Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

[Ramon Diaz-Uriarte]

Dear Martin,


Thanks a lot for looking into this. I'll wait then.


Best,


R.

On Mon, 03-04-2017, at 18:34, Martin Morgan  
wrote:
> On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:
>>
>> Dear All,
>>
>> A package I maintain, ADaCGH2, is failing to build in veracruz2 with a
>> segfault that seems to happen when plotting (in a call to plotting that
>> happens inside a mclapply)
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/veracruz2-buildsrc.html
>>
>>
>> these are some of the lines of the traceback:
>>
>> Traceback:
>>  1: dev.hold()
>>  2: plot.default(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 
>> 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 
>> 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 
>> 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 
>> 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 
>> 108945724, 120577571, 122947762.5, 124680401, 129086592, 144839226, 
>> 148940008.5, 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), 
>> c(0.397, 0.002, -0.179, -0.1385, -0.095, -0.611, -0.165, -0.54, -0.358, 
>> 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, 
>> -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, 
>> -0.099, -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, 
>> -0.33, -0.491, 0.138, -0.187, 0.21), ylab = "log ratio", xlab = 
>> quote("Chromosomal location"), col = c("orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange",
>>  "orange", "orange", "orange", "orange", "orange"), cex = 1, axes = 
>> FALSE, main = quote("Chr4@L.1"), pch = 20)
>>  3: plot(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 
>> 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 
>> 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 
>> 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 
>> 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 108945724, 
>> 120577571, 122947762.5, 124680401, 129086592, 144839226, 148940008.5, 
>> 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), c(0.397, 
>> 0.002, -0.179, -0.1385, -0.095, -0.611, -0.165, -0.54, -0.358, 0.172, 
>> -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, -0.406, 
>> 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, -0.099, 
>> -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, 
>> -0.491, 0.138, -0.187, 0.21), ylab = "log ratio", xlab = quote("Chromosomal 
>> location"), col = c("orange", "orange", "orange", "orange", "orange",
>>  "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
>> "orange", "orange", "orange"), cex = 1, axes = FALSE, main = 
>> quote("Chr4@L.1"), pch = 20)
>>  4: do.call(funname, c(list(mf[[i]], y, ylab = yl, xlab = xl), dots))
>>
>>
>>
>> It seems that what triggers the problem is an innocuous plot.default
>> followed by dev.hold? (none of which I call explicitly in my code)
>
> I was able to reproduce this with
>
> $ cat segfault-test.R
> xx <- parallel::mclapply(1:2, function(i) {
>  Cairo::CairoPNG(filename = paste("plt", i, ".png", sep=''))
>  dev.hold()
> })
>
> $ R -f segfault-test.R
>
> The El-Capitain builds are still in a great deal of flux, and in 
> particular the Cairo package requires a binary installation that is not 
> yet available (the Cairo package is used is actually from Mavericks). 
> The best strategy is probably to wait until binaries become available.
>
> Martin
>
>>
>>
>> At least another package, arrayQualityMetrics seems to experience a
>> somewhat similar problem:
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/arrayQualityMetrics/veracruz2-buildsrc.html
>>
>> where, again, an apparently innocuous plot.default followed by dev.hold
>> triggers a segfault (and there is no mclapply here)
>>
>> Traceback:
>>  1: dev.hold()
>>  2: plot.default(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])), ylim 
>> = range(min(as.vector(mns)) - 1, max(as.vector(mns)) + 1), xlab = 
>> "5' <-> 3'\n Probe Number ", ylab = ylab, axes = FALSE, main = "RNA 
>> degradation plot", ...)
>>  3: 

Re: [Bioc-devel] segfault when building in veracruz2 for BioC 3.5

[Martin Morgan]

On 03/31/2017 04:19 AM, Ramon Diaz-Uriarte wrote:


Dear All,

A package I maintain, ADaCGH2, is failing to build in veracruz2 with a
segfault that seems to happen when plotting (in a call to plotting that
happens inside a mclapply)

http://bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/veracruz2-buildsrc.html


these are some of the lines of the traceback:

