key pairs, see https://help.github.com/articl
>> es/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> --
>> *From:* Bioc-devel  on behalf of
>> Simina Boca 
>> *Sent:* Tuesday, September 5, 2017 11:40:37 PM
>> *To:* bioc-devel@r-project.org
>> *Subject:* [Bioc-devel] updating Bioconductor package that is already on
>> Github
>>
>> Dear all,
>>
>> I hope this isn't a duplicate of another question. Here goes:
>>
>> - I would like to update my swfdr package, which is already on
>> Bioconductor. It is also on Github and my submission process was via
>> opening an issue at https://github.com/Bioconducto
>> r/Contributions/issues/213
>>
>> - At this point there are some slight differences between the Github and
>> Bioconductor versions, for example the Bioconductor version number got
>> automatically bumped to 1.0.0 upon acceptance
>>
>> - I would like to first synchronize what is on Github to have the current
>> version that is on Bioconductor before updating and also include any
>> updates in the next version of the package on Bioconductor
>>
>> - I did "git remote add upstream g...@git.bioconductor.org:packa
>> ges/swfdr.git"
>> as per some of the instructions for developers, so that now I have:
>> ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git remote -v
>> origin  https://github.com/leekgroup/swfdr.git (fetch)
>> origin  https://github.com/leekgroup/swfdr.git (push)
>> upstreamg...@git.bioconductor.org:packages/swfdr.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/swfdr.git (push)
>>
>> *but* when I try to fetch upstream content, via:
>> git fetch upstream
>>
>> I get an error:
>> ~\Documents\GitHub\swfdr [master ≡ +0 ~0 -1 !]> git fetch upstream
>> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
>> to
>> the list of known hosts.
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights
>>
>> Am I missing something here? Alternatively, I suppose I can just make the
>> changes I want and simply open another issue, although it would be nice to
>> have an easy to sync it with what is already on Bioconductor.
>>
>> Thank you in advance for your help and I apologize if I missed anything
>> obvious!
>>
>> Cheers,
>> Simina
>>
>> --
>> Simina M. Boca
>> Assistant Professor
>> Innovation Center for Biomedical Informatics  (ICBI)
>> Department of Oncology | Georgetown University Medical Center
>> Department of Biostatistics, Bioinformatics and Biomathematics |
>> Georgetown
>> University Medical Center
>> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>> Center
>>
>> 2115 Wisconsin Ave NW, Suite 110
>> Washington, DC 20007
>> Phone: (202) 687-1545
>> Fax: (202)

Re: [Bioc-devel] Upstream permission denied

Hi Nitesh,

Many thanks, I will check it in a couple of days.

Cheers,
Vlad

On Mon, 11 Sep 2017, 19:01 Turaga, Nitesh 
wrote:

