[Bioc-devel] questions about windows build execute permissions and R version dependency

2017-03-22 Thread Alicia Schep 
Hi,

I have a two questions about the bioconductor build and BiocCheck process
when submitting packages.

1) My submitted package ('motifmatchr') returns the following warning on
the Windows computer:

Warning: file 'motifmatchr/cleanup' did not have execute permissions: corrected

How can this warning be averted?  How to give the file permission? I tried
fixing this issue by making the file executable on my computer-- on GitHub
it shows up as marked as "Executable File". This did not prevent the
warning though.

2) The same package also gives a warning in BiocCheck related to the
version of R required in DESCRIPTION.  As the package is currently hosted
on GitHub and tested against the current release of R using travis, I would
like the github version to have a dependency of only R 3.3 rather than R
3.4. Is it possible to have a different dependency for the R version on
GitHub versus on Bioconductor?

Appreciate any guidance on these question.  Thanks,

Alicia

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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś 
On Wed, Mar 22, 2017 at 6:12 PM, Hervé Pagès  wrote:

>
>   setClass("A", representation(stuff="numeric"))
>   as.vector.A <- function (x, mode="any") x@stuff
>   a <- new("A", stuff=c(3.5, 0.1))
>   x <- numeric(10)
>   x[3:4] <- a
>
> then the code is now valid and we still get the segfault on Mac.
>

Thanks Hervé for the updated MWE.  As suggested by Martin and Dan I've run
it through valgrind on Linux but it didn't give any errors...

Andrzej

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Re: [Bioc-devel] builds: veracruz2 Mac builder

2017-03-22 Thread Obenchain, Valerie 
Minor correction below:

On 03/22/2017 12:56 PM, Obenchain, Valerie wrote:
> Hi,
>
> We recently learned that R 3.4.0, to be released on April 21, will use
> OS X 10.11 (El Capitan).  This means we need a new devel Mac builder up
> and running before the next release. toluca2 will also become an El
> Capitan builder but not until after the release.

We won't be reusing the toluca2 machine or name. Post-release we'll get
a new machine and it will get a new name ... some TBD city in Mexico.

Valerie


>
> Over the past week, Herve has been configuring the new machine,
> veracruz2, and you may have noticed it's been added to the build report:
>
>   https://bioconductor.org/checkResults/3.5/bioc-LATEST/
>
> In today's report there were a few segfault errors which may be related
> to the fact that we're using the wrong C and C++ compilers right now. We
> hope to have these issues sorted out soon.
>
> Valerie
>
>
>
> This email message may contain legally privileged and/or confidential 
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>



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[Bioc-devel] builds: veracruz2 Mac builder

2017-03-22 Thread Obenchain, Valerie 
Hi,

We recently learned that R 3.4.0, to be released on April 21, will use
OS X 10.11 (El Capitan).  This means we need a new devel Mac builder up
and running before the next release. toluca2 will also become an El
Capitan builder but not until after the release.

Over the past week, Herve has been configuring the new machine,
veracruz2, and you may have noticed it's been added to the build report:

  https://bioconductor.org/checkResults/3.5/bioc-LATEST/

In today's report there were a few segfault errors which may be related
to the fact that we're using the wrong C and C++ compilers right now. We
hope to have these issues sorted out soon.

Valerie



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[Bioc-devel] Annotation packages maintained by Francesco Ferrari

2017-03-22 Thread Obenchain, Valerie 
Hi,

We have 24 annotation packages in the repo maintained by Francesco
Ferrari, the majority of which are broken (output below). The last time
these were updated was for Bioconductor 2.8 (3 years ago). We've tried a
number of times to contact Francesco but did not get a response.

The plan is to remove these 24 from the Bioconductor 3.5 release:

> pkgs
 [1] "gahgu133acdf"   "gahgu133a.db"   "gahgu133aprobe"   
 [4] "gahgu133bcdf"   "gahgu133b.db"   "gahgu133bprobe"   
 [7] "gahgu133plus2cdf"   "gahgu133plus2.db"   "gahgu133plus2probe"
[10] "gahgu95av2cdf"  "gahgu95av2.db"  "gahgu95av2probe"  
[13] "gahgu95bcdf""gahgu95b.db""gahgu95bprobe"
[16] "gahgu95ccdf""gahgu95c.db""gahgu95cprobe"
[19] "gahgu95dcdf""gahgu95d.db""gahgu95dprobe"
[22] "gahgu95ecdf""gahgu95e.db""gahgu95eprobe" 

If anyone is interested in taking over as maintainer please let me know.

Valerie


Sample R CMD check error:

   * checking examples ... ERROR
   Running examples in ‘gahgu95av2.db-Ex.R’ failed
   The error most likely occurred in:

   > ### Name: gahgu95av2_dbconn
   > ### Title: Collect information about the package annotation DB
   > ### Aliases: gahgu95av2_dbconn gahgu95av2_dbfile gahgu95av2_dbschema
   > ###   gahgu95av2_dbInfo
   > ### Keywords: utilities datasets
   >
   > ### ** Examples
   >
   >   ## Count the number of rows in the "probes" table:
   >   dbGetQuery(gahgu95av2_dbconn(), "SELECT COUNT(*) FROM probes")
   Error: could not find function "dbGetQuery"
   Execution halted
   * checking PDF version of manual ... OK
   * DONE

   Status: 1 ERROR, 4 NOTEs
   See
 ‘/home/biocbuild/bbs-3.4-bioc/gahgu95av2.db.Rcheck/00check.log’
   for details.