Traceback:
 1: dev.hold()
 2: plot.default(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 108945724, 120577571, 122947762.5, 124680401, 129086592, 144839226, 148940008.5, 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), c(0.397, 0.002, -0.179, -0.1385, -0.095, 
-0.611, -0.165, -0.54, -0.358, 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, -0.099, -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, -0.491, 0.138, -0.187, 0.21), ylab = "log ratio", xlab = quote("Chromosomal location"), col = c("orange", "orange", "orange", "orange", "orange", "orange", "orange", 
"orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
"orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange"), cex = 1, axes = FALSE, main = quote("Chr4@L.1"), pch = 20)
 3: plot(c(2925836, 5135683.5, 6415674.5, 7169722, 9715199, 13220514.5, 15307852, 41589471, 44534348, 47975338, 52729020, 54225865, 54970734, 55406435.5, 57169693.5, 57359284.5, 66362289.5, 69947314.5, 72243027.5, 75218239, 75268559.5, 75683700, 76272391, 76901797, 77282738, 83724180, 88707195.5, 89536816.5, 102463647.5, 104082964, 107610854, 108945724, 120577571, 122947762.5, 124680401, 129086592, 144839226, 148940008.5, 154240128.5, 155887373.5, 178034441.5, 184199138, 184552484), c(0.397, 0.002, -0.179, -0.1385, -0.095, -0.611, 
-0.165, -0.54, -0.358, 0.172, -0.2435, -0.044, -0.048, 0.078, -0.344, -0.139, -0.513, -0.681, -0.406, 0.083, -0.325, -0.186, -0.138, 0.393, -0.075, -0.655, 0.123, -0.346, -0.099, -0.3465, 0.463, -0.18, -0.101, -0.175, -0.101, 0.371, -0.642, -0.13, -0.33, -0.491, 0.138, -0.187, 0.21), ylab = "log ratio", xlab = quote("Chromosomal location"), col = c("orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
"orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", 
"orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange", "orange"), cex = 1, axes = FALSE, main = quote("Chr4@L.1"), pch = 20)
 4: do.call(funname, c(list(mf[[i]], y, ylab = yl, xlab = xl), dots))



It seems that what triggers the problem is an innocuous plot.default
followed by dev.hold? (none of which I call explicitly in my code)


I was able to reproduce this with

$ cat segfault-test.R
xx <- parallel::mclapply(1:2, function(i) {
Cairo::CairoPNG(filename = paste("plt", i, ".png", sep=''))
dev.hold()
})

$ R -f segfault-test.R

The El-Capitain builds are still in a great deal of flux, and in 
particular the Cairo package requires a binary installation that is not 
yet available (the Cairo package is used is actually from Mavericks). 
The best strategy is probably to wait until binaries become available.


Martin




At least another package, arrayQualityMetrics seems to experience a
somewhat similar problem:

http://bioconductor.org/checkResults/devel/bioc-LATEST/arrayQualityMetrics/veracruz2-buildsrc.html

where, again, an apparently innocuous plot.default followed by dev.hold
triggers a segfault (and there is no mclapply here)

Traceback:
 1: dev.hold()
 2: plot.default(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])), ylim = range(min(as.vector(mns)) 
- 1, max(as.vector(mns)) + 1), xlab = "5' <-> 3'\n Probe Number ", ylab = ylab, 
axes = FALSE, main = "RNA degradation plot", ...)
 3: plot(-2, -1, pch = "", xlim = range(-1, (dim(mns)[2])), ylim = range(min(as.vector(mns)) - 1, 
max(as.vector(mns)) + 1), xlab = "5' <-> 3'\n Probe Number ", ylab = ylab, axes = FALSE, 
main = "RNA degradation plot", ...)
 4: plotAffyRNAdeg(AffyRNAdeg(expressionset, log.it = TRUE), lwd = 1, cols 
= x$arrayColors)




I am not sure how to proceed here. Any suggestions?


Thanks,


R.

--
Ramon Diaz-Uriarte
Department of 

Re: [Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

[Hervé Pagès]

Hi Maarten,

identical() is not reliable on DNAStringSet objects or other objects
that contain external pointers as it can return false negatives as well
as false positives. We'll fix the "cbind" and "rbind" methods for
SummarizedExperiment to work around this problem.