> Hi
>
> Your key will be added in the next run of our script. You can change your
> GitHub keys, our script will take in the new one, and you don’t have to
> resubmit on the google-form.
>
> It is run manually at the moment at noon EST everyday.
>
> Nitesh
> > On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
> >
> > Thanks Simina,
> >
> > I think I've done all the steps described there before and was able to
> push
> > to upstream. I can't do it anymore and try to figure out why.
> >
> > Could anyone else please help?
> >
> > Cheers,
> > Vlad
> >
> > On Mon, 11 Sep 2017, 18:03 Simina Boca  wrote:
> >
> >> Hi, Simina.
> >>
> >> Take a look at the FAQ, #3, here:
> >>
> >> http://bioconductor.org/developers/how-to/git/faq/
> >>
> >> Have you submitted an SSH key somehow?
> >>
> >>
> >>>
> >>> Am I missing something here? Alternatively, I suppose I can just make
> the
> >>> changes I want and simply open another issue, although it would be
> nice to
> >>> have an easy to sync it with what is already on Bioconductor.
> >>>
> >>
> >> When everything is working, you will "own" the bioconductor git repo, so
> >> working it will be roughly equivalent to working with github. Opening an
> >> issue on the package submission repo will not get you what you want and
> is
> >> only for new packages.
> >>
> >> Sean
> >>
> >>
> >> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
> >> vladimir.yu.kise...@gmail.com> wrote:
> >>
> >>> Hi Simina,
> >>>
> >>> Thanks for your quick reply, but it looks like to forgot to paste your
> >>> response from Sean (at least I couldn't find it in your email).
> >>>
> >>> Cheers,
> >>> Vlad
> >>>
> >>> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca 
> >>> wrote:
> >>>
>  Hi Vladimir,
>  This seems like the same error I was getting. Here is the helpful
> advice
>  I got from Sean:
> 
>  Hi, Simina.
> 
>  On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>  vladimir.yu.kise...@gmail.com> wrote:
> 
> > Hello,
> >
> > I am trying to push a new version of my package to
> git.bioconductor.org.
> > I
> > was able to do that in the past. But I've recently changed my public
> key
> > and not sure whether this causes a problem. However, I can see my new
> > public key here - https://github.com/wikiselev.keys - and it is the
> > first
> > one in the list.
> >
> > When I look at the remote I can see git.bioconductor.org there but
> > when I
> > try to push to upstream I get an error:
> >
> > git remote -v
> > origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> > origin  g...@github.com:hemberg-lab/scmap.git (push)
> > upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
> > upstreamg...@git.bioconductor.org:packages/scmap.git (push)
> >
> > git push origin master
> > Everything up-to-date
> >
> > git push upstream master
> > Permission denied (publickey).
> > fatal: Could not read from remote repository.
> > Please make sure you have the correct access rights
> > and the repository exists.
> >
> > Could anyone please help?
> > Many thanks in advance,
> > Kind regards,
> > Vladimir
> >
>  --
> > http://genat.uk
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> 
> 
> 
>  --
>  Simina M. Boca
>  Assistant Professor
>  Innovation Center for Biomedical Informatics  (ICBI)
>  Department of Oncology | Georgetown University Medical Center
>  Department of Biostatistics, Bioinformatics and Biomathematics |
>  Georgetown University Medical Center
>  Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>  Center
> 
>  2115 Wisconsin Ave NW, Suite 110
>  <
> https://maps.google.com/?q=2115+Wisconsin+Ave+NW,+Suite+110Washington,+DC+20007=gmail=g
> >
>  Washington, DC 20007
>  <
> https://maps.google.com/?q=2115+Wisconsin+Ave+NW,+Suite+110Washington,+DC+20007=gmail=g
> >
>  Phone: (202) 687-1545
>  Fax: (202) 687-5011
>  http://icbi.georgetown.edu/boca
> 
> 
>  On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>  vladimir.yu.kise...@gmail.com> wrote:
> 
> > Hello,
> >
> > I am trying to push a new version of my package to
> git.bioconductor.org.
> > I
> > was able to do that in the past. But I've recently changed my public
> key
> > and not sure whether this causes a problem. However, I can see my new
> > public key here -

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi,

I added coercion from ExpressionSet to SummarizedExperiment in
SummarizedExperiment 1.7.6.

The current behavior of the SummarizedExperiment() constructor
when called on a ExpressionSet object doesn't make much sense to
me. I'd rather have it consistent with what the coercion does.
Will fix it.

Cheers,
H.

On 09/11/2017 09:58 AM, Michael Lawrence wrote:

It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.

Michael

On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
wrote:

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.

SummarizedExperiment(mouseData)

puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not accordingly
transferred to colData and rowData.

Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.

While I can understand that this is by design of `SummarizedExperiment`, I
really wonder whether there are use cases where somebody would like to put
an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
would like to coerce it that way.

Furthermore, if you would indeed like to have several `ExpressionSet`s in
a `SummarizedExperiment`, haven't you already arrived at a scenario where
use of `MultiAssayExperiment` is indicated?

I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

[[alternative HTML version deleted]]

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--
Hervé Pagès

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

___
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Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Turaga, Nitesh

Hi

Your key will be added in the next run of our script. You can change your 
GitHub keys, our script will take in the new one, and you don’t have to 
resubmit on the google-form.

It is run manually at the moment at noon EST everyday.

