[Bioc-devel] GateFinder: Windows Server Error

[Tony Culos]

Hello,

I'm working on resolving the error with the GateFinder package for Windows
Server 2012 R2 Standard, it appears that the issue is a calculation
difference between 32 and 64-bit systems. Is it possible to have the
package be included in the next release only with support for 64-bit
systems? I couldn't find any explicit reference to this sort of situation
so any clarification would be greatly appreciated.

Thank You,
Tony C.

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Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

[Elizabeth Purdom]

Dear Michael,

Thanks, that fixed the problem. The new version hasn’t shown up in a call to 
biocLite, but I was able to get it from the github repository and check it; 
also our package is now clearing bioconductor checks.

Just to note, our package has always gotten messages about the class conflicts 
during installation too. This was true with the previous patch to 
SummarizedExperiment and that is still the case with this new patch for 
S4Vectors. It doesn’t affect the user or our tests, so we’ve never tracked it 
down or asked about it, but since there has been a wider discussion about the 
question, I thought I’d mention it. You can see this in the output of our build 
of our 1.99.2 build in bioconductor:

http://bioconductor.org/checkResults/devel/bioc-LATEST/clusterExperiment/tokay2-install.html

(I have to assume it is using the new patch, 0.17.42, because before the 
package was not passing the checks and now it is)
> * installing *source* package 'clusterExperiment' ...
> ** R
> ** data
> ** byte-compile and prepare package for lazy loading
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by 'RNeXML'
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by 'RNeXML'
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by 'RNeXML'
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by 'RNeXML'
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by 'RNeXML'


All of the best,
Elizabeth

> On Apr 14, 2018, at 9:25 PM, Michael Lawrence  
> wrote:
> 
> Last night I checked in a workaround to S4Vectors. It just calls
> getClass("Annotated") instead of passing the class name directly.
> 
> I'll check in a simple fix for is() today maybe to R 3.6 (devel) and
> then we'll be good for now.
> 
> On Sat, Apr 14, 2018 at 8:59 AM, Martin Morgan
>  wrote:
>> On 04/14/2018 07:21 AM, Vincent Carey wrote:
>>> 
>>> But Annotated is defined in S4Vectors and RNeXML; the latter is not a
>>> Bioconductor package.
>>> 
>>> The likelihood of collisions among class names defined in different
>>> packages seems pretty high
>>> as S4 adoption grows.  So requiring a systematic approach to
>>> disambiguating
>>> class references seems inevitable.
>> 
>> 
>> I agree that renaming is not a robust solution, and would encourage Michael
>> to commit the change using the class definition in `is()` with more
>> elaborate solutions (really this is a problem with is(), where it should be
>> fixed, rather than introducing complicated syntax?) left for a later day.
>> 
>> Martin
>> 
>>> 
>>> 
>>> On Sat, Apr 14, 2018 at 4:05 AM, Hervé Pagès  wrote:
>>> 
 How about renaming Annotated? Isn't having 2 classes around with the
 same name fundamentally a bad situation? No amount of workarounds will
 change that.
 
 H.
 
 
 On 04/12/2018 04:06 PM, Michael Lawrence wrote:
 
> Yea, good idea, I was thinking of supporting :: in class names and
> parsing them out. In code is better.  Maybe %::%? It wouldn't have to
> get a class object (for one thing, a class might not exist), because
> the methods package supports a 'package' attribute on the character
> vector, abstracted by packageSlot().
> 
> 
> 
> On Thu, Apr 12, 2018 at 3:26 PM, Vincent Carey
>  wrote:
> 
>> If we need to disambiguate class references, perhaps an operator
>> 
>> could help?  Along the lines of base::"::" ...
>> 
>> 
>> "%c%" <- function(package,class) {
>> 
>> pk = as.character(substitute(package))
>> 
>> cl = as.character(substitute(class))
>> 
>> getClass(cl, where=getNamespace(pk))
>> 
>> }
>> 
>> 
>> Biobase %c% ExpressionSet  # a classRepresentation instance
>> 
>> 
>> is(1:5, Biobase %c% ExpressionSet)  # FALSE
>> 
>> 
>> is(Biobase::ExpressionSet(), "ExpressionSet")  # TRUE
>> 
>> 
>> is(Biobase::ExpressionSet(),  Biobase %c% ExpressionSet) # TRUE
>> 
>> 
>> 
>> 
>> 
>> 
>> On Thu, Apr 12, 2018 at 3:57 PM, Michael Lawrence
>>  wrote:
>> 
>>> 
>>> Hi Davide,
>>> 
>>> We can get this fixed soon, but I was hoping to hear e.g. Herve's
>>> opinion first if he has one.
>>> 
>>> Michael
>>> 
>>> On Thu, Apr 12, 2018 at 12:53 PM, Davide Risso
>>> >> wrote:
>>> 
 Hi Michael,
 
 Thanks for looking into this.
 
 Can you or someone with push permission to S4Vectors implement the
 

Re: [Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

[Ryan Thompson]

Hi again,

I just had a thought. Would it be possible to extend the citation pages
that you linked to also provide the bibtex source at a similar URL, e.g.
http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/bibtex.html

 ?

Regards,

Ryan Thompson

On Tue, Apr 17, 2018 at 12:23 PM Ryan Thompson  wrote:

> I wasn't specific about what I meant by "structured" because I'm not
> certain what kind of citation data types CiteAs can handle, though I'd
> assume bibtex would probably be fine. It's possible that the unprocessed
> CITATION file might also be good enough (I'm not familiar with the format).
>
> On Tue, Apr 17, 2018 at 11:57 AM Marcel Ramos <
> marcel.ra...@roswellpark.org> wrote:
>
>> Hi Ryan,
>>
>> Thanks for pointing this out.
>>
>> I'm not sure what you mean by "structured" or "format". We do have
>> public facing citations
>> which can be found at:
>>
>> http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html
>>
>> (Thanks Lori for locating these pages!)
>>
>>
>> And even with a web-browsable git repository (as you mentioned), one
>> would still only be able
>> to get the "unprocessed" CITATION file. The best way to programmatically
>> get these at the moment
>> is through the git repository via:
>>
>> git archive
>> --remote=g...@git.bioconductor.org:packages/MultiAssayExperiment.git \
>>HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt
>>
>> although, we would have to provide the CiteAs service with a key for
>> read-only access.
>>
>> Best regards,
>>
>> Marcel
>>
>>
>> On 04/17/2018 12:44 PM, Ryan Thompson wrote:
>> > There's a nice online tool called CiteAs which tries to figure out the
>> > proper citation for a given URL. I've recently helped the author to add
>> > support for extracting the DOI from Bioconductor package information
>> pages:
>> > https://github.com/Impactstory/citeas-api/issues/12
>> >
>> > This is a good start, but is suboptimal, since some many packages have
>> > actual published articles which should be used as the canonical citation
>> > instead of the package's URL. However, I'm not sure how to get this
>> > citation information in a structured format short of running R and
>> > installing the package, which isn't really an option for a web service
>> like
>> > this, which wants to return a result quickly. Does anyone know a good
>> way
>> > to access this info?
>> >
>> > Thanks,
>> >
>> > Ryan Thompson
>> >
>> >   [[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...{{dropped:4}}
>>
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>>
>

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Re: [Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

[Ryan Thompson]

I wasn't specific about what I meant by "structured" because I'm not
certain what kind of citation data types CiteAs can handle, though I'd
assume bibtex would probably be fine. It's possible that the unprocessed
CITATION file might also be good enough (I'm not familiar with the format).