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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Dan Tenenbaum 


- Original Message -
> From: "Hervé Pagès" 
> To: "Martin Morgan" , "lcollado" 
> , "bioc-devel"
> 
> Cc: "Jeff Leek" , "Andrew Jaffe" 
> Sent: Wednesday, March 22, 2017 10:21:43 AM
> Subject: Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that 
> sometimes popped up, sometimes it didn't.
> Related to IRanges/S4Vectors '$<-'

> On 03/21/2017 05:28 PM, Martin Morgan wrote:
>> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>>> Hi Leonardo,
>>>
>>> Thanks for hunting down and isolating that bug! I tried to simplify
>>> your code even more and was able to get a segfault with just:
>>>
>>>   setClass("A", representation(stuff="numeric"))
>>>   x <- logical(10)
>>>   x[TRUE] <- new("A")
>>>
>>> I get the segfault about 50% of the time on a fresh R session on Mac.
>>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>>> on El Capitan. I get the segfault on both.
>>>
>>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>
>> Any insight from
>>
>>   R -d valgrind -f herve.R
>>
>> where herve.R contains the code above?
> 
> That's a little bit complicated for me at the moment. I was
> actually running this code on build machines toluca2 and (upcoming)
> veracruz2 and we don't have valgrind there for now. I don't have
> access to other Macs so hopefully someone else will be able to help
> with this.
> 

Just running valgrind on linux should reveal something
Dan


> H.
> 
>>
>> Martin
>>
>>>
>>> Cheers,
>>> H.
>>>
>>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
 Hi bioc-devel,

 This is a story about a bug that took me a long time to trace. The
 behaviour was really weird, so I'm sharing the story in case this
 helps others in the future. I was originally writing it to request
 help, but then I was able to find the issue ^^. The story ends right
 now with code that will reproduce the problem with '$<-' from
 IRanges/S4Vectors.




 During this Bioc cycle, frequently my package derfinder has failed to
 pass R CMD check in OSX. The error is always the same when it appears
 and sometimes it shows up in release, but not devel and viceversa.
 Right now (3/21/2017) it's visible in both
 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_derfinder_morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLkVy9RxxshXWAJaBZa_Yc=


 and
 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=a_K-yK7w2LEV72lpHrpp0UoKRru_7Aad74T5Uk0R-Fo=

 .
 The end of "test-all.Rout.fail" looks like this:

 Loading required package: foreach
 Loading required package: iterators
 Loading required package: locfit
 locfit 1.5-9.1 2013-03-22
 getSegments: segmenting
 getSegments: splitting
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 16.3681899295041
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 19.7936614060235
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52 findRegions: smoothing

  *** caught segfault ***
 address 0x7f87d2f917e0, cause 'memory not mapped'

 Traceback:
  1: (function (y, x, cluster, weights, smoothFun, ...) {
 hostPackage <- environmentName(environment(smoothFun))
 requireNamespace(hostPackage)smoothed <- .runFunFormal(smoothFun,
 y = y, x = x, cluster = cluster, weights = weights, ...)if
 (any(!smoothed$smoothed)) {smoothed$fitted[!smoothed$smoothed]
 <- y[!smoothed$smoothed]}res <- Rle(smoothed$fitted)
 return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
 dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
 weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
 verbose = TRUE) {if (is.null(dim(y))) y <-
 matrix(y, ncol = 1)if

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Alina Selega 
This is very useful, thank you very much! I will stay tuned for any further
advice on this.

Thanks,
Alina

On 22 March 2017 at 16:53, Gabe Becker  wrote:

> Alina,
>
> Typically in cases like the one you describe, people want users to use the
> paper citation when citing use of the package. Whether this is what they
> "should" want is somewhat debatable, but at least it seems reasonable, as
> by using the package users are, assumedly, applying the method your package
> implements.
>
> That said, a package can (from a mechanical perspective) have list more
> than one citation in it's CITATION file. Xie's knitr does this, for example
> (seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
> returned from citation(package="knitr") ) .
>
> Whether it's good to do this, and more generally whether package users
> should be expected to cite a (theory-based) methods paper and software
> which implements the method, particularly when they are by the same author,
> is again debatable. I have my thoughts on that but it's somewhat tangential
> to your question.
>
> It might be valuable for the Bioconductor team to have guidelines/an
> official view of how to navigate these issues.
>
> Best,
> ~G
>
> On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
>> If you do not have a CITATION file, a citation is automatically generated.
>> So yes, effectively it would overwrite.  See details in R-exts.
>>
>> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega 
>> wrote:
>>
>> > Hi Monther,
>> >
>> > Thank you for your reply!
>> >
>> > Would that overwrite the package citation that currently shows up on the
>> > page though? My paper doesn't cite the Bioconductor package (as it was
>> > accepted before I had a valid link to include), it just refers to the
>> same
>> > name of the computational method. Is there a way to include both
>> citations?
>> > And if not, which one should I keep?
>> >
>> > Thanks,
>> > Alina
>> >
>> > On 21 March 2017 at 22:13, Monther Alhamdoosh 
>> > wrote:
>> >
>> > > Hi Alina,
>> > >
>> > > I think you need to add a file named CITATION in your package (usually
>> > > under the inst folder) and use bibentry as follows
>> > >
>> > > bibentry(bibtype = "Article",
>> > >
>> > >  title = "Combining multiple tools outperforms individual
>> methods
>> > > in gene set enrichment analyses",
>> > >
>> > >  author = c(person("Monther", "Alhamdoosh"),
>> > >
>> > > person("Milica", "Ng"),
>> > >
>> > > person("Nicholas", "Wilson"),
>> > >
>> > > person("Julie", "Sheridan"),
>> > >
>> > > person("Huy", "Huynh"),
>> > >
>> > > person("Michael", "Wilson"),
>> > >
>> > > person("Matthew", "Ritchie")),
>> > >
>> > >  journal = "Bioinformatics",
>> > >
>> > >  page = "414-424",
>> > >
>> > >  volume = 33,
>> > >
>> > >  number = 3,
>> > >
>> > >  year = 2017,
>> > >
>> > >  doi = "10.1093/bioinformatics/btw623")
>> > >
>> > >
>> > >
>> > > Cheers,
>> > >
>> > > Monther
>> > >
>> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega > >
>> > > wrote:
>> > >
>> > >> Hi,
>> > >>
>> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
>> > >> BUMHMM
>> > >> was accepted before I submitted the package for revision at
>> > Bioconductor.
>> > >> I
>> > >> would like the package page to also hold the citation to the paper.
>> What
>> > >> is
>> > >> the best way to add this paper citation? (I cite it in the vignette,
>> but
>> > >> it
>> > >> would be nice to also have it on the main page.)
>> > >>
>> > >> Thank you,
>> > >> Alina Selega
>> > >>
>> > >> [[alternative HTML version deleted]]
>> > >>
>> > >> ___
>> > >> Bioc-devel@r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >>
>> > >
>> > >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>>
>
>
>
> --
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>

