Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Leonardo Collado Torres]

Hi,

Thank you for all the work in this transition Andrzej, Lori, Valerie,
Nitesh and Hervé!


I have a few questions about the new system.

1) I already had a github repo (that I manually kept in sync with the
subversion one) for the recountWorkflow. Should I just follow the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
I guess that I'll need to do this too
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-

2) Is repo/vignettes/.html_output still needed?

3) Related to (2), the .html_output file used to ignore the `output`
line in the vignette YAML. I got an email from Lori saying that
output: BiocWorkflowTools::f1000_article is not working for
recountWorfkflow for now (no html vignette). My guess is that the
`output` line now matters, and in my case, that would build a pdf file
which is ignored due to
https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
in my .Rbuildignore.

4) Related to the last 2. What setup do you recommend so I can
maintain a single git repo that produces the files needed for
uploading them to F1000research? Before this transition, I had to
maintain 3 repos: the subversion one for Bioc, my git copy (well,
main), and another one with the files setup for F1000. At some point
in the past, Andrzej recommended that I use "output:
BiocWorkflowTools::f1000_article" to try to have all the files in 1
place. I imagine that I would still need some ifelse() statements for
sentences like the one I have at
https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
I think that this question could be generalized and documented in the
Bioc website.

5) Is there anything else I should be aware of so I can reproduce any
errors? In the past, the Bioc workflow system would trigger a build
immediately after a new push, and due to the custom way workflows were
built (like .html_output), I relied on these builds to check if my
changes had worked or not: specially early on where I had issues with
figures, links to figures and figure captions.

Best,
Leo






On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori
 wrote:
>
> For now the page at
>
> https://www.bioconductor.org/help/workflows/
>
> will remain and be updated accordingly however there is discussion about 
> having this page be removed or redirected.
>
>
> In the next few days I hope to have the new landing pages up and running and 
> will make an announcement when they are live. The new changes involve having 
> a link to the workflows on the biocViews page, that will directly link to a 
> workflow package landing page (like the software, annotation, and experiment 
> package do).
>
>
> Until the release your changes will be visible in devel which will transition 
> over to the new release just as done for software packages -
>
> The workflow are built monday, wednesday, and friday and the new landing 
> pages will reflect when the package is propagated like the other types of 
> packages.
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
> 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 Aaron Lun 
> 
> Sent: Sunday, April 1, 2018 2:17:09 PM
> To: Herv� Pag�s; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Workflows are now in git (and other Important 
> workflow-related changes)
>
> Thanks everybody, this is much appreciated.
>
> On that note, will the compiled workflows shown at:
>
> https://www.bioconductor.org/help/workflows/
>
> ... be updated to reflect changes in the git repositories for the
> workflows?
>
> Or will the workflow page just directly link to the landing page for
> each package? This would be very convenient, not least because it will
> avoid me having to make pull requests to the bioconductor.org
> repository every time I want to change my workflow blurb.
>
> I'm in the process of fixing and updating my various workflows, and I'm
> wondering when/how my changes will be visible to users.
>
> Cheers,
>
> Aaron
>
> On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> > To the authors/maintainers of the workflows:
> >
> >
> > Following the svn-to-git migration of the software and data
> > experiment
> > packages last summer, we've completed the migration of the workflow
> > packages.
> >
> > The canonical location for the workflow source code now is
> > git.bioconductor.org
> >
> > Please use your git client to access/maintain your workflow the same
> > way you would do it for a software or data-experiment package.
> >
> > We've also migrated the workflows to our in-house build system.
> > Starting with Bioc 3.7, the build report for the devel versions of
> > the 

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

[Shepherd, Lori]

For now the page at

https://www.bioconductor.org/help/workflows/

will remain and be updated accordingly however there is discussion about having 
this page be removed or redirected.


In the next few days I hope to have the new landing pages up and running and 
will make an announcement when they are live. The new changes involve having a 
link to the workflows on the biocViews page, that will directly link to a 
workflow package landing page (like the software, annotation, and experiment 
package do).