On Tue, Apr 17, 2018 at 11:57 AM Marcel Ramos 
wrote:

> Hi Ryan,
>
> Thanks for pointing this out.
>
> I'm not sure what you mean by "structured" or "format". We do have
> public facing citations
> which can be found at:
>
> http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html
>
> (Thanks Lori for locating these pages!)
>
>
> And even with a web-browsable git repository (as you mentioned), one
> would still only be able
> to get the "unprocessed" CITATION file. The best way to programmatically
> get these at the moment
> is through the git repository via:
>
> git archive
> --remote=g...@git.bioconductor.org:packages/MultiAssayExperiment.git \
>HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt
>
> although, we would have to provide the CiteAs service with a key for
> read-only access.
>
> Best regards,
>
> Marcel
>
>
> On 04/17/2018 12:44 PM, Ryan Thompson wrote:
> > There's a nice online tool called CiteAs which tries to figure out the
> > proper citation for a given URL. I've recently helped the author to add
> > support for extracting the DOI from Bioconductor package information
> pages:
> > https://github.com/Impactstory/citeas-api/issues/12
> >
> > This is a good start, but is suboptimal, since some many packages have
> > actual published articles which should be used as the canonical citation
> > instead of the package's URL. However, I'm not sure how to get this
> > citation information in a structured format short of running R and
> > installing the package, which isn't really an option for a web service
> like
> > this, which wants to return a result quickly. Does anyone know a good way
> > to access this info?
> >
> > Thanks,
> >
> > Ryan Thompson
> >
> >   [[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...{{dropped:4}}
>
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>

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[Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

[Marcel Ramos]

Hi Ryan,

Thanks for pointing this out.

I'm not sure what you mean by "structured" or "format". We do have
public facing citations
which can be found at:
http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html

(Thanks Lori for locating these pages!)


And even with a web-browsable git repository (as you mentioned), one
would still only be able
to get the "unprocessed" CITATION file. The best way to programmatically
get these at the moment
is through the git repository via:

git archive
--remote=g...@git.bioconductor.org:packages/MultiAssayExperiment.git \
   HEAD inst/CITATION | tar -xO inst/CITATION > citation.txt

although, we would have to provide the CiteAs service with a key for
read-only access.

Best regards,

Marcel


On 04/17/2018 12:44 PM, Ryan Thompson wrote:
> There's a nice online tool called CiteAs which tries to figure out the
> proper citation for a given URL. I've recently helped the author to add
> support for extracting the DOI from Bioconductor package information pages:
> https://github.com/Impactstory/citeas-api/issues/12
>
> This is a good start, but is suboptimal, since some many packages have
> actual published articles which should be used as the canonical citation
> instead of the package's URL. However, I'm not sure how to get this
> citation information in a structured format short of running R and
> installing the package, which isn't really an option for a web service like
> this, which wants to return a result quickly. Does anyone know a good way
> to access this info?
>
> Thanks,
>
> Ryan Thompson
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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[Bioc-devel] TxDbs, OrgDbs, GO.db, and PFAM.db packages available

[Van Twisk, Daniel]

Hello all!


The newest TxDbs, OrgDbs, GO.db, and PFAM.db packages have been pushed to 
Bioconductor 3.7 devel and should propagate by tomorrow.  The following 
packages have been updated/added:


Updated GO.db:

GO.db_3.6.0.tar.gz


Updated PFAM.db:

PFAM.db_3.6.0.tar.gz


Updated org dbs:

org.Ag.eg.db_3.6.0.tar.gz
org.At.tair.db_3.6.0.tar.gz
org.Bt.eg.db_3.6.0.tar.gz
org.Ce.eg.db_3.6.0.tar.gz
org.Cf.eg.db_3.6.0.tar.gz
org.Dm.eg.db_3.6.0.tar.gz
org.Dr.eg.db_3.6.0.tar.gz
org.EcK12.eg.db_3.6.0.tar.gz
org.EcSakai.eg.db_3.6.0.tar.gz
org.Gg.eg.db_3.6.0.tar.gz
org.Hs.eg.db_3.6.0.tar.gz
org.Mm.eg.db_3.6.0.tar.gz
org.Mmu.eg.db_3.6.0.tar.gz
org.Pf.plasmo.db_3.6.0.tar.gz
org.Pt.eg.db_3.6.0.tar.gz
org.Rn.eg.db_3.6.0.tar.gz
org.Sc.sgd.db_3.6.0.tar.gz
org.Ss.eg.db_3.6.0.tar.gz
org.Xl.eg.db_3.6.0.tar.gz


New TxDbs:

TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.3.tar.gz

TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.3.tar.gz


Updated TxDbs:

TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.3.tar.gz
TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz
TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.3.tar.gz
TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz
TxDb.Ggallus.UCSC.galGal4.refGene_3.4.3.tar.gz
TxDb.Ggallus.UCSC.galGal5.refGene_3.4.3.tar.gz
TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.3.tar.gz
TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.3.tar.gz
TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.3.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz
TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz
TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.3.tar.gz




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

[Obenchain, Valerie]

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 
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[Bioc-devel] Accessing package citation info programmatically without running R?

[Ryan Thompson]

There's a nice online tool called CiteAs which tries to figure out the
proper citation for a given URL. I've recently helped the author to add
support for extracting the DOI from Bioconductor package information pages:
https://github.com/Impactstory/citeas-api/issues/12

This is a good start, but is suboptimal, since some many packages have
actual published articles which should be used as the canonical citation
instead of the package's URL. However, I'm not sure how to get this
citation information in a structured format short of running R and
installing the package, which isn't really an option for a web service like
this, which wants to return a result quickly. Does anyone know a good way
to access this info?

Thanks,

Ryan Thompson

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Re: [Bioc-devel] RareVariantVis failed

[Shepherd, Lori]

I just checked and it is indeed updated on the git.bioconductor.org server.  So 
you should be all set.