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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Hervé Pagès 

On 03/21/2017 05:28 PM, Martin Morgan wrote:

On 03/21/2017 08:21 PM, Hervé Pagès wrote:

Hi Leonardo,

Thanks for hunting down and isolating that bug! I tried to simplify
your code even more and was able to get a segfault with just:

  setClass("A", representation(stuff="numeric"))
  x <- logical(10)
  x[TRUE] <- new("A")

I get the segfault about 50% of the time on a fresh R session on Mac.
I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
on El Capitan. I get the segfault on both.

So it looks like a bug in the `[<-` primitive to me (subassignment).


Any insight from

  R -d valgrind -f herve.R

where herve.R contains the code above?


That's a little bit complicated for me at the moment. I was
actually running this code on build machines toluca2 and (upcoming)
veracruz2 and we don't have valgrind there for now. I don't have
access to other Macs so hopefully someone else will be able to help
with this.

H.



Martin



Cheers,
H.

On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:

Hi bioc-devel,

This is a story about a bug that took me a long time to trace. The
behaviour was really weird, so I'm sharing the story in case this
helps others in the future. I was originally writing it to request
help, but then I was able to find the issue ^^. The story ends right
now with code that will reproduce the problem with '$<-' from
IRanges/S4Vectors.




During this Bioc cycle, frequently my package derfinder has failed to
pass R CMD check in OSX. The error is always the same when it appears
and sometimes it shows up in release, but not devel and viceversa.
Right now (3/21/2017) it's visible in both
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_derfinder_morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLkVy9RxxshXWAJaBZa_Yc=


and
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=a_K-yK7w2LEV72lpHrpp0UoKRru_7Aad74T5Uk0R-Fo=

.
The end of "test-all.Rout.fail" looks like this:

Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
getSegments: segmenting
getSegments: splitting
2017-03-20 02:36:52 findRegions: smoothing
2017-03-20 02:36:52 findRegions: identifying potential segments
2017-03-20 02:36:52 findRegions: segmenting information
2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
16.3681899295041
2017-03-20 02:36:52 findRegions: identifying candidate regions
2017-03-20 02:36:52 findRegions: identifying region clusters
2017-03-20 02:36:52 findRegions: smoothing
2017-03-20 02:36:52 findRegions: identifying potential segments
2017-03-20 02:36:52 findRegions: segmenting information
2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
19.7936614060235
2017-03-20 02:36:52 findRegions: identifying candidate regions
2017-03-20 02:36:52 findRegions: identifying region clusters
2017-03-20 02:36:52 findRegions: smoothing

 *** caught segfault ***
address 0x7f87d2f917e0, cause 'memory not mapped'

Traceback:
 1: (function (y, x, cluster, weights, smoothFun, ...) {
hostPackage <- environmentName(environment(smoothFun))
requireNamespace(hostPackage)smoothed <- .runFunFormal(smoothFun,
y = y, x = x, cluster = cluster, weights = weights, ...)if
(any(!smoothed$smoothed)) {smoothed$fitted[!smoothed$smoothed]
<- y[!smoothed$smoothed]}res <- Rle(smoothed$fitted)
return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
verbose = TRUE) {if (is.null(dim(y))) y <-
matrix(y, ncol = 1)if (!is.null(weights) &&
is.null(dim(weights))) weights <- matrix(weights, ncol =
1)if (is.null(x)) x <- seq(along = y)if
(is.null(weights)) weights <- matrix(1, nrow = nrow(y),
ncol = ncol(y))Indexes <- split(seq(along = cluster), cluster)
   clusterL <- sapply(Indexes, length)smoothed <-
rep(TRUE, nrow(y))for (i in seq(along = Indexes)) {
if (verbose) if (i%%1 == 0)
cat(".")Index <- Indexes[[i]]if (clusterL[i]

= minNum & sum(rowSums(is.na(y[Index, , drop =

FALSE])) == 0) >= minNum) {nn <-
minInSpan/length(Index)for (j in 1:ncol(y)) {
sdata <- data.frame(pos = x[Index], y = y[Index,
  j], weights = weights[Index, j])  fit <-
locfit(y ˜ lp(pos, nn = nn, h = bpSpan), data =
sdata, weights = weights, family = "gaussian",
maxk = 1)

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Leonardo Collado Torres 
Awesome, thanks everyone! I'm tempted to write a blog post about this
whole story.