Until the release your changes will be visible in devel which will transition 
over to the new release just as done for software packages -

The workflow are built monday, wednesday, and friday and the new landing pages 
will reflect when the package is propagated like the other types of packages.
http://bioconductor.org/checkResults/3.7/workflows-LATEST/


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 Aaron Lun 

Sent: Sunday, April 1, 2018 2:17:09 PM
To: Herv� Pag�s; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Workflows are now in git (and other Important 
workflow-related changes)

Thanks everybody, this is much appreciated.

On that note, will the compiled workflows shown at:

https://www.bioconductor.org/help/workflows/

... be updated to reflect changes in the git repositories for the
workflows?

Or will the workflow page just directly link to the landing page for
each package? This would be very convenient, not least because it will
avoid me having to make pull requests to the bioconductor.org
repository every time I want to change my workflow blurb.

I'm in the process of fixing and updating my various workflows, and I'm
wondering when/how my changes will be visible to users.

Cheers,

Aaron

On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> To the authors/maintainers of the workflows:
>
>
> Following the svn-to-git migration of the software and data
> experiment
> packages last summer, we've completed the migration of the workflow
> packages.
>
> The canonical location for the workflow source code now is
> git.bioconductor.org
>
> Please use your git client to access/maintain your workflow the same
> way you would do it for a software or data-experiment package.
>
> We've also migrated the workflows to our in-house build system.
> Starting with Bioc 3.7, the build report for the devel versions of
> the workflows can be found here:
>
>https://bioconductor.org/checkResults/devel/workflows-LATEST/
>
> We run these builds every other day (Mondays, Wednesdays, Fridays).
> Because of limited build resources, we now run the data-experiment
> builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
>
> The links to the package landing pages are not working yet. This
> will be addressed in the next few days.
>
> Please address any error you see on the report for the workflow
> you maintain.
>
> Note that, from now on, we're also following the same version scheme
> for these packages as for the software and data-experiment packages.
> That is, we're using an even y (in x.y.z) in release and an odd y in
> devel. We'll take care of bumping y at release time (like we do for
> software and data-experiment packages).
>
> After the next Bioconductor release (scheduled for May 1), we'll
> start
> building the release versions of the workflows in addition to the
> devel versions. The build report for the release versions will be
> here:
>
>https://bioconductor.org/checkResults/release/workflows-LATEST/
>
> Finally, please note that with the latest version of BiocInstaller
> (1.29.5), workflow packages can be installed with biocLite(), like
> any other Bioconductor package. We'll deprecate the old mechanism
> (workflowInstall()) at some point in the future.
>
> Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> migration.
>
> Let us know if you have any question about this.
>
> H.
>
>

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


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

[Bioc-devel] AAString - Amino acid code enforced?

[Felix Ernst]

Dear all,

probably this is for Hervé Pagès:

I tried the following code, which should according to ?AAString not work, since 
ÜÖÄ are not part of any AA code.

> AAString("ÜÄÖ")
  3-letter "AAString" instance
seq: ÜÄÖ
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
LC_MONETARY=German_Germany.1252 LC_NUMERIC=C   
[5] LC_TIME=German_Germany.1252

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets  
methods   base 

other attached packages:
[1] Biostrings_2.46.0   XVector_0.18.0  IRanges_2.12.0  
S4Vectors_0.16.0BiocGenerics_0.24.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0 compiler_3.4.4  tools_3.4.4 yaml_2.1.18


I don’t have access right now to the devel version of Biostrings, bit I checked 
out the current Code in the github repo and its recent changes. I am pretty 
sure, that this behavior is also in the current devel branch. Can someone 
confirm this?

My current interest is in using the XString classes and methods for an 
additional biological string representation. The initial question was, how can 
I restrict this to a certain character set, if the characters are not saved 
byte encoded? The latter option is not available to me, since characters like 
‚«‘ or ‚=‘ result in a two byte code using the charToRaw function. This trips 
up the build of the internal lookup table, which are passed down to the C 
backend.

Therefore I looked into, how this is done for an AAString differing from a 
BString. I discovered, that it currently doesn‘t. I also looked into the 
current 2.47.12 repo, which as far as I can tell does not use the 
AMINO_ACID_CODE constant in the creation of an AAString object.