Nitesh 
> On Sep 11, 2017, at 1:12 PM, Vladimir Kiselev  
> wrote:
> 
> Thanks Simina,
> 
> I think I've done all the steps described there before and was able to push
> to upstream. I can't do it anymore and try to figure out why.
> 
> Could anyone else please help?
> 
> Cheers,
> Vlad
> 
> On Mon, 11 Sep 2017, 18:03 Simina Boca  wrote:
> 
>> Hi, Simina.
>> 
>> Take a look at the FAQ, #3, here:
>> 
>> http://bioconductor.org/developers/how-to/git/faq/
>> 
>> Have you submitted an SSH key somehow?
>> 
>> 
>>> 
>>> Am I missing something here? Alternatively, I suppose I can just make the
>>> changes I want and simply open another issue, although it would be nice to
>>> have an easy to sync it with what is already on Bioconductor.
>>> 
>> 
>> When everything is working, you will "own" the bioconductor git repo, so
>> working it will be roughly equivalent to working with github. Opening an
>> issue on the package submission repo will not get you what you want and is
>> only for new packages.
>> 
>> Sean
>> 
>> 
>> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
>> vladimir.yu.kise...@gmail.com> wrote:
>> 
>>> Hi Simina,
>>> 
>>> Thanks for your quick reply, but it looks like to forgot to paste your
>>> response from Sean (at least I couldn't find it in your email).
>>> 
>>> Cheers,
>>> Vlad
>>> 
>>> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca 
>>> wrote:
>>> 
 Hi Vladimir,
 This seems like the same error I was getting. Here is the helpful advice
 I got from Sean:
 
 Hi, Simina.
 
 On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
 vladimir.yu.kise...@gmail.com> wrote:
 
> Hello,
> 
> I am trying to push a new version of my package to git.bioconductor.org.
> I
> was able to do that in the past. But I've recently changed my public key
> and not sure whether this causes a problem. However, I can see my new
> public key here - https://github.com/wikiselev.keys - and it is the
> first
> one in the list.
> 
> When I look at the remote I can see git.bioconductor.org there but
> when I
> try to push to upstream I get an error:
> 
> git remote -v
> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> origin  g...@github.com:hemberg-lab/scmap.git (push)
> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
> 
> git push origin master
> Everything up-to-date
> 
> git push upstream master
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> Could anyone please help?
> Many thanks in advance,
> Kind regards,
> Vladimir
> 
 --
> http://genat.uk
> 
>[[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
 
 
 
 --
 Simina M. Boca
 Assistant Professor
 Innovation Center for Biomedical Informatics  (ICBI)
 Department of Oncology | Georgetown University Medical Center
 Department of Biostatistics, Bioinformatics and Biomathematics |
 Georgetown University Medical Center
 Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
 Center
 
 2115 Wisconsin Ave NW, Suite 110
 
 Washington, DC 20007
 
 Phone: (202) 687-1545
 Fax: (202) 687-5011
 http://icbi.georgetown.edu/boca
 
 
 On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
 vladimir.yu.kise...@gmail.com> wrote:
 
> Hello,
> 
> I am trying to push a new version of my package to git.bioconductor.org.
> I
> was able to do that in the past. But I've recently changed my public key
> and not sure whether this causes a problem. However, I can see my new
> public key here - https://github.com/wikiselev.keys - and it is the
> first
> one in the list.
> 
> When I look at the remote I can see git.bioconductor.org there but
> when I
> try to push to upstream I get an error:
> 
> git remote -v
> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> origin  g...@github.com:hemberg-lab/scmap.git (push)
> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)

[Bioc-devel] clarifying initialization for BiocCheck

2017-09-11 Thread Vincent Carey

"Consider clarifying how 6 object(s) are initialized"

Suppose an object is initialized via data() ... how can I make

this note go away?  I don't understand how to clarify the situation.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Upstream permission denied

Thanks Simina,

I think I've done all the steps described there before and was able to push
to upstream. I can't do it anymore and try to figure out why.

Could anyone else please help?

Cheers,
Vlad

On Mon, 11 Sep 2017, 18:03 Simina Boca  wrote:

> Hi, Simina.
>
> Take a look at the FAQ, #3, here:
>
> http://bioconductor.org/developers/how-to/git/faq/
>
> Have you submitted an SSH key somehow?
>
>
>>
>> Am I missing something here? Alternatively, I suppose I can just make the
>> changes I want and simply open another issue, although it would be nice to
>> have an easy to sync it with what is already on Bioconductor.
>>
>
> When everything is working, you will "own" the bioconductor git repo, so
> working it will be roughly equivalent to working with github. Opening an
> issue on the package submission repo will not get you what you want and is
> only for new packages.
>
> Sean
>
>
> On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hi Simina,
>>
>> Thanks for your quick reply, but it looks like to forgot to paste your
>> response from Sean (at least I couldn't find it in your email).
>>
>> Cheers,
>> Vlad
>>
>> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca 
>> wrote:
>>
>>> Hi Vladimir,
>>> This seems like the same error I was getting. Here is the helpful advice
>>> I got from Sean:
>>>
>>> Hi, Simina.
>>>
>>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>>> vladimir.yu.kise...@gmail.com> wrote:
>>>
 Hello,

 I am trying to push a new version of my package to git.bioconductor.org.
 I
 was able to do that in the past. But I've recently changed my public key
 and not sure whether this causes a problem. However, I can see my new
 public key here - https://github.com/wikiselev.keys - and it is the
 first
 one in the list.