Thanks for the report.

H.

On 04/03/2017 12:58 AM, Maarten van Iterson wrote:

Dear list,

Combining SummarizedExperiment object, containing a DNAStringSet in the
rowData seems not to work properly. If I cbind two SummarizedExperiment
objects, which I know are identical, an error is reported:

Error in FUN(X[[i]], ...) (from #2) :
  column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not match

I think I traced the problem existing in `SummarizedExperiment:::.compare`
in that `identical` is used to compare DNAStringSets which is not behaving
as expected. Whereas it should return all identical it returns it is not!

Here is a counter example (which was easier to construct) showing that
`identical` returns FALSE where it should return TRUE.


library(Biostrings)
seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")

seq1

[1] "GACTC"

seq2

[1] "GAATG"


s1 <- DNAStringSet(seq1)
s2 <- DNAStringSet(seq2)

str(s1)

Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :
  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()

str(s2)

Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :

  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()


identical(seq1, seq2)

[1] FALSE

identical(s1, s2)

[1] TRUE

seq1 == seq2

[1] FALSE

s1 == s2

[1] FALSE


sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

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] Biostrings_2.42.1  XVector_0.14.1
 [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
 [5] Biobase_2.34.0 GenomicRanges_1.26.4
 [7] GenomeInfoDb_1.10.3IRanges_2.8.2
 [9] S4Vectors_0.12.2   BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
hms_0.3
 [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
BiocParallel_1.8.1
 [7] BSgenome_1.42.0  lattice_0.20-35
R6_2.2.0
[10] httr_1.2.1   tools_3.3.2
grid_3.3.2
[13] DBI_0.6  assertthat_0.1
digest_0.6.12
[16] tibble_1.2   Matrix_1.2-8
readr_1.1.0
[19] rtracklayer_1.34.2   bitops_1.0-6
biomaRt_2.30.0
[22] RCurl_1.95-4.8   memoise_1.0.0
RSQLite_1.1-2
[25] compiler_3.3.2   GenomicFeatures_1.26.3
Rsamtools_1.26.1
[28] XML_3.98-1.5 jsonlite_1.3
VariantAnnotation_1.20.3




I don't completely understand understand why `identical` is not working
properly is it comparing the environment address in the above example they
are the same although the sequences are not? In my case the two
SummarizedExperiments contained the same DNAStringSets but had a different
environment address?

Regards,
Maarten

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[Bioc-devel] Bioconductor 3.5 Release: db0 packages

[Obenchain, Valerie]

The new db0 packages (all version 3.4.2) are now available in the devel
repo. Let me know if you notice any problems.

Thanks.

Valerie



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Re: [Bioc-devel] Using LaTeX packages in vignettes

[Andrzej Oleś]

Dear Roel,

to override the default \bibliographystyle{unsrt} use
`BiocStyle::latex(use.unsrturl=FALSE)` as documented in ?BiocStyle::latex

Best, Andrzej

On Mon, Apr 3, 2017 at 2:29 PM, Janssen-10, R.R.E. <
r.r.e.janssen...@umcutrecht.nl> wrote:

> Obenchain, Valerie writes:
> > Hi,
> >
> > On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote:
> >> Hello all,
> >>
> >> We wrote our vignette in Sweave/LaTeX, and I am running into a problem
> with citing to other papers.
> >> I would like to use the APA style of citing which looks like:
> "Determine the optimal factorization rank using the
> >> NMF package (Gaujoux and Seoighe, 2010). ..."
> >>
> >> Now, to achieve that, I could use the package "apacite", but I wonder
> whether it's available on the build nodes of
> >> Bioconductor, and whether it's desired to choose our own citation
> style.  Can we choose our own citation style in
> >> vignettes? And if so, is "apacite" available on the build
> infrastructure of Bioconductor?
> >
> > apacite is included in TeXLive which is on the build machines.
> >
> > Valerie
>
> Thanks!  There's one problem left now.  I think the Bioconductor theme
> sets the \bibliographystyle to "unsrt".  I would like to add the following
> to my vignette:
> > \usepackage[natbibapa]{apacite}
> > \bibliographystyle{apacite}
>
> The problem is that there can only be a single \bibliographystyle
> definition in the TeX file:
> > Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet,  :
> >   Running 'texi2dvi' on 'Introduction_to_MutationalPatterns.tex' failed.
> > BibTeX errors:
> > The top-level auxiliary file: Introduction_to_MutationalPatterns.aux
> > The style file: apacite.bst
> > Illegal, another \bibstyle command---line 20 of file Introduction_to_
> MutationalPatterns.aux
> >  : \bibstyle
> >  :  {/gnu/store/87z400wdxx9ii0h2nfi8864wl0c3vs
> aq-r-biocstyle-2.2.1/site-library/BiocStyle/resources/tex/unsrturl}
>
> Do you know how I can get around this?
>
> Thanks for your time.
>
> Kind regards,
> Roel Janssen
>
> 
> --
>
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender
> direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd
> bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>
> 
> --
>
> This message may contain confidential information and ...{{dropped:10}}