So my questions are:
- What is the best practice for extending a class from XString with a 
restricted character set, which is not byte encoded?
- Is there a way to use byte encoding for chars with two ore more bytes?

 Thanks in advance for any help and suggestions.

Best regards,
Felix

PS: regarding the second question: One could change 
„as.integer(charToRaw(paste(letters, collapse="")))“ to 
„lapply(lapply(letters,charToRaw),as.integer)“ in .letterAsByteVal, but in any 
case it will not be atomic anymore, which I think is required to be excepted by 
the C backend. I didn’t test it.






[[alternative HTML version deleted]]

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

[Bioc-devel] Final List of Deprecated Packages for Bioc3.7

[Shepherd, Lori]

The Bioconductor Team has identified the following list of deprecated packages:



Maintainer requested deprecation:



Software Package:

ontoCAT

spliceR (functionalities moved to IsoformSwitchAnalyzeR)

mvGST





Experiment Data Package:

RnaSeqTutorial

cheung2010

MEALData (replaced with brgedata)





Unresponsive/not-maintained packages:

Software:

GMRP

MBttest

OperaMate

DASC

htSeqTools

PAnnBuilder

DMRScan

phenoDist





We did not announce that the following is also no longer available Experiment 
Data Package: IlluminaHumanMethylation450k.db



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

[Bioc-devel] Release Deadline: Passing R CMD build and R CMD check

[Shepherd, Lori]

As stated in the release schedule The Deadline for all packages passing R CMD 
build and R CMD check without errors or warnings in devel is Wednesday April 
25th. This includes software, data experiment and workflow packages. Some 
warnings will be accepted, with clarification on the bioc-devel mailing list.

If you are having trouble please feel free to email bioc-devel@r-project.org 
with questions.

Please also note Wednesday April 11 is the last day to submit changes to the 
current release 3.6 branch.
If ERRORS are not fixed by this date, the package will be frozen broken in this 
release.


See the release schedule for other important deadlines

http://bioconductor.org/developers/release-schedule/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Need some help to submit a R package.

[Turaga, Nitesh]

Hi,

Please read through this documentation.

http://bioconductor.org/developers/package-submission/


Nitesh

> On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:
> 
> Dear Sir,
> 
> 
> 
> I have developed an R package. I want to submit this package in
> Bioconductor.
> Please help me to submit the R package.
> 
> 
> 
> 
> 
> 
> 
> 
> 
> regards
> Pijush Das
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] BiocGenerics::unique Bug? "Error: node stack overflow" in package esATAC

[Zheng Wei]

Dear all,


I am a maintainer of package 'esATAC'.


I find this error if calling library(rJava) before using BiocGenerics::unique.


This error makes esATAC under bioc_3_7 check error because esATAC has to import 
rJava.


The error reproduce-able code and session information is pasted below. 


Thanks,
Zheng


R Under development (unstable) (2018-03-12 r74392) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.


  Natural language support but running in an English locale


R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.


Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


> library(rJava)
> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel


Attaching package: ‘BiocGenerics’


The following objects are masked from ‘package:parallel’:


clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB


The following objects are masked from ‘package:rJava’:


anyDuplicated, duplicated, sort, unique


The following objects are masked from ‘package:stats’:


IQR, mad, sd, var, xtabs


The following objects are masked from ‘package:base’:


anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min


Loading required package: S4Vectors


Attaching package: ‘S4Vectors’


The following object is masked from ‘package:base’:


expand.grid


Loading required package: IRanges
Loading required package: GenomeInfoDb
> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
+ ranges=IRanges(16:21, 20),
+ strand=rep(c("+", "-", "*"), 2))
> unique(gr1)
Error: node stack overflow
> BiocGenerics::unique(gr1)
Error: node stack overflow
> sessionInfo()
R Under development (unstable) (2018-03-12 r74392)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)


Matrix products: default
BLAS: /home/software/R/R-devel/lib64/R/lib/libRblas.so
LAPACK: /home/software/R/R-devel/lib64/R/lib/libRlapack.so


locale:
 [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C 
 [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C   
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C  


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


other attached packages:
[1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5   IRanges_2.13.28  
[4] S4Vectors_0.17.38 BiocGenerics_0.25.3   rJava_0.9-9  


loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0compiler_3.5.0 XVector_0.19.9
[4] GenomeInfoDbData_1.1.0 RCurl_1.95-4.10bitops_1.0-6   
[[alternative HTML version deleted]]

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

[Bioc-devel] Need some help to submit a R package.