 When I look at the remote I can see git.bioconductor.org there but
 when I
 try to push to upstream I get an error:

 git remote -v
 origin  g...@github.com:hemberg-lab/scmap.git (fetch)
 origin  g...@github.com:hemberg-lab/scmap.git (push)
 upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
 upstreamg...@git.bioconductor.org:packages/scmap.git (push)

 git push origin master
 Everything up-to-date

 git push upstream master
 Permission denied (publickey).
 fatal: Could not read from remote repository.
 Please make sure you have the correct access rights
 and the repository exists.

 Could anyone please help?
 Many thanks in advance,
 Kind regards,
 Vladimir

>>> --
 http://genat.uk

 [[alternative HTML version deleted]]

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

>>>
>>>
>>>
>>> --
>>> Simina M. Boca
>>> Assistant Professor
>>> Innovation Center for Biomedical Informatics  (ICBI)
>>> Department of Oncology | Georgetown University Medical Center
>>> Department of Biostatistics, Bioinformatics and Biomathematics |
>>> Georgetown University Medical Center
>>> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>>> Center
>>>
>>> 2115 Wisconsin Ave NW, Suite 110
>>> 
>>> Washington, DC 20007
>>> 
>>> Phone: (202) 687-1545
>>> Fax: (202) 687-5011
>>> http://icbi.georgetown.edu/boca
>>>
>>>
>>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>>> vladimir.yu.kise...@gmail.com> wrote:
>>>
 Hello,

 I am trying to push a new version of my package to git.bioconductor.org.
 I
 was able to do that in the past. But I've recently changed my public key
 and not sure whether this causes a problem. However, I can see my new
 public key here - https://github.com/wikiselev.keys - and it is the
 first
 one in the list.

 When I look at the remote I can see git.bioconductor.org there but
 when I
 try to push to upstream I get an error:

 git remote -v
 origin  g...@github.com:hemberg-lab/scmap.git (fetch)
 origin  g...@github.com:hemberg-lab/scmap.git (push)
 upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
 upstreamg...@git.bioconductor.org:packages/scmap.git (push)

 git push origin master
 Everything up-to-date

 git push upstream master
 Permission denied (publickey).
 fatal: Could not read from remote repository.
 Please make sure you have the correct access rights
 and the repository exists.

 Could anyone please help?
 Many thanks in advance,
 Kind regards,
 Vladimir

>>> --
 http://genat.uk

 [[alternative HTML version deleted]]

Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Simina Boca

Hi, Simina.

Take a look at the FAQ, #3, here:

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

Have you submitted an SSH key somehow?


>
> Am I missing something here? Alternatively, I suppose I can just make the
> changes I want and simply open another issue, although it would be nice to
> have an easy to sync it with what is already on Bioconductor.
>

When everything is working, you will "own" the bioconductor git repo, so
working it will be roughly equivalent to working with github. Opening an
issue on the package submission repo will not get you what you want and is
only for new packages.

Sean


On Mon, Sep 11, 2017 at 1:01 PM, Vladimir Kiselev <
vladimir.yu.kise...@gmail.com> wrote:

> Hi Simina,
>
> Thanks for your quick reply, but it looks like to forgot to paste your
> response from Sean (at least I couldn't find it in your email).
>
> Cheers,
> Vlad
>
> On Mon, Sep 11, 2017 at 5:58 PM Simina Boca  wrote:
>
>> Hi Vladimir,
>> This seems like the same error I was getting. Here is the helpful advice
>> I got from Sean:
>>
>> Hi, Simina.
>>
>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>> vladimir.yu.kise...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I am trying to push a new version of my package to git.bioconductor.org.
>>> I
>>> was able to do that in the past. But I've recently changed my public key
>>> and not sure whether this causes a problem. However, I can see my new
>>> public key here - https://github.com/wikiselev.keys - and it is the
>>> first
>>> one in the list.
>>>
>>> When I look at the remote I can see git.bioconductor.org there but when
>>> I
>>> try to push to upstream I get an error:
>>>
>>> git remote -v
>>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>>
>>> git push origin master
>>> Everything up-to-date
>>>
>>> git push upstream master
>>> Permission denied (publickey).
>>> fatal: Could not read from remote repository.
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>>
>>> Could anyone please help?
>>> Many thanks in advance,
>>> Kind regards,
>>> Vladimir
>>>
>> --
>>> http://genat.uk
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>> --
>> Simina M. Boca
>> Assistant Professor
>> Innovation Center for Biomedical Informatics  (ICBI)
>> Department of Oncology | Georgetown University Medical Center
>> Department of Biostatistics, Bioinformatics and Biomathematics |
>> Georgetown University Medical Center
>> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
>> Center
>>
>> 2115 Wisconsin Ave NW, Suite 110
>> 
>> Washington, DC 20007
>> 
>> Phone: (202) 687-1545
>> Fax: (202) 687-5011
>> http://icbi.georgetown.edu/boca
>>
>>
>> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
>> vladimir.yu.kise...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I am trying to push a new version of my package to git.bioconductor.org.
>>> I
>>> was able to do that in the past. But I've recently changed my public key
>>> and not sure whether this causes a problem. However, I can see my new
>>> public key here - https://github.com/wikiselev.keys - and it is the
>>> first
>>> one in the list.
>>>
>>> When I look at the remote I can see git.bioconductor.org there but when
>>> I
>>> try to push to upstream I get an error:
>>>
>>> git remote -v
>>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>>
>>> git push origin master
>>> Everything up-to-date
>>>
>>> git push upstream master
>>> Permission denied (publickey).
>>> fatal: Could not read from remote repository.
>>> Please make sure you have the correct access rights
>>> and the repository exists.
>>>
>>> Could anyone please help?
>>> Many thanks in advance,
>>> Kind regards,
>>> Vladimir
>>>
>> --
>>> http://genat.uk
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>> --
>> Simina M. Boca
>> Assistant Professor
>> Innovation Center for Biomedical Informatics  (ICBI)
>> Department of Oncology | Georgetown University Medical Center
>> Department of Biostatistics, Bioinformatics and Biomathematics |
>> Georgetown University Medical Center

Re: [Bioc-devel] Upstream permission denied

Hi Simina,

Thanks for your quick reply, but it looks like to forgot to paste your
response from Sean (at least I couldn't find it in your email).

Cheers,
Vlad

On Mon, Sep 11, 2017 at 5:58 PM Simina Boca  wrote:

> Hi Vladimir,
> This seems like the same error I was getting. Here is the helpful advice I
> got from Sean:
>
> Hi, Simina.
>
> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to push a new version of my package to git.bioconductor.org.
>> I
>> was able to do that in the past. But I've recently changed my public key
>> and not sure whether this causes a problem. However, I can see my new
>> public key here - https://github.com/wikiselev.keys - and it is the first
>> one in the list.
>>
>> When I look at the remote I can see git.bioconductor.org there but when I
>> try to push to upstream I get an error:
>>
>> git remote -v
>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>
>> git push origin master
>> Everything up-to-date
>>
>> git push upstream master
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights
>> and the repository exists.
>>
>> Could anyone please help?
>> Many thanks in advance,
>> Kind regards,
>> Vladimir
>>
> --
>> http://genat.uk
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Department of Oncology | Georgetown University Medical Center
> Department of Biostatistics, Bioinformatics and Biomathematics |
> Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110
> Washington, DC 20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
>
> On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
> vladimir.yu.kise...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to push a new version of my package to git.bioconductor.org.
>> I
>> was able to do that in the past. But I've recently changed my public key
>> and not sure whether this causes a problem. However, I can see my new
>> public key here - https://github.com/wikiselev.keys - and it is the first
>> one in the list.
>>
>> When I look at the remote I can see git.bioconductor.org there but when I
>> try to push to upstream I get an error:
>>
>> git remote -v
>> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
>> origin  g...@github.com:hemberg-lab/scmap.git (push)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
>> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>>
>> git push origin master
>> Everything up-to-date
>>
>> git push upstream master
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>> Please make sure you have the correct access rights
>> and the repository exists.
>>
>> Could anyone please help?
>> Many thanks in advance,
>> Kind regards,
>> Vladimir
>>
> --
>> http://genat.uk
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Simina M. Boca
> Assistant Professor
> Innovation Center for Biomedical Informatics  (ICBI)
> Department of Oncology | Georgetown University Medical Center
> Department of Biostatistics, Bioinformatics and Biomathematics |
> Georgetown University Medical Center
> Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
> Center
>
> 2115 Wisconsin Ave NW, Suite 110
> Washington, DC 20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
>
-- 
http://genat.uk

[[alternative HTML version deleted]]

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Michael Lawrence

It's probably good keeping coercion and construction distinct,
although we have violated that recently with GRanges(). It now
attempts to coerce its first argument to a GRanges. Don't want to
derail the discussion, but it's another data point.