Best,
Leo

On Wed, Mar 22, 2017 at 6:36 AM, Martin Morgan
 wrote:
> On 03/22/2017 06:17 AM, Martin Maechler wrote:
>>>
>>> Andrzej Oleś 
>>> on Wed, 22 Mar 2017 10:29:57 +0100 writes:
>>
>>
>> > Just for the record, on R-3.3.2 Herve's code fails with the
>> following error:
>> > Error in x[TRUE] <- new("A") :
>> > incompatible types (from S4 to logical) in subassignment type fix
>>
>> yes, (of course) and I would be interested in a small
>> reproducible example which uses _valid_ code.
>> We have seen such examples with something (more complicated
>> than, but basically like)
>>
>>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>>   M <- Matrix::Matrix(exp(0:3),2)
>>   df[1:2,1:2] <- M
>>
>> which actually calls `[<-`, and then `[<-.data.frame`  and
>> always works for me but does seg.fault (in the CRAN checks of
>> package FastImputation (on 3 of the dozen platforms,
>> https://cran.r-project.org/web/checks/check_results_FastImputation.html
>>
>> one of them is
>>
>>
>> https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64-clang/FastImputation-00check.html
>>
>> I strongly suspect this is the same bug as yours, but for a case
>> where the correct behavior is *not* giving an error.
>>
>> I have also written and shown  Herve's example  to the R-core team.
>
>
> On Linux, if I run Leonardo's or Martin's example under gctorture(TRUE) I
> see a PROTECT problem; I don't see this with Herve's code, and I don't think
> his code goes through this execution path.
>
> e.g.
>
>> library(Matrix)
>> gctorture(TRUE)
>>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>>   M <- Matrix::Matrix(exp(0:3),2)
>>   df[1:2,1:2] <- M
> Error in `[<-.data.frame`(`*tmp*`, 1:2, 1:2, value =  "dgeMatrix">) :
>   unimplemented type 'integer' in 'coerceToInteger'
>
> This is addressed in r72383.
>
> R-devel$ svn diff -c72383
> Index: src/main/array.c
> ===
> --- src/main/array.c(revision 72382)
> +++ src/main/array.c(revision 72383)
> @@ -436,8 +436,12 @@
> DispatchOrEval(call, op, "length", args, rho, , 0, 1)) {
> if (length(ans) == 1 && TYPEOF(ans) == REALSXP) {
> double d = REAL(ans)[0];
> -   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d)
> -   return coerceVector(ans, INTSXP);
> +   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d) {
> +PROTECT(ans);
> +ans = coerceVector(ans, INTSXP);
> +UNPROTECT(1);
> +return(ans);
> +}
> }
> return(ans);
>  }
>
>
> Martin Morgan
>
>
>>
>> Unfortunately, I have no platform where I can trigger the bug.
>> Martin
>>
>>
>>
>> > Cheers,
>> > Andrzej
>>
>>
>>
>> > On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
>> > martin.mor...@roswellpark.org> wrote:
>>
>> >> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>> >>
>> >>> Hi Leonardo,
>> >>>
>> >>> Thanks for hunting down and isolating that bug! I tried to
>> simplify
>> >>> your code even more and was able to get a segfault with just:
>> >>>
>> >>> setClass("A", representation(stuff="numeric"))
>> >>> x <- logical(10)
>> >>> x[TRUE] <- new("A")
>> >>>
>> >>> I get the segfault about 50% of the time on a fresh R session on
>> Mac.
>> >>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>> >>> on El Capitan. I get the segfault on both.
>> >>>
>> >>> So it looks like a bug in the `[<-` primitive to me
>> (subassignment).
>> >>>
>> >>
>> >> Any insight from
>> >>
>> >> R -d valgrind -f herve.R
>> >>
>> >> where herve.R contains the code above?
>> >>
>> >> Martin
>> >>
>> >>
>> >>
>> >>> Cheers,
>> >>> H.
>> >>>
>> >>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
>> >>>
>>  Hi bioc-devel,
>> 
>>  This is a story about a bug that took me a long time to trace.
>> The
>>  behaviour was really weird, so I'm sharing the story in case this
>>  helps others in the future. I was originally writing it to
>> request
>>  help, but then I was able to find the issue ^^. The story ends
>> right
>>  now with code that will reproduce the problem with '$<-' from
>>  IRanges/S4Vectors.
>> 
>> 
>> 
>> 
>>  During this Bioc cycle, frequently my package derfinder has
>> failed to
>>  pass R CMD check in OSX. The error is always the same when it
>> appears
>>  and sometimes it shows up in release, but not devel and
>> viceversa.
>>  Right now (3/21/2017) it's visible in both
>>

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Leonardo Collado Torres 
You can include both like I do in
https://github.com/leekgroup/derfinderPlot/blob/master/inst/CITATION
which is similar to what Xie's knitr does.