[Pijush Das]

Dear Sir,



I have developed an R package. I want to submit this package in
Bioconductor.
Please help me to submit the R package.









regards
Pijush Das

[[alternative HTML version deleted]]

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

[Bioc-devel] Bioconductor New Package Submission Deadline Today!

[Shepherd, Lori]

Today is the final day to submit new packages to the Bioconductor contributions 
tracker to have a shot at being included in the upcoming 3.7 release at the end 
of the month.

https://github.com/Bioconductor/Contributions


Please note: submission today does not guarantee it will be included - the 
package must undergo an official review and be accepted by April 16th.


Submissions after today and those that are not accepted by April 16th will 
still be able to be in Bioconductor but will be included in the 3.8 release 
later in the year.


Please see the release schedule for other important deadlines

http://bioconductor.org/developers/release-schedule/


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Error: node stack overflow

[Hervé Pagès]

Hi Zheng,

Thanks for the report. I will look into this and will let you know.

H.

On 04/01/2018 02:38 AM, Zheng Wei wrote:

Dear all,

I find this error if calling library(rJava) before using 
BiocGenerics::unique


The code is pasted below.

Thanks,
Zheng

 > library(rJava)
 > library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ??BiocGenerics??

The following objects are masked from ??package:parallel??:

 ?0?2 ?0?2 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ
 ?0?2 ?0?2 clusterExport, clusterMap, parApply, parCapply, parLapp
 ?0?2 ?0?2 parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ??package:rJava??:

 ?0?2 ?0?2 anyDuplicated, duplicated, sort, unique

The following objects are masked from ??package:stats??:

 ?0?2 ?0?2 IQR, mad, sd, var, xtabs

The following objects are masked from ??package:base??:

 ?0?2 ?0?2 anyDuplicated, append, as.data.frame, basename, cbind,
 ?0?2 ?0?2 colnames, colSums, dirname, do.call, duplicated, eval,
 ?0?2 ?0?2 Filter, Find, get, grep, grepl, intersect, is.unsorted,
 ?0?2 ?0?2 lengths, Map, mapply, match, mget, order, paste, pmax,
 ?0?2 ?0?2 pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans
 ?0?2 ?0?2 rowSums, sapply, setdiff, sort, table, tapply, union, u
 ?0?2 ?0?2 unsplit, which, which.max, which.min

Loading required package: S4Vectors


Attaching package: ??S4Vectors??

The following object is masked from ??package:base??:

 ?0?2 ?0?2 expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
 > gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
+?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ranges=IRanges(16:21, 20),
+?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 ?0?2 strand=rep(c("+", "-", "*"), 2))
 > unique(gr1)
Error: node stack overflow
 > BiocGenerics::unique(gr1)
Error: node stack overflow




--
Herv?? Pag??s

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

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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

[Bioc-devel] Matrix::(cBind|rBind) to base::(cbind|rbind)

[Turaga, Nitesh]

Hello Maintainers,

The following packages have been identified for changing the functions 
‘Matrix::cBind’ and ‘Matrix::rBind’ to the ‘base::cbind’ and ‘base::rbind’. The 
functions  ‘Matrix::cBind’ and ‘Matrix::rBind’ have been deprecated by the 
author of the Matrix package. 
(https://cran.r-project.org/web/packages/Matrix/news.html). 

List of packages:  

chromVAR, gCMAP, gespeR, HiTC, Mirsynergy, monocle, Ringo

I’ve issued a version bump along with the switch to the new functions. These 
commits should be merged into your Github repos if you are maintaining your 
packages on both Bioconductor and Github. 

The commit should look like this:



Commit message from Nitesh Turaga , 

Change from cBind and rBind to 'cbind' and 'rbind'.

- version bump
- Reference to NEWS file from Matrix package indicating
deprecated 'cBind' and 'rBind'

https://cran.r-project.org/web/packages/Matrix/news.html


Please reply to this thread if you have any further questions regarding this 
change. 