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Re: [Bioc-devel] Using LaTeX packages in vignettes

[Janssen-10, R.R.E.]

Obenchain, Valerie writes:
> Hi,
> 
> On 03/30/2017 03:20 AM, Janssen-10, R.R.E. wrote:
>> Hello all,
>>
>> We wrote our vignette in Sweave/LaTeX, and I am running into a problem with 
>> citing to other papers.
>> I would like to use the APA style of citing which looks like: "Determine the 
>> optimal factorization rank using the
>> NMF package (Gaujoux and Seoighe, 2010). ..."
>>
>> Now, to achieve that, I could use the package "apacite", but I wonder 
>> whether it's available on the build nodes of
>> Bioconductor, and whether it's desired to choose our own citation style.  
>> Can we choose our own citation style in
>> vignettes? And if so, is "apacite" available on the build infrastructure of 
>> Bioconductor?
>
> apacite is included in TeXLive which is on the build machines.
>
> Valerie

Thanks!  There's one problem left now.  I think the Bioconductor theme sets the 
\bibliographystyle to "unsrt".  I would like to add the following to my 
vignette:
> \usepackage[natbibapa]{apacite}
> \bibliographystyle{apacite}

The problem is that there can only be a single \bibliographystyle definition in 
the TeX file:
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
>   Running 'texi2dvi' on 'Introduction_to_MutationalPatterns.tex' failed.
> BibTeX errors:
> The top-level auxiliary file: Introduction_to_MutationalPatterns.aux
> The style file: apacite.bst
> Illegal, another \bibstyle command---line 20 of file 
> Introduction_to_MutationalPatterns.aux
>  : \bibstyle
>  :  
> {/gnu/store/87z400wdxx9ii0h2nfi8864wl0c3vsaq-r-biocstyle-2.2.1/site-library/BiocStyle/resources/tex/unsrturl}

Do you know how I can get around this?

Thanks for your time.

Kind regards,
Roel Janssen

--

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

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[Bioc-devel] Installing EBImage with custom packages dir?

[Guillaume MULLER]

Hi,

I've been installing EBImage several time these past months on multiple 
machines, using instructions at: 
http://bioconductor.org/packages/release/bioc/html/EBImage.html.

I've noticed a few strange things with the installer:

- When the installer installs the dependencies and one of them fails (e.g. 
"tiff" or "png", because the headers are not installed on the system), and I 
run again biocLite("EBImage"), then even the dependencies that previously 
installed successfully (I saw the "DONE (xxx)" line in the logs) are 
re-downloaded and re-installed...

- The script asks if I want to upgrade my packages. If I says yes, then the 
system-wide installation fails because I'm not root, thus the biocLite() asks 
if I want to install the packages in my "personal library". If I answer "yes", 
it installs the packages in the default personal library location 
("~/R/x86_64-pc-linux-gnu-library/3.2"), whereas I've hardcoded my personal 
library location by using (.libPaths("~/.R/x86_64-pc-linux-gnu-library/3.1.2" 
in my .Rprofile)... Also, I'm not sure the script does not takes into account 
the packages already installed installed in my personal library, thus 
redundantly (re)-installs some packages in the default location.

Is there any work-around so that I don't have to move all the (redundantly) 
installed packages into my actual personal library?