On Wed, Mar 22, 2017 at 12:53 PM, Gabe Becker  wrote:
> Alina,
>
> Typically in cases like the one you describe, people want users to use the
> paper citation when citing use of the package. Whether this is what they
> "should" want is somewhat debatable, but at least it seems reasonable, as
> by using the package users are, assumedly, applying the method your package
> implements.
>
> That said, a package can (from a mechanical perspective) have list more
> than one citation in it's CITATION file. Xie's knitr does this, for example
> (seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
> returned from citation(package="knitr") ) .
>
> Whether it's good to do this, and more generally whether package users
> should be expected to cite a (theory-based) methods paper and software
> which implements the method, particularly when they are by the same author,
> is again debatable. I have my thoughts on that but it's somewhat tangential
> to your question.
>
> It might be valuable for the Bioconductor team to have guidelines/an
> official view of how to navigate these issues.
>
> Best,
> ~G
>
> On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
>> If you do not have a CITATION file, a citation is automatically generated.
>> So yes, effectively it would overwrite.  See details in R-exts.
>>
>> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega 
>> wrote:
>>
>> > Hi Monther,
>> >
>> > Thank you for your reply!
>> >
>> > Would that overwrite the package citation that currently shows up on the
>> > page though? My paper doesn't cite the Bioconductor package (as it was
>> > accepted before I had a valid link to include), it just refers to the
>> same
>> > name of the computational method. Is there a way to include both
>> citations?
>> > And if not, which one should I keep?
>> >
>> > Thanks,
>> > Alina
>> >
>> > On 21 March 2017 at 22:13, Monther Alhamdoosh 
>> > wrote:
>> >
>> > > Hi Alina,
>> > >
>> > > I think you need to add a file named CITATION in your package (usually
>> > > under the inst folder) and use bibentry as follows
>> > >
>> > > bibentry(bibtype = "Article",
>> > >
>> > >  title = "Combining multiple tools outperforms individual
>> methods
>> > > in gene set enrichment analyses",
>> > >
>> > >  author = c(person("Monther", "Alhamdoosh"),
>> > >
>> > > person("Milica", "Ng"),
>> > >
>> > > person("Nicholas", "Wilson"),
>> > >
>> > > person("Julie", "Sheridan"),
>> > >
>> > > person("Huy", "Huynh"),
>> > >
>> > > person("Michael", "Wilson"),
>> > >
>> > > person("Matthew", "Ritchie")),
>> > >
>> > >  journal = "Bioinformatics",
>> > >
>> > >  page = "414-424",
>> > >
>> > >  volume = 33,
>> > >
>> > >  number = 3,
>> > >
>> > >  year = 2017,
>> > >
>> > >  doi = "10.1093/bioinformatics/btw623")
>> > >
>> > >
>> > >
>> > > Cheers,
>> > >
>> > > Monther
>> > >
>> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega 
>> > > wrote:
>> > >
>> > >> Hi,
>> > >>
>> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
>> > >> BUMHMM
>> > >> was accepted before I submitted the package for revision at
>> > Bioconductor.
>> > >> I
>> > >> would like the package page to also hold the citation to the paper.
>> What
>> > >> is
>> > >> the best way to add this paper citation? (I cite it in the vignette,
>> but
>> > >> it
>> > >> would be nice to also have it on the main page.)
>> > >>
>> > >> Thank you,
>> > >> Alina Selega
>> > >>
>> > >> [[alternative HTML version deleted]]
>> > >>
>> > >> ___
>> > >> Bioc-devel@r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >>
>> > >
>> > >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

___
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Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Gabe Becker 
Alina,

Typically in cases like the one you describe, people want users to use the
paper citation when citing use of the package. Whether this is what they
"should" want is somewhat debatable, but at least it seems reasonable, as
by using the package users are, assumedly, applying the method your package
implements.

That said, a package can (from a mechanical perspective) have list more
than one citation in it's CITATION file. Xie's knitr does this, for example
(seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
returned from citation(package="knitr") ) .

Whether it's good to do this, and more generally whether package users
should be expected to cite a (theory-based) methods paper and software
which implements the method, particularly when they are by the same author,
is again debatable. I have my thoughts on that but it's somewhat tangential
to your question.

It might be valuable for the Bioconductor team to have guidelines/an
official view of how to navigate these issues.

Best,
~G

On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> If you do not have a CITATION file, a citation is automatically generated.
> So yes, effectively it would overwrite.  See details in R-exts.
>
> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega 
> wrote:
>
> > Hi Monther,
> >
> > Thank you for your reply!
> >
> > Would that overwrite the package citation that currently shows up on the
> > page though? My paper doesn't cite the Bioconductor package (as it was
> > accepted before I had a valid link to include), it just refers to the
> same
> > name of the computational method. Is there a way to include both
> citations?
> > And if not, which one should I keep?
> >
> > Thanks,
> > Alina
> >
> > On 21 March 2017 at 22:13, Monther Alhamdoosh 
> > wrote:
> >
> > > Hi Alina,
> > >
> > > I think you need to add a file named CITATION in your package (usually
> > > under the inst folder) and use bibentry as follows
> > >
> > > bibentry(bibtype = "Article",
> > >
> > >  title = "Combining multiple tools outperforms individual
> methods
> > > in gene set enrichment analyses",
> > >
> > >  author = c(person("Monther", "Alhamdoosh"),
> > >
> > > person("Milica", "Ng"),
> > >
> > > person("Nicholas", "Wilson"),
> > >
> > > person("Julie", "Sheridan"),
> > >
> > > person("Huy", "Huynh"),
> > >
> > > person("Michael", "Wilson"),
> > >
> > > person("Matthew", "Ritchie")),
> > >
> > >  journal = "Bioinformatics",
> > >
> > >  page = "414-424",
> > >
> > >  volume = 33,
> > >
> > >  number = 3,
> > >
> > >  year = 2017,
> > >
> > >  doi = "10.1093/bioinformatics/btw623")
> > >
> > >
> > >
> > > Cheers,
> > >
> > > Monther
> > >
> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega 
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
> > >> BUMHMM
> > >> was accepted before I submitted the package for revision at
> > Bioconductor.
> > >> I
> > >> would like the package page to also hold the citation to the paper.
> What
> > >> is
> > >> the best way to add this paper citation? (I cite it in the vignette,
> but
> > >> it
> > >> would be nice to also have it on the main page.)
> > >>
> > >> Thank you,
> > >> Alina Selega
> > >>
> > >> [[alternative HTML version deleted]]
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Kasper Daniel Hansen 
If you do not have a CITATION file, a citation is automatically generated.
So yes, effectively it would overwrite.  See details in R-exts.