Best regards,

Nitesh Turaga
Bioconductor Core Team

This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Error: node stack overflow

[Vincent Carey]

I get the following on MacOSX, after library(rJava); library(GenomicRanges)
-- take rJava out of the mix and
there is no error.  I ran into this originally as an interaction between
rJava and Gviz, and have reported to
Florian.  That seemed to be MacOSX-specific.

> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),

+  ranges=IRanges(16:21, 20),

+  strand=rep(c("+", "-", "*"), 2))

>  unique(gr1)

*Error in validObject(.Object) : *

*  invalid class "MethodWithNext" object: Error : C stack usage  7969864 is
too close to the limit*

*Error during wrapup: C stack usage  7969656 is too close to the limit*


*> sessionInfo()*







* R Under development (unstable) (2018-02-14 r74250) Platform:
x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6
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  [8] methods   base  other attached
packages: [1] GenomicRanges_1.31.23 GenomeInfoDb_1.15.5   IRanges_2.13.28
[4] S4Vectors_0.17.38 BiocGenerics_0.25.3   rJava_0.9-9
[7] rmarkdown_1.9 loaded via a namespace (and not attached):  [1]
Rcpp_0.12.16   digest_0.6.15  rprojroot_1.3-2 [4]
bitops_1.0-6   backports_1.1.2magrittr_1.5[7]
evaluate_0.10.1zlibbioc_1.25.0stringi_1.1.7  [10]
XVector_0.19.9 tools_3.5.0stringr_1.3.0  [13]
RCurl_1.95-4.10compiler_3.5.0 htmltools_0.3.6[16]
knitr_1.20 GenomeInfoDbData_1.1.0 *



On Mon, Apr 2, 2018 at 2:25 PM, Hervé Pagès  wrote:

> Hi Zheng,
>
> Thanks for the report. I will look into this and will let you know.
>
> H.
>
> On 04/01/2018 02:38 AM, Zheng Wei wrote:
>
>> Dear all,
>>
>> I find this error if calling library(rJava) before using
>> BiocGenerics::unique
>>
>> The code is pasted below.
>>
>> Thanks,
>> Zheng
>>
>>  > library(rJava)
>>  > library(GenomicRanges)
>> Loading required package: stats4
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>>
>>  clusterApply, clusterApplyLB, clusterCall, clusterEvalQ
>>  clusterExport, clusterMap, parApply, parCapply, parLapp
>>  parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following objects are masked from ‘package:rJava’:
>>
>>  anyDuplicated, duplicated, sort, unique
>>
>> The following objects are masked from ‘package:stats’:
>>
>>  IQR, mad, sd, var, xtabs
>>
>> The following objects are masked from ‘package:base’:
>>
>>  anyDuplicated, append, as.data.frame, basename, cbind,
>>  colnames, colSums, dirname, do.call, duplicated, eval,
>>  Filter, Find, get, grep, grepl, intersect, is.unsorted,
>>  lengths, Map, mapply, match, mget, order, paste, pmax,
>>  pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans
>>  rowSums, sapply, setdiff, sort, table, tapply, union, u
>>  unsplit, which, which.max, which.min
>>
>> Loading required package: S4Vectors
>>
>>
>> Attaching package: ‘S4Vectors’
>>
>> The following object is masked from ‘package:base’:
>>
>>  expand.grid
>>
>> Loading required package: IRanges
>> Loading required package: GenomeInfoDb
>>  > gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
>> +ranges=IRanges(16:21, 20),
>> +strand=rep(c("+", "-", "*"), 2))
>>  > unique(gr1)
>> Error: node stack overflow
>>  > BiocGenerics::unique(gr1)
>> Error: node stack overflow
>>
>>
>>
> --
> 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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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

[Bioc-devel] Problem getting updated checkResults

[Lorena Pantano]

Hi,

I am trying to get the last version of my package(isomiRs) to be build by the 
testing system, but it seems it doesn’t get 
updated(http://bioconductor.org/checkResults/release/bioc-LATEST/isomiRs/). 