Michael

On Mon, Sep 11, 2017 at 9:26 AM, Levi Waldron
 wrote:
> On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
> ludwig.geistlin...@bio.ifi.lmu.de> wrote:
>
>> I guess we discussed this with Davide Risso @Bioc2017 in the
>> MultiAssayExperiment workshop.
>>
>> > SummarizedExperiment(mouseData)
>>
>> puts the eSet (rather counterintuitively) into `assays` of
>> `SummarizedExperiment`, it does not really coerce it to
>> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
>> transferred to colData and rowData.
>>
>
> Right, I had forgotten about that - this isn't a coercion but a
> construction, which should be obvious from the use of a constructor
> function. This behavior is intuitive if you remember that
> SummarizedExperiment(assays, ...) is a constructor that accepts as assays
> any object or list of objects supporting square bracket matrix-like
> subsetting. Sorry for my brain hiccup there.
>
>
>> While I can understand that this is by design of `SummarizedExperiment`, I
>> really wonder whether there are use cases where somebody would like to put
>> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
>> would like to coerce it that way.
>>
>> Furthermore, if you would indeed like to have several `ExpressionSet`s in
>> a `SummarizedExperiment`, haven't you already arrived at a scenario where
>> use of `MultiAssayExperiment` is indicated?
>>
>
> I think the behavior of the constructor SummarizedExperiment() here is
> correct and expected, the issue here is that we're actually looking for
> coercion methods.
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Upstream permission denied

2017-09-11 Thread Simina Boca

Hi Vladimir,
This seems like the same error I was getting. Here is the helpful advice I
got from Sean:

Hi, Simina.

On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
vladimir.yu.kise...@gmail.com> wrote:

> Hello,
>
> I am trying to push a new version of my package to git.bioconductor.org. I
> was able to do that in the past. But I've recently changed my public key
> and not sure whether this causes a problem. However, I can see my new
> public key here - https://github.com/wikiselev.keys - and it is the first
> one in the list.
>
> When I look at the remote I can see git.bioconductor.org there but when I
> try to push to upstream I get an error:
>
> git remote -v
> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> origin  g...@github.com:hemberg-lab/scmap.git (push)
> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>
> git push origin master
> Everything up-to-date
>
> git push upstream master
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
>
> Could anyone please help?
> Many thanks in advance,
> Kind regards,
> Vladimir
> --
> http://genat.uk
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics | Georgetown
University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca


On Mon, Sep 11, 2017 at 12:55 PM, Vladimir Kiselev <
vladimir.yu.kise...@gmail.com> wrote:

> Hello,
>
> I am trying to push a new version of my package to git.bioconductor.org. I
> was able to do that in the past. But I've recently changed my public key
> and not sure whether this causes a problem. However, I can see my new
> public key here - https://github.com/wikiselev.keys - and it is the first
> one in the list.
>
> When I look at the remote I can see git.bioconductor.org there but when I
> try to push to upstream I get an error:
>
> git remote -v
> origin  g...@github.com:hemberg-lab/scmap.git (fetch)
> origin  g...@github.com:hemberg-lab/scmap.git (push)
> upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
> upstreamg...@git.bioconductor.org:packages/scmap.git (push)
>
> git push origin master
> Everything up-to-date
>
> git push upstream master
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
>
> Could anyone please help?
> Many thanks in advance,
> Kind regards,
> Vladimir
> --
> http://genat.uk
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics | Georgetown
University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

[[alternative HTML version deleted]]

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[Bioc-devel] Upstream permission denied

Hello,

I am trying to push a new version of my package to git.bioconductor.org. I
was able to do that in the past. But I've recently changed my public key
and not sure whether this causes a problem. However, I can see my new
public key here - https://github.com/wikiselev.keys - and it is the first
one in the list.