On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega 
wrote:

> Hi Monther,
>
> Thank you for your reply!
>
> Would that overwrite the package citation that currently shows up on the
> page though? My paper doesn't cite the Bioconductor package (as it was
> accepted before I had a valid link to include), it just refers to the same
> name of the computational method. Is there a way to include both citations?
> And if not, which one should I keep?
>
> Thanks,
> Alina
>
> On 21 March 2017 at 22:13, Monther Alhamdoosh 
> wrote:
>
> > Hi Alina,
> >
> > I think you need to add a file named CITATION in your package (usually
> > under the inst folder) and use bibentry as follows
> >
> > bibentry(bibtype = "Article",
> >
> >  title = "Combining multiple tools outperforms individual methods
> > in gene set enrichment analyses",
> >
> >  author = c(person("Monther", "Alhamdoosh"),
> >
> > person("Milica", "Ng"),
> >
> > person("Nicholas", "Wilson"),
> >
> > person("Julie", "Sheridan"),
> >
> > person("Huy", "Huynh"),
> >
> > person("Michael", "Wilson"),
> >
> > person("Matthew", "Ritchie")),
> >
> >  journal = "Bioinformatics",
> >
> >  page = "414-424",
> >
> >  volume = 33,
> >
> >  number = 3,
> >
> >  year = 2017,
> >
> >  doi = "10.1093/bioinformatics/btw623")
> >
> >
> >
> > Cheers,
> >
> > Monther
> >
> > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega 
> > wrote:
> >
> >> Hi,
> >>
> >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
> >> BUMHMM
> >> was accepted before I submitted the package for revision at
> Bioconductor.
> >> I
> >> would like the package page to also hold the citation to the paper. What
> >> is
> >> the best way to add this paper citation? (I cite it in the vignette, but
> >> it
> >> would be nice to also have it on the main page.)
> >>
> >> Thank you,
> >> Alina Selega
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Martin Morgan 

On 03/22/2017 06:17 AM, Martin Maechler wrote:

Andrzej Oleś 
on Wed, 22 Mar 2017 10:29:57 +0100 writes:


> Just for the record, on R-3.3.2 Herve's code fails with the following 
error:
> Error in x[TRUE] <- new("A") :
> incompatible types (from S4 to logical) in subassignment type fix

yes, (of course) and I would be interested in a small
reproducible example which uses _valid_ code.
We have seen such examples with something (more complicated
than, but basically like)

  df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
  M <- Matrix::Matrix(exp(0:3),2)
  df[1:2,1:2] <- M

which actually calls `[<-`, and then `[<-.data.frame`  and
always works for me but does seg.fault (in the CRAN checks of
package FastImputation (on 3 of the dozen platforms,
https://cran.r-project.org/web/checks/check_results_FastImputation.html

one of them is

 
https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64-clang/FastImputation-00check.html

I strongly suspect this is the same bug as yours, but for a case
where the correct behavior is *not* giving an error.

I have also written and shown  Herve's example  to the R-core team.


On Linux, if I run Leonardo's or Martin's example under gctorture(TRUE) 
I see a PROTECT problem; I don't see this with Herve's code, and I don't 
think his code goes through this execution path.


e.g.

> library(Matrix)
> gctorture(TRUE)
>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>   M <- Matrix::Matrix(exp(0:3),2)
>   df[1:2,1:2] <- M
Error in `[<-.data.frame`(`*tmp*`, 1:2, 1:2, value = "dgeMatrix">) :

  unimplemented type 'integer' in 'coerceToInteger'

This is addressed in r72383.

R-devel$ svn diff -c72383
Index: src/main/array.c
===
--- src/main/array.c(revision 72382)
+++ src/main/array.c(revision 72383)
@@ -436,8 +436,12 @@
DispatchOrEval(call, op, "length", args, rho, , 0, 1)) {
if (length(ans) == 1 && TYPEOF(ans) == REALSXP) {
double d = REAL(ans)[0];
-   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d)
-   return coerceVector(ans, INTSXP);
+   if (R_FINITE(d) && d >= 0. && d <= INT_MAX && floor(d) == d) {
+PROTECT(ans);
+ans = coerceVector(ans, INTSXP);
+UNPROTECT(1);
+return(ans);
+}
}
return(ans);
 }


Martin Morgan



Unfortunately, I have no platform where I can trigger the bug.
Martin



> Cheers,
> Andrzej



> On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:

>> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>>
>>> Hi Leonardo,
>>>
>>> Thanks for hunting down and isolating that bug! I tried to simplify
>>> your code even more and was able to get a segfault with just:
>>>
>>> setClass("A", representation(stuff="numeric"))
>>> x <- logical(10)
>>> x[TRUE] <- new("A")
>>>
>>> I get the segfault about 50% of the time on a fresh R session on Mac.
>>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>>> on El Capitan. I get the segfault on both.
>>>
>>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>>
>>
>> Any insight from
>>
>> R -d valgrind -f herve.R
>>
>> where herve.R contains the code above?
>>
>> Martin
>>
>>
>>
>>> Cheers,
>>> H.
>>>
>>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
>>>
 Hi bioc-devel,

 This is a story about a bug that took me a long time to trace. The
 behaviour was really weird, so I'm sharing the story in case this
 helps others in the future. I was originally writing it to request
 help, but then I was able to find the issue ^^. The story ends right
 now with code that will reproduce the problem with '$<-' from
 IRanges/S4Vectors.




 During this Bioc cycle, frequently my package derfinder has failed to
 pass R CMD check in OSX. The error is always the same when it appears
 and sometimes it shows up in release, but not devel and viceversa.
 Right now (3/21/2017) it's visible in both
 https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
 ctor.org_checkResults_release_bioc-2DLATEST_derfinder_
 morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfh
 Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_
 t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLk
 Vy9RxxshXWAJaBZa_Yc=

 and
 https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
 ctor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca
 2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3X

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Alina Selega 
Hi Monther,

Thank you for your reply!

Would that overwrite the package citation that currently shows up on the
page though? My paper doesn't cite the Bioconductor package (as it was
accepted before I had a valid link to include), it just refers to the same
name of the computational method. Is there a way to include both citations?
And if not, which one should I keep?