It is still seeing the version from last year even when I updated the package 
last week (however the last version -1.7.3 is ok when downloading from 
https://git.bioconductor.org/packages/isomiRs). My other package (DEGreport) is 
good though.

Can somebody help me to know what I am doing wrong?

Thanks in advance
[[alternative HTML version deleted]]

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

[Bioc-devel] "convert" graphics error for new submission

[Vincent Carey]

for two host-types I am seeing an error that I do not know how to address

Loading required package: ontologyIndex
sh: line 1: 76907 Abort trap: 6   'convert'
'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim
'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null
sh: line 1: 76914 Abort trap: 6   'convert'
'BiocOncoTK_files/figure-html/dopogmock-1.png' -trim
'BiocOncoTK_files/figure-html/dopogmock-1.png' > /dev/null
Quitting from lines 351-363 (BiocOncoTK.Rmd)
Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:

[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Problem getting updated checkResults

[Lorena Pantano]

Yep, silly mistake, it seems I was in the stable version. Dummy me. I’ll kick 
myself for make you waste your time.

Thanks for your time.

> On Apr 2, 2018, at 5:30 PM, Obenchain, Valerie 
>  wrote:
> 
> Hi Lorena,
> 
> You'll have to supply more information for us to help you. The build report 
> shows version 1.7.3:
> 
>   https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ 
> 
> 
> What version are you expecting? Have you pushed all local changes to 
> git.bioconductor.org? What does `git log` say? How about your remotes?
> 
> This is the last commit I see for isomiRs on git.bioconductor.org. The 
> DESCRIPTION file says version 1.7.3.
> 
> commit ab2b609c01bdfc7e833b08c57cb74c9515d89a12 (HEAD -> master, 
> origin/master, origin/HEAD)
> Author: Lorena Pantano  
> 
> Date:   Fri Mar 30 08:29:28 2018 -0400
> 
> Pass check
> 
> .travis.yml
> DESCRIPTION
> NEWS
> R/targets.R
> man/isoNetwork.Rd
> 
> 
> Valerie
> 
> 
> 
> 
> 
> On 04/02/2018 01:48 PM, Lorena Pantano wrote:
>> Hi,
>> 
>> I am trying to get the last version of my package(isomiRs) to be build by 
>> the testing system, but it seems it doesn’t get 
>> updated(http://bioconductor.org/checkResults/release/bioc-LATEST/isomiRs/ 
>> ). 
>> 
>> It is still seeing the version from last year even when I updated the 
>> package last week (however the last version -1.7.3 is ok when downloading 
>> from https://git.bioconductor.org/packages/isomiRs 
>> ). My other package 
>> (DEGreport) is good though.
>> 
>> Can somebody help me to know what I am doing wrong?
>> 
>> Thanks in advance
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org  mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
>> 
>> 
> 
> 
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.


[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Problem getting updated checkResults

[Obenchain, Valerie]

Hi Lorena,

You'll have to supply more information for us to help you. The build report 
shows version 1.7.3:

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

What version are you expecting? Have you pushed all local changes to 
git.bioconductor.org? What does `git log` say? How about your remotes?

This is the last commit I see for isomiRs on git.bioconductor.org. The 
DESCRIPTION file says version 1.7.3.

commit ab2b609c01bdfc7e833b08c57cb74c9515d89a12 (HEAD -> master, origin/master, 
origin/HEAD)
Author: Lorena Pantano 

Date:   Fri Mar 30 08:29:28 2018 -0400

Pass check

.travis.yml
DESCRIPTION
NEWS
R/targets.R
man/isoNetwork.Rd


Valerie





On 04/02/2018 01:48 PM, Lorena Pantano wrote:

Hi,

I am trying to get the last version of my package(isomiRs) to be build by the 
testing system, but it seems it doesn�t get 
updated(http://bioconductor.org/checkResults/release/bioc-LATEST/isomiRs/).

It is still seeing the version from last year even when I updated the package 
last week (however the last version -1.7.3 is ok when downloading from 
https://git.bioconductor.org/packages/isomiRs). My other package (DEGreport) is 
good though.

Can somebody help me to know what I am doing wrong?