The version number in the build report should be updated either tomorrow or 
thur to indicate it is building the new 2.7.1 version of the package.

http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html



If you didn't want to wait until the build report coming out to check that the 
version was updated -  you could create a temporary directory and clone the 
repository from the git server -

git clone g...@git.bioconductor.org:packages/RareVariantVis.git


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tomasz Stokowy 
Sent: Tuesday, April 17, 2018 11:39:59 AM
To: bioc-devel@r-project.org; Shepherd, Lori
Subject: Re: [Bioc-devel] RareVariantVis failed

Ok, I pushed to upstream master. Where could I check that version "to be 
checked" was updated to 2.7.1?

--
Tomasz

On Tue, 17 Apr 2018 17:35:18 +0200, Shepherd, Lori 
 wrote:


Yes that is correct.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tomasz Stokowy 
Sent: Tuesday, April 17, 2018 11:30:17 AM
To: bioc-devel@r-project.org; Shepherd, Lori
Subject: Re: [Bioc-devel] RareVariantVis failed


Output of git remote -v seems to be ok:

Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v
origin https://github.com/tstokowy/RareVariantVis.git (fetch)
origin https://github.com/tstokowy/RareVariantVis.git (push)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (fetch)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (push)

According to push instructions I should do
git push upstream master

Is that right?


--
Tomasz

On Tue, 17 Apr 2018 17:25:42 +0200, Shepherd, Lori 
 wrote:


You need to push the changes to the git.bioconductor.org server.


What is the result of

`git remote -v`


You should have set up the upstream remote to point the the Bioconductor git 
server where you will also have to push changes.

See the following help page:



http://bioconductor.org/developers/how-to/git/push-to-github-bioc/




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 Tomasz Stokowy 

Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,

I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
 wrote:

> Dear Robert,
>
> Thank you for clarification. I updated package following your
> instructions and committed changes to
> https://github.com/tstokowy/RareVariantVis.
>
> I will verify if the R CMD check goes through this time.
>
> Kind regards,
>
> --
> Tomasz
>
>
> On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo
>  wrote:
>
>> hi Tomasz,
>>
>> regarding the warning caused by GenomicScores:
>>
>>  > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
>>  > GRanges(seqnames = paste0("chr",  :
>>  >The 'scores()' method has been deprecated and will become defunct
>> in
>>  > the next release version of Biocondcutor 3.8. Please use its
>> replacement functions 'gscores()' and 'score()'.
>>
>> for this one just replace, the call:
>>
>> scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...
>>
>> by
>>
>> score(phastCons100way.UCSC.hg19, etc...
>>
>> i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.
>>
>>  > Warning in gscores(object, ranges, ...) :
>>  >assuming query ranges genome build is the one of the GScores
>> object
>>  > (Genome Reference Consortium GRCh37).
>>
>> here the 'genome' column in the sequence information ('seqinfo()') from
>> the input ranges ranges is probably something like "hg19" or NA, while
>> the one in the GScores object is "Genome Reference Consortium GRCh37".
>> if you know both objects have positions over the same reference genome,
>> you can forget about this warning. however, probably a warning is not
>> necessary here, i'll replace it by a message and the warning will
>> dissappear in a couple 

Re: [Bioc-devel] RareVariantVis failed

[Shepherd, Lori]

Yes that is correct.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Tomasz Stokowy 
Sent: Tuesday, April 17, 2018 11:30:17 AM
To: bioc-devel@r-project.org; Shepherd, Lori
Subject: Re: [Bioc-devel] RareVariantVis failed


Output of git remote -v seems to be ok:

Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v
origin https://github.com/tstokowy/RareVariantVis.git (fetch)
origin https://github.com/tstokowy/RareVariantVis.git (push)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (fetch)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (push)

According to push instructions I should do
git push upstream master

Is that right?


--
Tomasz

On Tue, 17 Apr 2018 17:25:42 +0200, Shepherd, Lori 
 wrote:


You need to push the changes to the git.bioconductor.org server.


What is the result of

`git remote -v`


You should have set up the upstream remote to point the the Bioconductor git 
server where you will also have to push changes.

See the following help page:



http://bioconductor.org/developers/how-to/git/push-to-github-bioc/




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 Tomasz Stokowy 

Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,

I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
 wrote:

> Dear Robert,
>
> Thank you for clarification. I updated package following your
> instructions and committed changes to
> https://github.com/tstokowy/RareVariantVis.
>
> I will verify if the R CMD check goes through this time.
>
> Kind regards,
>
> --
> Tomasz
>
>
> On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo
>  wrote:
>
>> hi Tomasz,
>>
>> regarding the warning caused by GenomicScores:
>>
>>  > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
>>  > GRanges(seqnames = paste0("chr",  :
>>  >The 'scores()' method has been deprecated and will become defunct
>> in
>>  > the next release version of Biocondcutor 3.8. Please use its
>> replacement functions 'gscores()' and 'score()'.
>>
>> for this one just replace, the call:
>>
>> scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...
>>
>> by
>>
>> score(phastCons100way.UCSC.hg19, etc...
>>
>> i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.
>>
>>  > Warning in gscores(object, ranges, ...) :
>>  >assuming query ranges genome build is the one of the GScores
>> object
>>  > (Genome Reference Consortium GRCh37).
>>
>> here the 'genome' column in the sequence information ('seqinfo()') from
>> the input ranges ranges is probably something like "hg19" or NA, while
>> the one in the GScores object is "Genome Reference Consortium GRCh37".
>> if you know both objects have positions over the same reference genome,
>> you can forget about this warning. however, probably a warning is not
>> necessary here, i'll replace it by a message and the warning will
>> dissappear in a couple of days.
>>
>> btw, i'm assuming we're talking here about the current 'development'
>> branch of Bioconductor, i.e., GenomicScores version 1.3.21.
>>
>> cheers,
>>
>> robert.
>>
>>
>> On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:
>>> Dear bioc-devel,
>>>  My package RareVariantVis currently failed check because of examples
>>> warnings/error. I am not able to reproduce this on my system, despite
>>> updating R and Bioconductor.
>>> It seems that recent changes in dependencies are causing this trouble.
>>> Should I go for useDevel() to solve this issues?
>>>
>>> http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html
>>>  https://github.com/tstokowy/RareVariantVis
>>>  Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
>>>GRanges object contains 2 out-of-bound ranges located on sequence
>>>68559. Note that ranges located on a sequence whose length is
>>> unknown
>>>(NA) or on a circular sequence are not considered out-of-bound (use
>>>seqlengths() and isCircular() to get the lengths and circularity
>>> flags
>>>of the underlying sequences). You can use trim() to trim these
>>> ranges.
>>>See 

Re: [Bioc-devel] RareVariantVis failed

[Shepherd, Lori]

You need to push the changes to the git.bioconductor.org server.


What is the result of

`git remote -v`


You should have set up the upstream remote to point the the Bioconductor git 
server where you will also have to push changes.