Thanks,
Alina

On 21 March 2017 at 22:13, Monther Alhamdoosh  wrote:

> Hi Alina,
>
> I think you need to add a file named CITATION in your package (usually
> under the inst folder) and use bibentry as follows
>
> bibentry(bibtype = "Article",
>
>  title = "Combining multiple tools outperforms individual methods
> in gene set enrichment analyses",
>
>  author = c(person("Monther", "Alhamdoosh"),
>
> person("Milica", "Ng"),
>
> person("Nicholas", "Wilson"),
>
> person("Julie", "Sheridan"),
>
> person("Huy", "Huynh"),
>
> person("Michael", "Wilson"),
>
> person("Matthew", "Ritchie")),
>
>  journal = "Bioinformatics",
>
>  page = "414-424",
>
>  volume = 33,
>
>  number = 3,
>
>  year = 2017,
>
>  doi = "10.1093/bioinformatics/btw623")
>
>
>
> Cheers,
>
> Monther
>
> On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega 
> wrote:
>
>> Hi,
>>
>> My methods paper (doi:10.1038/nmeth.4068) associated with my package
>> BUMHMM
>> was accepted before I submitted the package for revision at Bioconductor.
>> I
>> would like the package page to also hold the citation to the paper. What
>> is
>> the best way to add this paper citation? (I cite it in the vignette, but
>> it
>> would be nice to also have it on the main page.)
>>
>> Thank you,
>> Alina Selega
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Martin Maechler 
> Andrzej Oleś 
> on Wed, 22 Mar 2017 10:29:57 +0100 writes:

> Just for the record, on R-3.3.2 Herve's code fails with the following 
error:
> Error in x[TRUE] <- new("A") :
> incompatible types (from S4 to logical) in subassignment type fix

yes, (of course) and I would be interested in a small
reproducible example which uses _valid_ code.
We have seen such examples with something (more complicated
than, but basically like)

  df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
  M <- Matrix::Matrix(exp(0:3),2)
  df[1:2,1:2] <- M

which actually calls `[<-`, and then `[<-.data.frame`  and
always works for me but does seg.fault (in the CRAN checks of
package FastImputation (on 3 of the dozen platforms,
https://cran.r-project.org/web/checks/check_results_FastImputation.html

one of them is

 
https://www.r-project.org/nosvn/R.check/r-devel-macos-x86_64-clang/FastImputation-00check.html

I strongly suspect this is the same bug as yours, but for a case
where the correct behavior is *not* giving an error.

I have also written and shown  Herve's example  to the R-core team.

Unfortunately, I have no platform where I can trigger the bug.
Martin



> Cheers,
> Andrzej



> On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:

>> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>> 
>>> Hi Leonardo,
>>> 
>>> Thanks for hunting down and isolating that bug! I tried to simplify
>>> your code even more and was able to get a segfault with just:
>>> 
>>> setClass("A", representation(stuff="numeric"))
>>> x <- logical(10)
>>> x[TRUE] <- new("A")
>>> 
>>> I get the segfault about 50% of the time on a fresh R session on Mac.
>>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>>> on El Capitan. I get the segfault on both.
>>> 
>>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>> 
>> 
>> Any insight from
>> 
>> R -d valgrind -f herve.R
>> 
>> where herve.R contains the code above?
>> 
>> Martin
>> 
>> 
>> 
>>> Cheers,
>>> H.
>>> 
>>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
>>> 
 Hi bioc-devel,
 
 This is a story about a bug that took me a long time to trace. The
 behaviour was really weird, so I'm sharing the story in case this
 helps others in the future. I was originally writing it to request
 help, but then I was able to find the issue ^^. The story ends right
 now with code that will reproduce the problem with '$<-' from
 IRanges/S4Vectors.
 
 
 
 
 During this Bioc cycle, frequently my package derfinder has failed to
 pass R CMD check in OSX. The error is always the same when it appears
 and sometimes it shows up in release, but not devel and viceversa.
 Right now (3/21/2017) it's visible in both
 https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
 ctor.org_checkResults_release_bioc-2DLATEST_derfinder_
 morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfh
 Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_
 t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLk
 Vy9RxxshXWAJaBZa_Yc=
 
 and
 https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
 ctor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca
 2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3X
 eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_
 t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=a_K-yK7w2LEV72lpHrpp0UoK
 Rru_7Aad74T5Uk0R-Fo=
 .
 The end of "test-all.Rout.fail" looks like this:
 
 Loading required package: foreach
 Loading required package: iterators
 Loading required package: locfit
 locfit 1.5-9.1 2013-03-22
 getSegments: segmenting
 getSegments: splitting
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 16.3681899295041
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52 findRegions: smoothing
 2017-03-20 02:36:52 findRegions: identifying potential segments
 2017-03-20 02:36:52 findRegions: segmenting information
 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
 19.7936614060235
 2017-03-20 02:36:52 findRegions: identifying candidate regions
 2017-03-20 02:36:52 findRegions: identifying region clusters
 2017-03-20 02:36:52

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś 
On Wed, Mar 22, 2017 at 10:29 AM, Andrzej Oleś 
wrote:

> Just for the record, on R-3.3.2 Herve's code fails with the following
> error:
>
> Error in x[TRUE] <- new("A") :
>   incompatible types (from S4 to logical) in subassignment type fix
>

Quick update: I also get the above error on my Linux box under R-3.3.3.

Andrzej

[[alternative HTML version deleted]]

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Re: [Bioc-devel] segfault in csaw native code

2017-03-22 Thread Aaron Lun 
Thanks Ryan. I've determined the issue - a rather embarrassing one, 
actually, where the C array wasn't of the right length - I'm not quite 
sure why it didn't show up earlier. Anyway, patches have been committed 
to release and devel.