Cheers


GM
-- 
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
http://www.presans.com
http://feeds.feedburner.com/OYI/fr

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[Bioc-devel] cbind SummarizedExperiments containing a DNAStringSet not working

[Maarten van Iterson]

Dear list,

Combining SummarizedExperiment object, containing a DNAStringSet in the
rowData seems not to work properly. If I cbind two SummarizedExperiment
objects, which I know are identical, an error is reported:

Error in FUN(X[[i]], ...) (from #2) :
  column(s) 'sourceSeq' in ‘mcols’ are duplicated and the data do not match

I think I traced the problem existing in `SummarizedExperiment:::.compare`
in that `identical` is used to compare DNAStringSets which is not behaving
as expected. Whereas it should return all identical it returns it is not!

Here is a counter example (which was easier to construct) showing that
`identical` returns FALSE where it should return TRUE.

> library(Biostrings)
> seq1 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
> seq2 <- paste(DNA_BASES[sample(1:4,5,replace=T)], collapse="")
>
> seq1
[1] "GACTC"
> seq2
[1] "GAATG"
>
> s1 <- DNAStringSet(seq1)
> s2 <- DNAStringSet(seq2)
>
> str(s1)
Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :
  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()
> str(s2)
Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
  ..@ pool   :Formal class 'SharedRaw_Pool' [package "XVector"]
with 2 slots
  .. .. ..@ xp_list:List of 1
  .. .. .. ..$ :
  .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. ..$ :

  ..@ ranges :Formal class 'GroupedIRanges' [package "XVector"]
with 7 slots
  .. .. ..@ group  : int 1
  .. .. ..@ start  : int 1
  .. .. ..@ width  : int 5
  .. .. ..@ NAMES  : NULL
  .. .. ..@ elementType: chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata   : list()
  ..@ elementType: chr "DNAString"
  ..@ elementMetadata: NULL
  ..@ metadata   : list()
>
> identical(seq1, seq2)
[1] FALSE
> identical(s1, s2)
[1] TRUE
> seq1 == seq2
[1] FALSE
> s1 == s2
[1] FALSE
>
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

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] Biostrings_2.42.1  XVector_0.14.1
 [3] BBMRIomics_1.0.3   SummarizedExperiment_1.4.0
 [5] Biobase_2.34.0 GenomicRanges_1.26.4
 [7] GenomeInfoDb_1.10.3IRanges_2.8.2
 [9] S4Vectors_0.12.2   BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10 AnnotationDbi_1.36.2
hms_0.3
 [4] GenomicAlignments_1.10.1 zlibbioc_1.20.0
BiocParallel_1.8.1
 [7] BSgenome_1.42.0  lattice_0.20-35
R6_2.2.0
[10] httr_1.2.1   tools_3.3.2
grid_3.3.2
[13] DBI_0.6  assertthat_0.1
digest_0.6.12
[16] tibble_1.2   Matrix_1.2-8
readr_1.1.0
[19] rtracklayer_1.34.2   bitops_1.0-6
biomaRt_2.30.0
[22] RCurl_1.95-4.8   memoise_1.0.0
RSQLite_1.1-2
[25] compiler_3.3.2   GenomicFeatures_1.26.3
Rsamtools_1.26.1
[28] XML_3.98-1.5 jsonlite_1.3
VariantAnnotation_1.20.3
>

I don't completely understand understand why `identical` is not working
properly is it comparing the environment address in the above example they
are the same although the sequences are not? In my case the two
SummarizedExperiments contained the same DNAStringSets but had a different
environment address?

Regards,
Maarten

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[Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

[Rainer Johannes]

Dear all,

I've just committed a change in ensembldb (version 1.99.13) that removes all 
filter classes from it and imports them from the AnnotationFilter package. This 
change will break biovizBase and ggbio (and all packages downstream of them, 
e.g. Gviz). I've already sent Michael Lawrence patches to fix both packages, 
but  there might still be some problems in the upcoming build reports I guess.

I've also contacted the developers of the TVTB and chimeraviz packages and made 
them aware of the change. Could be that there are other packages out there 
possibly affected by the change. If so, let me know and I'll assist fixing the 
problems (if needed).

cheers, jo

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