When I look at the remote I can see git.bioconductor.org there but when I
try to push to upstream I get an error:

git remote -v
origin  g...@github.com:hemberg-lab/scmap.git (fetch)
origin  g...@github.com:hemberg-lab/scmap.git (push)
upstreamg...@git.bioconductor.org:packages/scmap.git (fetch)
upstreamg...@git.bioconductor.org:packages/scmap.git (push)

git push origin master
Everything up-to-date

git push upstream master
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

Could anyone please help?
Many thanks in advance,
Kind regards,
Vladimir
-- 
http://genat.uk

[[alternative HTML version deleted]]

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Re: [Bioc-devel] requesting more infrastructure on build/bot system


Hi Vince,

No particular procedure. Asking here is fine. I installed librdf0-dev
on the Linux builders and will install redland on the Mac builders.
Out of curiosity, what is the name of the Bioconductor package that
will depend on CRAN package redland?

Thanks,
H.

On 09/11/2017 07:29 AM, Vincent Carey wrote:

I have looked through the docs but cannot see where this
is addressed.  I would like to use the redland package
from CRAN but it has SystemRequirements:

Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>=
1.0.14)

is there a particular procedure for requesting such installations?

thanks

[[alternative HTML version deleted]]

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--
Hervé Pagès

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

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:

> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `SummarizedExperiment`, it does not really coerce it to
> SummarizedExperiment, eg. `fData` and `pData` are not accordingly
> transferred to colData and rowData.
>

Right, I had forgotten about that - this isn't a coercion but a
construction, which should be obvious from the use of a constructor
function. This behavior is intuitive if you remember that
SummarizedExperiment(assays, ...) is a constructor that accepts as assays
any object or list of objects supporting square bracket matrix-like
subsetting. Sorry for my brain hiccup there.

> While I can understand that this is by design of `SummarizedExperiment`, I
> really wonder whether there are use cases where somebody would like to put
> an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
> would like to coerce it that way.
>
> Furthermore, if you would indeed like to have several `ExpressionSet`s in
> a `SummarizedExperiment`, haven't you already arrived at a scenario where
> use of `MultiAssayExperiment` is indicated?
>

I think the behavior of the constructor SummarizedExperiment() here is
correct and expected, the issue here is that we're actually looking for
coercion methods.

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Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

2017-09-11 Thread Ludwig Geistlinger

I guess we discussed this with Davide Risso @Bioc2017 in the
MultiAssayExperiment workshop.

> SummarizedExperiment(mouseData)

puts the eSet (rather counterintuitively) into `assays` of
`SummarizedExperiment`, it does not really coerce it to
SummarizedExperiment, eg. `fData` and `pData` are not accordingly
transferred to colData and rowData.

While I can understand that this is by design of `SummarizedExperiment`, I
really wonder whether there are use cases where somebody would like to put
an `ExpressionSet` in `assays` of `SummarizedExperiment`, and not rather
would like to coerce it that way.

Furthermore, if you would indeed like to have several `ExpressionSet`s in
a `SummarizedExperiment`, haven't you already arrived at a scenario where
use of `MultiAssayExperiment` is indicated?


> Thanks Martin! I see the RangedSummarizedExperiment coercion method works
> when there are no mappable ranges (for example curatedMetagenomicData
> ExpressionSet objects), although the rowRanges is a GRangesList of empty
> elements. It might be worth also having a SummarizedExperiment coercion
> method it it's not a problematic or big job. And now I suppose I can ask
> the question I *really* wanted to know, which is why can't I coerce an
> object that extends eSet? I can still use the SummarizedExperiment()
> constructor, but for example:
>
>> library(metagenomeSeq)> data(mouseData)> class(mouseData)[1]
>> "MRexperiment"
> attr(,"package")
> [1] "metagenomeSeq"> is(mouseData, "ExpressionSet")[1] FALSE>
> is(mouseData, "eSet")[1] TRUE
>
>> SummarizedExperiment(mouseData)class: SummarizedExperiment
> dim: 10172 139
> metadata(0):
> assays(1): ''
> rownames(10172): Prevotellaceae:1 Lachnospiraceae:1 ... Bryantella:103
>   Parabacteroides:956
> rowData names(0):
> colnames(139): PM1:20080107 PM1:20080108 ... PM9:20080225 PM9:20080303
> colData names(0):
>
>> as(mouseData, "RangedSummarizedExperiment") Error in as(mouseData,
> "RangedSummarizedExperiment") : no method or default for coercing
> âMRexperimentâ to âRangedSummarizedExperimentâ > as(mouseData,
> "SummarizedExperiment") Error in as(mouseData, "SummarizedExperiment") :
> no
> method or default for coercing âMRexperimentâ to
> âSummarizedExperimentâ > as(mouseData,
> "ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot
> of
> name "pData" for this object of class "AnnotatedDataFrame" >
>
>
>
>
> On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> On 09/10/2017 08:38 PM, Levi Waldron wrote:
>>
>>> I just dug up this old thread because I realized we still don't have a
>>> coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since
>>> we
>>>
>>
>> try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see
>> ?makeSummarizedExperimentFromExpressionSet
>>
>> do have SummarizedExperiment(sample.ExpressionSet), could the coercion
>>> method also be added easily?
>>>
>>> library(Biobase) > library(SummarizedExperiment) >