Thanks in advance
[[alternative HTML version deleted]]

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





This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

[Bioc-devel] BiocGenerics::unique Bug? Error: node stack overflow

[魏征]

Dear all,


I am a maintainer of package 'esATAC'


I find this error if calling library(rJava) before using BiocGenerics::unique


The code is pasted below. 


Thanks,
Zheng


> library(rJava)
> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel


Attaching package: ‘BiocGenerics’


The following objects are masked from ‘package:parallel’:


clusterApply, clusterApplyLB, clusterCall, clusterEvalQ
clusterExport, clusterMap, parApply, parCapply, parLapp
parLapplyLB, parRapply, parSapply, parSapplyLB


The following objects are masked from ‘package:rJava’:


anyDuplicated, duplicated, sort, unique


The following objects are masked from ‘package:stats’:


IQR, mad, sd, var, xtabs


The following objects are masked from ‘package:base’:


anyDuplicated, append, as.data.frame, basename, cbind,
colnames, colSums, dirname, do.call, duplicated, eval,
Filter, Find, get, grep, grepl, intersect, is.unsorted,
lengths, Map, mapply, match, mget, order, paste, pmax,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans
rowSums, sapply, setdiff, sort, table, tapply, union, u
unsplit, which, which.max, which.min


Loading required package: S4Vectors




Attaching package: ‘S4Vectors’


The following object is masked from ‘package:base’:


expand.grid


Loading required package: IRanges
Loading required package: GenomeInfoDb
> gr1 <- GRanges(seqnames=Rle(c("ch1", "chMT"), c(2, 4)),
+ranges=IRanges(16:21, 20),
+strand=rep(c("+", "-", "*"), 2))
> unique(gr1)
Error: node stack overflow
> BiocGenerics::unique(gr1)
Error: node stack overflow
[[alternative HTML version deleted]]

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

Re: [Bioc-devel] Problem getting updated checkResults

[Obenchain, Valerie]

No problem. I'm glad you figured it out.

Valerie


On 04/02/2018 03:16 PM, Lorena Pantano wrote:
Yep, silly mistake, it seems I was in the stable version. Dummy me. I�ll kick 
myself for make you waste your time.

Thanks for your time.

On Apr 2, 2018, at 5:30 PM, Obenchain, Valerie 
> 
wrote:

Hi Lorena,

You'll have to supply more information for us to help you. The build report 
shows version 1.7.3:

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

What version are you expecting? Have you pushed all local changes to 
git.bioconductor.org? What does `git log` say? How 
about your remotes?

This is the last commit I see for isomiRs on 
git.bioconductor.org. The DESCRIPTION file says 
version 1.7.3.

commit ab2b609c01bdfc7e833b08c57cb74c9515d89a12 (HEAD -> master, origin/master, 
origin/HEAD)
Author: Lorena Pantano 

Date:   Fri Mar 30 08:29:28 2018 -0400

Pass check

.travis.yml
DESCRIPTION
NEWS
R/targets.R
man/isoNetwork.Rd


Valerie





On 04/02/2018 01:48 PM, Lorena Pantano wrote:

Hi,

I am trying to get the last version of my package(isomiRs) to be build by the 
testing system, but it seems it doesn�t get 
updated(http://bioconductor.org/checkResults/release/bioc-LATEST/isomiRs/).

It is still seeing the version from last year even when I updated the package 
last week (however the last version -1.7.3 is ok when downloading from 
https://git.bioconductor.org/packages/isomiRs). My other package (DEGreport) is 
good though.

Can somebody help me to know what I am doing wrong?

Thanks in advance
[[alternative HTML version deleted]]

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




This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), you 
are hereby notified that any disclosure, copying, distribution, or use of this 
email message is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail and delete this email message from your 
computer. Thank you.




This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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

[Bioc-devel] Release of R package

[Watson Zhang]

Hi,

I submitted R package MAGeCKFlute last year, which should be released
recently. However, I checked the release list from "
https://bioconductor.org/checkResults/release/bioc-LATEST/;, and I didn't
find my package "MAGeCKFlute". Can you help to check that? And tell me why?

Look forward for your reply.

Thanks

-- 
Watson Wubing Zhang
Shirley Liu lab in Tongji University
Biostatistics and Computational Biology

[[alternative HTML version deleted]]

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