See the following help page:



http://bioconductor.org/developers/how-to/git/push-to-github-bioc/




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 Tomasz Stokowy 

Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,

I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
 wrote:

> Dear Robert,
>
> Thank you for clarification. I updated package following your
> instructions and committed changes to
> https://github.com/tstokowy/RareVariantVis.
>
> I will verify if the R CMD check goes through this time.
>
> Kind regards,
>
> --
> Tomasz
>
>
> On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo
>  wrote:
>
>> hi Tomasz,
>>
>> regarding the warning caused by GenomicScores:
>>
>>  > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
>>  > GRanges(seqnames = paste0("chr",  :
>>  >The 'scores()' method has been deprecated and will become defunct
>> in
>>  > the next release version of Biocondcutor 3.8. Please use its
>> replacement functions 'gscores()' and 'score()'.
>>
>> for this one just replace, the call:
>>
>> scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...
>>
>> by
>>
>> score(phastCons100way.UCSC.hg19, etc...
>>
>> i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.
>>
>>  > Warning in gscores(object, ranges, ...) :
>>  >assuming query ranges genome build is the one of the GScores
>> object
>>  > (Genome Reference Consortium GRCh37).
>>
>> here the 'genome' column in the sequence information ('seqinfo()') from
>> the input ranges ranges is probably something like "hg19" or NA, while
>> the one in the GScores object is "Genome Reference Consortium GRCh37".
>> if you know both objects have positions over the same reference genome,
>> you can forget about this warning. however, probably a warning is not
>> necessary here, i'll replace it by a message and the warning will
>> dissappear in a couple of days.
>>
>> btw, i'm assuming we're talking here about the current 'development'
>> branch of Bioconductor, i.e., GenomicScores version 1.3.21.
>>
>> cheers,
>>
>> robert.
>>
>>
>> On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:
>>> Dear bioc-devel,
>>>  My package RareVariantVis currently failed check because of examples
>>> warnings/error. I am not able to reproduce this on my system, despite
>>> updating R and Bioconductor.
>>> It seems that recent changes in dependencies are causing this trouble.
>>> Should I go for useDevel() to solve this issues?
>>>
>>> http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html
>>>  https://github.com/tstokowy/RareVariantVis
>>>  Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
>>>GRanges object contains 2 out-of-bound ranges located on sequence
>>>68559. Note that ranges located on a sequence whose length is
>>> unknown
>>>(NA) or on a circular sequence are not considered out-of-bound (use
>>>seqlengths() and isCircular() to get the lengths and circularity
>>> flags
>>>of the underlying sequences). You can use trim() to trim these
>>> ranges.
>>>See ?`trim,GenomicRanges-method` for more information.
>>> Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
>>> GRanges(seqnames = paste0("chr",  :
>>>The 'scores()' method has been deprecated and will become defunct
>>> in the next release version of Biocondcutor 3.8. Please use its
>>> replacement functions 'gscores()' and 'score()'.
>>> Warning in gscores(object, ranges, ...) :
>>>assuming query ranges genome build is the one of the GScores object
>>> (Genome Reference Consortium GRCh37).
>>> Error in match.names(clabs, nmi) : names do not match previous names
>>> Calls: chromosomeVis ... eval -> eval -> eval -> rbind -> rbind ->
>>> match.names
>>>  I will be thankful for any suggestions.
>>>  Kind regards,
>>>
>>
>
>


--
Tomasz Stokowy
Department of Clinical Science
University of Bergen

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


This email message 

Re: [Bioc-devel] RareVariantVis failed

[Tomasz Stokowy]

Ok, I pushed to upstream master. Where could I check that version "to be  
checked" was updated to 2.7.1?


--
Tomasz

On Tue, 17 Apr 2018 17:35:18 +0200, Shepherd, Lori  
 wrote:




Yes that is correct.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
From: Tomasz Stokowy 
Sent: Tuesday, April 17, 2018 11:30:17 AM
To: bioc-devel@r-project.org; Shepherd, Lori
Subject: Re: [Bioc-devel] RareVariantVis failed
Output of git remote -v seems to be ok:

Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v
origin https://github.com/tstokowy/RareVariantVis.git (fetch)origin  
https://github.com/tstokowy/RareVariantVis.git (push)upstream  
g...@git.bioconductor.org:packages/RareVariantVis.git (fetch)upstream  
g...@git.bioconductor.org:packages/RareVariantVis.git (push)


According to push instructions I should do
git push upstream master

Is that right?


--
Tomasz

On Tue, 17 Apr 2018 17:25:42 +0200, Shepherd, Lori  
 wrote:




You need to push the changes to the git.bioconductor.org server.


What is the result of
`git remote -v`


You should have set up the upstream remote to point the the  
Bioconductor git server where you will also have to push changes.

See the following help page:




http://bioconductor.org/developers/how-to/git/push-to-github-bioc/






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 Tomasz  
Stokowy 

Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,


I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
 wrote:


Dear Robert,

Thank you for clarification. I updated package following your  
instructions and committed changes to

https://github.com/tstokowy/RareVariantVis.

I will verify if the R CMD check goes through this time.

Kind regards,

--
Tomasz


On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo  
 wrote:



hi Tomasz,

regarding the warning caused by GenomicScores:

 > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
 > GRanges(seqnames = paste0("chr",  :
 >The 'scores()' method has been deprecated and will become  
defunct in
 > the next release version of Biocondcutor 3.8. Please use its  
replacement functions 'gscores()' and 'score()'.


for this one just replace, the call:

scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...

by

score(phastCons100way.UCSC.hg19, etc...

i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.

 > Warning in gscores(object, ranges, ...) :
 >assuming query ranges genome build is the one of the GScores  
object

 > (Genome Reference Consortium GRCh37).

here the 'genome' column in the sequence information ('seqinfo()')  
from the input ranges ranges is probably something like "hg19" or NA,  
while the one in the GScores object is "Genome Reference Consortium  
GRCh37". if you know both objects have positions over the same  
reference genome, you can forget about this warning. however,  
probably a warning is not necessary here, i'll replace it by a  
message and the warning will dissappear in a couple of days.


btw, i'm assuming we're talking here about the current 'development'  
branch of Bioconductor, i.e., GenomicScores version 1.3.21.


cheers,

robert.


On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:

Dear bioc-devel,
 My package RareVariantVis currently failed check because of  
examples warnings/error. I am not able to reproduce this on my  
system, despite updating R and Bioconductor.
It seems that recent changes in dependencies are causing this  
trouble. Should I go for useDevel() to solve this issues?
  
http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html  
 https://github.com/tstokowy/RareVariantVis

 Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
   GRanges object contains 2 out-of-bound ranges located on sequence
   68559. Note that ranges located on a sequence whose length is  
unknown
   (NA) or on a circular sequence are not considered out-of-bound  
(use
   seqlengths() and isCircular() to get the lengths and circularity  
flags
   of the underlying sequences). You can use trim() to trim these  
ranges.