>>> example("ExpressionSet")
>>>
>>> SummarizedExperiment(sample.ExpressionSet)class: SummarizedExperiment

>>> dim: 500 26
>>> metadata(0):
>>> assays(1): ''
>>> rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
>>> rowData names(0):
>>> colnames(26): A B ... Y Z
>>> colData names(0):> as(sample.ExpressionSet,
>>> "SummarizedExperiment")Error in as(sample.ExpressionSet,
>>> "SummarizedExperiment") :
>>>no method or default for coercing âExpressionSetâ to
>>> âSummarizedExperimentâ
>>>
>>> sessionInfo()R version 3.4.0 RC (2017-04-20 r72569)

>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 16.04.3 LTS
>>>
>>> Matrix products: default
>>> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
>>> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>>> LC_TIME=en_US.UTF-8
>>>   [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
>>> LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>>> LC_ADDRESS=C
>>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4parallel  stats graphics  grDevices utils
>>> datasets  methods   base
>>>
>>> other attached packages:
>>> [1] SummarizedExperiment_1.7.5 DelayedArray_0.3.16
>>> matrixStats_0.52.2
>>> [4] GenomicRanges_1.29.6   GenomeInfoDb_1.13.4
>>> IRanges_2.11.7
>>> [7] S4Vectors_0.15.5   Biobase_2.37.2
>>> BiocGenerics_0.23.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] lattice_0.20-35 bitops_1.0-6grid_3.4.0
>>>   [4] zlibbioc_1.23.0 XVector_0.17.0  Matrix_1.2-11
>>>   [7] tools_3.4.0 RCurl_1.95-4.8  compiler_3.4.0
>>> [10] GenomeInfoDbData_0.99.1
>>>
>>>

>>> On Mon, Sep 22, 2014 at 1:54 AM, HervÃ© PagÃ¨s 
>>> wrote:
>>>
>>> Hi,

 On 09/20/2014 11:14 AM, Martin Morgan wrote:

 On

[Bioc-devel] requesting more infrastructure on build/bot system

2017-09-11 Thread Vincent Carey

I have looked through the docs but cannot see where this
is addressed.  I would like to use the redland package
from CRAN but it has SystemRequirements:

Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>=
1.0.14)

is there a particular procedure for requesting such installations?

thanks

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Re: [Bioc-devel] Cannot push to master branch

2017-09-11 Thread Turaga, Nitesh

You need to use the SSH protocol not HTTPS.

So, your origin needs to be 
`g...@git.bioconductor.org:packages/MutationalPatterns.git`.

http://bioconductor.org/developers/how-to/git/maintain-bioc-only/

> On Sep 11, 2017, at 10:26 AM, Janssen-10, R.R.E. 
>  wrote:
> 
> Dear Bioconductor team,
> 
> I cannot push to the master branch of our package (MutationalPatterns).
> 
> $ git push origin master
> fatal: remote error: FATAL: W any packages/MutationalPatterns nobody DENIED 
> by fallthru
> (or you mis-spelled the reponame)
> 
> $ git remote -v
> origin  https://git.bioconductor.org/packages/MutationalPatterns.git (fetch)
> origin  https://git.bioconductor.org/packages/MutationalPatterns.git (push)
> 
> What's wrong?
> 
> Kind regards,
> Roel Janssen
> 
> --
> 
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
> 
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
> 
> --
> 
> This message may contain confidential information and ...{{dropped:17}}

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[Bioc-devel] Cannot push to master branch

2017-09-11 Thread Janssen-10, R.R.E.

Dear Bioconductor team,

I cannot push to the master branch of our package (MutationalPatterns).

$ git push origin master
fatal: remote error: FATAL: W any packages/MutationalPatterns nobody DENIED by 
fallthru
(or you mis-spelled the reponame)

$ git remote -v
origin  https://git.bioconductor.org/packages/MutationalPatterns.git (fetch)
origin  https://git.bioconductor.org/packages/MutationalPatterns.git (push)

What's wrong?

Kind regards,
Roel Janssen

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