Cheers,

Aaron

On 22/03/17 01:14, Ryan Thompson wrote:
> Hi Aaron,
>
> I'm making a ChIP-Seq analyisis pipeline using csaw, and I'm running
> into an inconsistent error/segfault. I've reduced it to a test case
> which you can find
> here: 
> https://www.dropbox.com/sh/2a2vpb5ek4413fx/AAAXwCaTzsAmfyPefwAbFg8Na?dl=0
>
> The test case consists of my R workspace saved with save.image right
> before the code that causes the segfault along with a script that loads
> the workspace and then runs the offending code. The code consists of
> running combineOverlaps on each of a list of topTags tables. Seemingly
> at random, some but not all of the calls to combineOverlaps will fail
> and error, and occasionally R will segfault. Since the bug is random,
> I've also included a transcript of me running the script until it
> crashes, as well as a text file with the traceback in it.
>
> Can you help me debug the issue here?
>
> Thanks,
>
> -Ryan
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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś 
Just for the record, on R-3.3.2 Herve's code fails with the following error:

Error in x[TRUE] <- new("A") :
  incompatible types (from S4 to logical) in subassignment type fix


Cheers,
Andrzej



On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 03/21/2017 08:21 PM, Hervé Pagès wrote:
>
>> Hi Leonardo,
>>
>> Thanks for hunting down and isolating that bug! I tried to simplify
>> your code even more and was able to get a segfault with just:
>>
>>   setClass("A", representation(stuff="numeric"))
>>   x <- logical(10)
>>   x[TRUE] <- new("A")
>>
>> I get the segfault about 50% of the time on a fresh R session on Mac.
>> I tried this with R 3.3.3 on Mavericks, and with R devel (r72372)
>> on El Capitan. I get the segfault on both.
>>
>> So it looks like a bug in the `[<-` primitive to me (subassignment).
>>
>
> Any insight from
>
>   R -d valgrind -f herve.R
>
> where herve.R contains the code above?
>
> Martin
>
>
>
>> Cheers,
>> H.
>>
>> On 03/21/2017 03:06 PM, Leonardo Collado Torres wrote:
>>
>>> Hi bioc-devel,
>>>
>>> This is a story about a bug that took me a long time to trace. The
>>> behaviour was really weird, so I'm sharing the story in case this
>>> helps others in the future. I was originally writing it to request
>>> help, but then I was able to find the issue ^^. The story ends right
>>> now with code that will reproduce the problem with '$<-' from
>>> IRanges/S4Vectors.
>>>
>>>
>>>
>>>
>>> During this Bioc cycle, frequently my package derfinder has failed to
>>> pass R CMD check in OSX. The error is always the same when it appears
>>> and sometimes it shows up in release, but not devel and viceversa.
>>> Right now (3/21/2017) it's visible in both
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>>> ctor.org_checkResults_release_bioc-2DLATEST_derfinder_
>>> morelia-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfh
>>> Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_
>>> t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=RS-lsygPtDdgWKAhjA2BcSLk
>>> Vy9RxxshXWAJaBZa_Yc=
>>>
>>> and
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>>> ctor.org_checkResults_devel_bioc-2DLATEST_derfinder_toluca
>>> 2-2Dchecksrc.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3X
>>> eAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Bw-1Kqy-M_
>>> t4kmpYWTpYkt5bvj_eTpxriUM3UvtOIzQ=a_K-yK7w2LEV72lpHrpp0UoK
>>> Rru_7Aad74T5Uk0R-Fo=
>>> .
>>> The end of "test-all.Rout.fail" looks like this:
>>>
>>> Loading required package: foreach
>>> Loading required package: iterators
>>> Loading required package: locfit
>>> locfit 1.5-9.1 2013-03-22
>>> getSegments: segmenting
>>> getSegments: splitting
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>> 2017-03-20 02:36:52 findRegions: identifying potential segments
>>> 2017-03-20 02:36:52 findRegions: segmenting information
>>> 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
>>> 16.3681899295041
>>> 2017-03-20 02:36:52 findRegions: identifying candidate regions
>>> 2017-03-20 02:36:52 findRegions: identifying region clusters
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>> 2017-03-20 02:36:52 findRegions: identifying potential segments
>>> 2017-03-20 02:36:52 findRegions: segmenting information
>>> 2017-03-20 02:36:52 .getSegmentsRle: segmenting with cutoff(s)
>>> 19.7936614060235
>>> 2017-03-20 02:36:52 findRegions: identifying candidate regions
>>> 2017-03-20 02:36:52 findRegions: identifying region clusters
>>> 2017-03-20 02:36:52 findRegions: smoothing
>>>
>>>  *** caught segfault ***
>>> address 0x7f87d2f917e0, cause 'memory not mapped'
>>>
>>> Traceback:
>>>  1: (function (y, x, cluster, weights, smoothFun, ...) {
>>> hostPackage <- environmentName(environment(smoothFun))
>>> requireNamespace(hostPackage)smoothed <- .runFunFormal(smoothFun,
>>> y = y, x = x, cluster = cluster, weights = weights, ...)if
>>> (any(!smoothed$smoothed)) {smoothed$fitted[!smoothed$smoothed]
>>> <- y[!smoothed$smoothed]}res <- Rle(smoothed$fitted)
>>> return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]],
>>> dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster,
>>> weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0,
>>> verbose = TRUE) {if (is.null(dim(y))) y <-
>>> matrix(y, ncol = 1)if (!is.null(weights) &&
>>> is.null(dim(weights))) weights <- matrix(weights, ncol =
>>> 1)if (is.null(x)) x <- seq(along = y)if
>>> (is.null(weights)) weights <- matrix(1, nrow = nrow(y),
>>> ncol = ncol(y))Indexes <- split(seq(along = cluster), cluster)
>>>clusterL <- sapply(Indexes, length)smoothed <-
>>> rep(TRUE, nrow(y))for (i in seq(along = Indexes)) {
>>> if (verbose) if (i%%1 == 0)
>>> cat(".")Index <- Indexes[[i]]if (clusterL[i]
>>>
 = minNum & sum(rowSums(is.na(y[Index, , drop =

>>> FALSE])) == 0)