   See 

Re: [Bioc-devel] RareVariantVis failed

[Tomasz Stokowy]

Output of git remote -v seems to be ok:

Tomaszs-MacBook-Pro:RareVariantVis tomaszstokowy$ git remote -v
origin https://github.com/tstokowy/RareVariantVis.git (fetch)
origin https://github.com/tstokowy/RareVariantVis.git (push)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (fetch)
upstream g...@git.bioconductor.org:packages/RareVariantVis.git (push)

According to push instructions I should do
git push upstream master

Is that right?


--
Tomasz

On Tue, 17 Apr 2018 17:25:42 +0200, Shepherd, Lori  
 wrote:




You need to push the changes to the git.bioconductor.org server.


What is the result of
`git remote -v`


You should have set up the upstream remote to point the the Bioconductor  
git server where you will also have to push changes.

See the following help page:




http://bioconductor.org/developers/how-to/git/push-to-github-bioc/






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 Tomasz  
Stokowy 

Sent: Tuesday, April 17, 2018 11:20:33 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] RareVariantVis failed

Dear Bioc-devel,


I updated my package to version 2.7.1 following instructions from Robert
(https://github.com/tstokowy/RareVariantVis).
Unfortunately, check still reports error on version 2.7.0

https://master.bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html

What should I do to have my git updated version checked?

--
Tomasz Stokowy



On Sun, 15 Apr 2018 18:31:46 +0200, Tomasz Stokowy
 wrote:


Dear Robert,

Thank you for clarification. I updated package following your  
instructions and committed changes to

https://github.com/tstokowy/RareVariantVis.

I will verify if the R CMD check goes through this time.

Kind regards,

--
Tomasz


On Tue, 03 Apr 2018 15:16:55 +0200, Robert Castelo  
 wrote:



hi Tomasz,

regarding the warning caused by GenomicScores:

 > Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,
 > GRanges(seqnames = paste0("chr",  :
 >The 'scores()' method has been deprecated and will become  
defunct in
 > the next release version of Biocondcutor 3.8. Please use its  
replacement functions 'gscores()' and 'score()'.


for this one just replace, the call:

scores(phastCons100way.UCSC.hg19, scores.only = TRUE, etc...

by

score(phastCons100way.UCSC.hg19, etc...

i.e., 'scores()' by 'score()' and remove 'scores.only=TRUE'.

 > Warning in gscores(object, ranges, ...) :
 >assuming query ranges genome build is the one of the GScores  
object

 > (Genome Reference Consortium GRCh37).

here the 'genome' column in the sequence information ('seqinfo()')  
from the input ranges ranges is probably something like "hg19" or NA,  
while the one in the GScores object is "Genome Reference Consortium  
GRCh37". if you know both objects have positions over the same  
reference genome, you can forget about this warning. however, probably  
a warning is not necessary here, i'll replace it by a message and the  
warning will dissappear in a couple of days.


btw, i'm assuming we're talking here about the current 'development'  
branch of Bioconductor, i.e., GenomicScores version 1.3.21.


cheers,

robert.


On 04/03/2018 12:43 PM, Tomasz Stokowy wrote:

Dear bioc-devel,
 My package RareVariantVis currently failed check because of examples  
warnings/error. I am not able to reproduce this on my system, despite  
updating R and Bioconductor.
It seems that recent changes in dependencies are causing this  
trouble. Should I go for useDevel() to solve this issues?
  
http://bioconductor.org/checkResults/3.7/bioc-LATEST/RareVariantVis/malbec2-checksrc.html  
 https://github.com/tstokowy/RareVariantVis

 Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
   GRanges object contains 2 out-of-bound ranges located on sequence
   68559. Note that ranges located on a sequence whose length is  
unknown

   (NA) or on a circular sequence are not considered out-of-bound (use
   seqlengths() and isCircular() to get the lengths and circularity  
flags
   of the underlying sequences). You can use trim() to trim these  
ranges.

   See ?`trim,GenomicRanges-method` for more information.
Warning in scores(phastCons100way.UCSC.hg19, scores.only = TRUE,  
GRanges(seqnames = paste0("chr",  :
   The 'scores()' method has been deprecated and will become defunct  
in the next release version of Biocondcutor 3.8. Please use its  
replacement functions 'gscores()' and 'score()'.

Warning in gscores(object, ranges, ...) :
   assuming query ranges genome build is the one of the GScores  
object (Genome Reference Consortium GRCh37).

Error in match.names(clabs, nmi) : names do not match previous names
Calls: chromosomeVis ... eval -> eval -> 

[Rd] Minor glitch in optim()

[J C Nash]

Having worked with optim() and related programs for years, it surprised me
that I haven't noticed this before, but optim() is inconsistent in how it
deals with bounds constraints specified at infinity. Here's an example:

# optim-glitch-Ex.R
x0<-c(1,2,3,4)
fnt <- function(x, fscale=10){
  yy <- length(x):1
  val <- sum((yy*x)^2)*fscale
}
grt <- function(x, fscale=10){
  nn <- length(x)
  yy <- nn:1
  #gg <- rep(NA,nn)
  gg <- 2*(yy^2)*x*fscale
  gg
}

npar <- 4
lower <- -Inf
l2 <- rep(-Inf,npar)

a1 <- optim(x0, fnt, grt, lower=lower, method="BFGS") # works
a1
a1a<- optim(x0, fnt, grt, lower=l2, method="BFGS") # changes method!
a1a

The first call uses BFGS method without warning. The second gives
a warning that L-BFGS-B should be used, and from the output uses
this.

This is a bit of an edge case. My own preference would be for optim()
to simply fail if bounds of any type are specified without L-BFGS-B
as the method. I believe that gives clarity, even though infinite
bounds imply an unconstrained problem.

The behaviour where a scalar infinite bound is treated as unconstrained
but a vector is not is inconsistent, however, and I think that at some
point should be fixed. Possibly the easiest way is to treat infinite
bounds specified as a vector the same as those specified as a scalar.
That is to adjust the code in File src/library/stats/R/optim.R
in the block

if((length(lower) > 1L || length(upper) > 1L ||
   lower[1L] != -Inf || upper[1L] != Inf)
   && !any(method == c("L-BFGS-B","Brent"))) {
warning("bounds can only be used with method L-BFGS-B (or Brent)")
method <- "L-BFGS-B"
}

Possibly

if((any(is.finite(lower) || any(is.finite(upper))
   && !any(method == c("L-BFGS-B","Brent"))) {
warning("bounds can only be used with method L-BFGS-B (or Brent)")
method <- "L-BFGS-B"
}

Best, JN

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Elizabeth Purdom]

Yes, thanks. That also fixed it for me; only DelayedArray had a different 
version number.

I have 0.17.42 of S4Vectors because there were also a fix in that package that 
I need which are also not yet available from bioCLite (the question of 
duplicated class names creating messages was breaking my package). 

Elizabeth

> On Apr 17, 2018, at 1:19 PM, Vincent Carey  wrote:
> 
> Thanks Pete -- indeed installing fresh HDF5Array scotches the error.  But the 
> package
> version number is the same as Elizabeth's:  HDF5Array_1.7.10 -- so is it new 
> code,
> or just the act of reinstalling, perhaps with a different packageset in place 
> than was
> present for the first HDF5Array installation, that solves the problem?
> 
> On Tue, Apr 17, 2018 at 7:06 AM, Vincent Carey  > wrote:
> confirmed with 
> R version 3.5.0 beta (2018-04-10 r74581) under macosx
> 
> sHDF5S> ## Save 'se0' as an HDF5-based SummarizedExperiment object:
> sHDF5S> dir <- sub("file", "h5_se0_", tempfile())
> 
> sHDF5S> h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
> Error: C stack usage  7969544 is too close to the limit
> 
> I've been running into this a lot and in my case it seemed
> sufficient to "remake" old serialized objects.  But this example
> is a good one.  Somehow you have  S4Vectors_0.17.42  while I am working with 
> 0.17.41.
> On a linux system this error was not thrown.
> 
> 
> On Tue, Apr 17, 2018 at 6:14 AM, Elizabeth Purdom  > wrote:
> Hello,
> 
> When I try to run the example code in the saveHDF5SummarizedExperiment 
> function, I get the error "Error: C stack usage  7969416 is too close to the 
> limit”. I am working with development R and have incorporated HDF5 
> functionality in my package. I did so many weeks ago on earlier versions of 
> the packages and didn’t use to get this error, but now my tests are failing, 
> etc, since I can’t create a basic object.
> 
> Perhaps I’m unknowingly using the wrong version or some other problem? 
> Otherwise, I expect this is already known by authors since its their own 
> example, but in that case I am also wondering if I should roll back to an 
> earlier version for now, and if so which one so that I’m still reasonably 
> current?
> 
> Thanks,
> Elizabeth Purdom
> 
> Following example from the help pages of saveHDF5SummarizedExperiment:
> > library(HDF5Array)
> > library(SummarizedExperiment)
> > nrows <- 200; ncols <- 6
> > counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> > colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
> +  row.names=LETTERS[1:6])
> > se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
> + colData=colData)
> > se0
> class: SummarizedExperiment 
> dim: 200 6 
> metadata(0):
> assays(1): counts
> rownames: NULL
> rowData names(0):
> colnames(6): A B ... E F
> colData names(1): Treatment
> > 
> > ## Save 'se0' as an HDF5-based SummarizedExperiment object:
> > dir <- sub("file", "h5_se0_", tempfile())
> > h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
> Error: C stack usage  7969416 is too close to the limit
> #only showing part of traceback, because as expected by error, hitting some 
> kind of loop
> > traceback()
> …..
> 28: nrow(x)
> 27: nrow(x)
> 26: dim(x)
> 25: dim(x)
> 24: nrow(x)
> 23: nrow(x)
> 22: dim(x)
> 21: dim(x)
> 20: nrow(x)
> 19: nrow(x)
> 18: dim(assay)
> 17: dim(assay)
> 16: FUN(X[[i]], ...)
> 15: lapply(as.list(X), match.fun(FUN), ...)
> 14: lapply(as.list(X), match.fun(FUN), ...)
> 13: lapply(X = X, FUN = FUN, ...)
> 12: lapply(X = X, FUN = FUN, ...)
> 11: sapply(assays, function(assay) dim(assay)[1:2])
> 10: sapply(assays, function(assay) dim(assay)[1:2])
> 9: valid.func(object)
> 8: validityMethod(as(object, superClass))
> 7: isTRUE(x)
> 6: anyStrings(validityMethod(as(object, superClass)))
> 5: validObject(ans)
> 4: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed", 
>filepath = 
> "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>  
>name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652, 
>chunkdim = c(200L, 6L
> 3: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed", 
>filepath = 
> "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>  
>name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652, 
>chunkdim = c(200L, 6L
> 2: .write_h5_assays(x@assays, h5_path, chunkdim, level, verbose)
> 1: saveHDF5SummarizedExperiment(se0, dir)
> > sessionInfo()
> R Under development (unstable) (2018-03-22 r74446)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: 
> 

Re: [Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Peter Hickey]

Hi Elizabeth,

Aaron and I were hit by this same error message. As a workaround,
installing DelayedArray and HDF5Array from the git(hub) repo fixed the
issue (https://github.com/Bioconductor/HDF5Array/issues/6). But this
needs to be propagated to the versions made available via BiocLite().

Martin: Might it be possible to trigger a re-build of these 2 packages
on the BioC build machines?

Cheers,
Pete

On 17 April 2018 at 06:14, Elizabeth Purdom  wrote:
> Hello,
>
> When I try to run the example code in the saveHDF5SummarizedExperiment 
> function, I get the error "Error: C stack usage  7969416 is too close to the 
> limit”. I am working with development R and have incorporated HDF5 
> functionality in my package. I did so many weeks ago on earlier versions of 
> the packages and didn’t use to get this error, but now my tests are failing, 
> etc, since I can’t create a basic object.
>
> Perhaps I’m unknowingly using the wrong version or some other problem? 
> Otherwise, I expect this is already known by authors since its their own 
> example, but in that case I am also wondering if I should roll back to an 
> earlier version for now, and if so which one so that I’m still reasonably 
> current?
>
> Thanks,
> Elizabeth Purdom
>
> Following example from the help pages of saveHDF5SummarizedExperiment:
>> library(HDF5Array)
>> library(SummarizedExperiment)
>> nrows <- 200; ncols <- 6
>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
> +  row.names=LETTERS[1:6])
>> se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
> + colData=colData)
>> se0
> class: SummarizedExperiment
> dim: 200 6
> metadata(0):
> assays(1): counts
> rownames: NULL
> rowData names(0):
> colnames(6): A B ... E F
> colData names(1): Treatment
>>
>> ## Save 'se0' as an HDF5-based SummarizedExperiment object:
>> dir <- sub("file", "h5_se0_", tempfile())
>> h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
> Error: C stack usage  7969416 is too close to the limit
> #only showing part of traceback, because as expected by error, hitting some 
> kind of loop
>> traceback()
> …..
> 28: nrow(x)
> 27: nrow(x)
> 26: dim(x)
> 25: dim(x)
> 24: nrow(x)
> 23: nrow(x)
> 22: dim(x)
> 21: dim(x)
> 20: nrow(x)
> 19: nrow(x)
> 18: dim(assay)
> 17: dim(assay)
> 16: FUN(X[[i]], ...)
> 15: lapply(as.list(X), match.fun(FUN), ...)
> 14: lapply(as.list(X), match.fun(FUN), ...)
> 13: lapply(X = X, FUN = FUN, ...)
> 12: lapply(X = X, FUN = FUN, ...)
> 11: sapply(assays, function(assay) dim(assay)[1:2])
> 10: sapply(assays, function(assay) dim(assay)[1:2])
> 9: valid.func(object)
> 8: validityMethod(as(object, superClass))
> 7: isTRUE(x)
> 6: anyStrings(validityMethod(as(object, superClass)))
> 5: validObject(ans)
> 4: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed",
>filepath = 
> "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652,
>chunkdim = c(200L, 6L
> 3: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed",
>filepath = 
> "/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
>name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652,
>chunkdim = c(200L, 6L
> 2: .write_h5_assays(x@assays, h5_path, chunkdim, level, verbose)
> 1: saveHDF5SummarizedExperiment(se0, dir)
>> sessionInfo()
> R Under development (unstable) (2018-03-22 r74446)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
>
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats4stats graphics  grDevices utils datasets  
> methods   base
>
> other attached packages:
>  [1] SummarizedExperiment_1.9.16 Biobase_2.39.2  
> GenomicRanges_1.31.23   GenomeInfoDb_1.15.5
>  [5] HDF5Array_1.7.10rhdf5_2.23.8
> DelayedArray_0.5.30 BiocParallel_1.13.3
>  [9] IRanges_2.13.28 S4Vectors_0.17.42   
> BiocGenerics_0.25.3 matrixStats_0.53.1
>
> loaded via a namespace (and not attached):
>  [1] lattice_0.20-35bitops_1.0-6   grid_3.5.0 
> zlibbioc_1.25.0XVector_0.19.9
>  [6] Matrix_1.2-14  Rhdf5lib_1.1.5 tools_3.5.0
> RCurl_1.95-4.10compiler_3.5.0
> [11] GenomeInfoDbData_1.1.0
>>
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[Bioc-devel] Problem with saveHDF5SummarizedExperiment in HDF5Array package

[Elizabeth Purdom]

Hello,

When I try to run the example code in the saveHDF5SummarizedExperiment 
function, I get the error "Error: C stack usage  7969416 is too close to the 
limit”. I am working with development R and have incorporated HDF5 
functionality in my package. I did so many weeks ago on earlier versions of the 
packages and didn’t use to get this error, but now my tests are failing, etc, 
since I can’t create a basic object.

Perhaps I’m unknowingly using the wrong version or some other problem? 
Otherwise, I expect this is already known by authors since its their own 
example, but in that case I am also wondering if I should roll back to an 
earlier version for now, and if so which one so that I’m still reasonably 
current?

Thanks,
Elizabeth Purdom

Following example from the help pages of saveHDF5SummarizedExperiment:
> library(HDF5Array)
> library(SummarizedExperiment)
> nrows <- 200; ncols <- 6
> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
+  row.names=LETTERS[1:6])
> se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
+ colData=colData)
> se0
class: SummarizedExperiment 
dim: 200 6 
metadata(0):
assays(1): counts
rownames: NULL
rowData names(0):
colnames(6): A B ... E F
colData names(1): Treatment
> 
> ## Save 'se0' as an HDF5-based SummarizedExperiment object:
> dir <- sub("file", "h5_se0_", tempfile())
> h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
Error: C stack usage  7969416 is too close to the limit
#only showing part of traceback, because as expected by error, hitting some 
kind of loop
> traceback()
…..
28: nrow(x)
27: nrow(x)
26: dim(x)
25: dim(x)
24: nrow(x)
23: nrow(x)
22: dim(x)
21: dim(x)
20: nrow(x)
19: nrow(x)
18: dim(assay)
17: dim(assay)
16: FUN(X[[i]], ...)
15: lapply(as.list(X), match.fun(FUN), ...)
14: lapply(as.list(X), match.fun(FUN), ...)
13: lapply(X = X, FUN = FUN, ...)
12: lapply(X = X, FUN = FUN, ...)
11: sapply(assays, function(assay) dim(assay)[1:2])
10: sapply(assays, function(assay) dim(assay)[1:2])
9: valid.func(object)
8: validityMethod(as(object, superClass))
7: isTRUE(x)
6: anyStrings(validityMethod(as(object, superClass)))
5: validObject(ans)
4: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed", 
   filepath = 
"/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
 
   name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652, 
   chunkdim = c(200L, 6L
3: `[[<-`(`*tmp*`, i, value = new("HDF5Matrix", seed = new("HDF5ArraySeed", 
   filepath = 
"/private/var/folders/h4/xtpbyfq55qd3rc882bm4zfjwgn/T/RtmpKIQALa/h5_se0_7d29f927618/assays.h5",
 
   name = "assay001", dim = c(200L, 6L), first_val = 2481.95574347652, 
   chunkdim = c(200L, 6L
2: .write_h5_assays(x@assays, h5_path, chunkdim, level, verbose)
1: saveHDF5SummarizedExperiment(se0, dir)
> sessionInfo()
R Under development (unstable) (2018-03-22 r74446)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets  
methods   base 

other attached packages:
 [1] SummarizedExperiment_1.9.16 Biobase_2.39.2  
GenomicRanges_1.31.23   GenomeInfoDb_1.15.5
 [5] HDF5Array_1.7.10rhdf5_2.23.8
DelayedArray_0.5.30 BiocParallel_1.13.3
 [9] IRanges_2.13.28 S4Vectors_0.17.42   
BiocGenerics_0.25.3 matrixStats_0.53.1 

loaded via a namespace (and not attached):
 [1] lattice_0.20-35bitops_1.0-6   grid_3.5.0 
zlibbioc_1.25.0XVector_0.19.9
 [6] Matrix_1.2-14  Rhdf5lib_1.1.5 tools_3.5.0
RCurl_1.95-4.10compiler_3.5.0
[11] GenomeInfoDbData_1.1.0
> 
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Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

[Carmen M. Livi]

Hi Shijia,

I guess you should update the dependency from 2.15 to 3.5.

In the DESCRIPTION file add R 3.5 as dependency:
Depends: R (>= 3.5)

This should fix the warning.

Carmen

On 17/04/2018 10:49, Shijia Zhu wrote:

Hi Everyone,

   I submitted my package to Bioconductor, but always meet with the
following warning:


** Checking R Version dependency...* WARNING: Update R version
dependency from 2.15 to 3.5.*

Does anyone know how to fix the warning?

Any help will be appreciated very much.

Best
Shijia




On Tue, Apr 17, 2018 at 4:18 AM, bioc-issue-bot 
wrote:


Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report

for more details.

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Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

[Mike Smith]

You had the right idea with your commit
https://github.com/zhushijia/GIGSEA/commit/431af209590f905452b5f10b0ad3a282ab2534e3
but the wrong version of R.  You need to put  Depends: R (>= 3.5) in your
DESCRIPTION file and it should be good.

Mike

On 17 April 2018 at 10:49, Shijia Zhu  wrote:

> Hi Everyone,
>
>   I submitted my package to Bioconductor, but always meet with the
> following warning:
>
>
> ** Checking R Version dependency...* WARNING: Update R version
> dependency from 2.15 to 3.5.*
>
> Does anyone know how to fix the warning?
>
> Any help will be appreciated very much.
>
> Best
> Shijia
>
>
>
>
> On Tue, Apr 17, 2018 at 4:18 AM, bioc-issue-bot 
> wrote:
>
> > Dear Package contributor,
> >
> > This is the automated single package builder at bioconductor.org.
> >
> > Your package has been built on Linux, Mac, and Windows.
> >
> > On one or more platforms, the build results were: "WARNINGS".
> > This may mean there is a problem with the package that you need to fix.
> > Or it may mean that there is a problem with the build system itself.
> >
> > Please see the build report
> >  20180417041834.html>
> > for more details.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> >  381894378>,
> > or mute the thread
> >  AFKtsVCF2VeX6vhwJ5S3toxysjFC10VDks5tpaVfgaJpZM4TPAoV>
> > .
> >
>
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Re: [Rd] strange warning: data() error?

[peter dalgaard]

> On 17 Apr 2018, at 01:08 , David Winsemius  wrote:
> 
> 
> Hypothesis:   datasets in a ..library/data/Rdata.rds file whose listing does 
> not match the name of the dataset from which it is derived will cause the 
> behavior in question.

Yes, because data() originally goes looking for a file with a matching name, 
then loads/reads/executes it depending on file extension. However, some files 
can generate objects with a different name - or several such objects. Turning 
LazyData on doesn't change the semantics of data() (by design, I guess).

So survival's source "data" directory has cgd.Rda with cgd and cgd0, but no 
cgd0.Rda, this is reflected in the "datalist" file in the installed package:

data pd$ more datalist 
bladder: bladder bladder1 bladder2
cancer
cgd: cgd cgd0
colon
flchain
genfan
heart: heart jasa jasa1

 
-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [Bioc-devel] [Bioconductor/Contributions] GIGSEA (#720)

[Shijia Zhu]

Hi Everyone,

  I submitted my package to Bioconductor, but always meet with the
following warning:


** Checking R Version dependency...* WARNING: Update R version
dependency from 2.15 to 3.5.*

Does anyone know how to fix the warning?

Any help will be appreciated very much.

Best
Shijia




On Tue, Apr 17, 2018 at 4:18 AM, bioc-issue-bot 
wrote:

> Dear Package contributor,
>
> This is the automated single package builder at bioconductor.org.
>
> Your package has been built on Linux, Mac, and Windows.
>
> On one or more platforms, the build results were: "WARNINGS".
> This may mean there is a problem with the package that you need to fix.
> Or it may mean that there is a problem with the build system itself.
>
> Please see the build report
> 
> for more details.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
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Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

[Thierry Onkelinx]

Dear Alex,

Have a look at drat
(http://eddelbuettel.github.io/drat/DratForPackageAuthors.html). This
makes it easier to distribute prepackaged R packages (including When
you uploaded a new version, then the student would only have to do
drat::addRepo("your_repo") and then install.pakages("LM2GLMM") or
update.packages()

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///




2018-04-16 19:38 GMT+02:00 Alexandre Courtiol :
> Re,
>
> On 16 April 2018 at 17:35, Georgi Boshnakov <
> georgi.boshna...@manchester.ac.uk> wrote:
>
>> Hi,
>>
>> The problem is indeed difficult to debug but there are things that can be
>> done to narrow it down.
>>
>> 1. Are there 1/3 unlucky computers fixed? (I.e does the problem occur
>> always on the same computers) Also, do you really mean computer or user?
>>
>
> Yes, I mean computer, not user.
>
>>
>> 2. Are the students working under R studio? If so, does the same problem
>> appear if the same procedure is run outside R studio.
>>
>
> I will try tomorrow (but from memory I think the answer will be yes).
>
>>
>> 3. Further to 2.,  You mention development mode - do (some) students also
>> have a copy of your repository? This may be aproblem if they don't update
>> it too.
>>
>
> No, only me has the devel version.
>
>>
>> 4. What happens if R is restarted?
>
>
> I will try tomorrow (but I think the answer will be nothing).
>
>
>> 5. It may be worth checking .Rprofle and similar for the concerned
>> computers (or users, see 1.)
>>
>
> I will try as well but most had a fresh install and did not mess with
> settings.
>
>>
>> Hope this is of some help.
>>
>
> I will look at all this and also gather the session infos as Ben suggested.
> I think I know how to proceed to get to the bottom of that, but I was just
> hoping that the problem was already well known and the answer as well...
> If it is for anyone, please reply. Otherwise, I will investigate.
> Thanks to everyone.
> Alex
>
>
>>
>>
>>  Georgi Boshnakov
>>
>>
>> 
>> From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf
>> of Alexandre Courtiol [alexandre.court...@gmail.com]
>> Sent: 16 April 2018 14:40
>> To: List r-package-devel
>> Subject: [R-pkg-devel] vignette via devtools: sometimes found, sometimes
>> not (same package)
>>
>> Dear all,
>> I am teaching a class and for that I created a R package that mostly
>> contains vignettes (the slides of the course).
>> I host the package on GitHub because I want the students to download every
>> day the latest version of the package.
>> Building the vignettes takes a couple of hours so I pre-build the vignettes
>> using devtools::build_vignettes before pushing my updates to GitHub.
>> The student install the package using
>> devtools::install_github("courtiol/LM2GLMM").
>> Then, they do library(LM2GLMM) and browseVignettes(package = "LM2GLMM")...
>>
>> ... and that works on 2/3 of the computers, for the others it says
>> vignettes not found.
>>
>> Any idea why and what can I do to make it 100% success?
>> Of course on my laptop it works, so I cannot investigate.
>> Also, since they all use different versions of R, devtools or OS... I would
>> like to know the one thing that must be changed if it comes from that (but
>> I am not sure it does).
>>
>> I have added a back up function that works for the 1/3 of unfortunate
>> students:
>>
>> get_vignettes <- function() {
>>   utils::browseURL(paste0(find.package("LM2GLMM"), "/doc/")) ## for
>> installed
>>   utils::browseURL(paste0(find.package("LM2GLMM"), "/inst/doc/")) ## for
>> development
>>   return(invisible(NULL))
>> }
>>
>> This functions opens de vignette folder and that shows that all the
>> students actually have the html files installed correctly. But it is ugly
>> because then they have to find the good html file and so forth, so I would
>> rather have a better solution.
>>
>> Many thanks,
>>
>> Alex
>>
>> --
>> Alexandre Courtiol
>>
>> http://sites.google.com/site/alexandrecourtiol/home
>>
>> *"Science is the belief in the ignorance of experts"*, R. Feynman
>>
>>