Re: [Bioc-devel] Update existing packages and change name

[Obenchain, Valerie]

Hi Sokratis,

Unfortunately you can't rename a package ... and there is no such thing as a 
'sub package'. Maybe you meant sub-package terms of dependencies. If you have 
new data to add that's independent of what's in pathprintGEOData you can create 
a new data package.

I'm not sure what you mean by 'considerably more data'. The pathprintGEOData 
package is currently 22MG:

~ >du -h pathprintGEOData_1.4.0.tar.gz
22MpathprintGEOData_1.4.0.tar.gz

We don't support git LFS yet in the experimental data repo. If you plan on 
making the package(s) very large we should consider making a ExperimentHub 
package where the data can be stored in S3.

Valerie



On 02/21/2018 05:16 AM, Sokratis Kariotis wrote:

Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData) with
considerably more data and a few code updates. I also want to change the
name of the data package to reflect the new content. Can the package name
be changed or do I have to create new sub-packages? Thanks in advance.

Cheers




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Re: [Bioc-devel] rsvg on mac

[Kevin Horan]

Ok, I understand. Is it safe to assume that the rsvg package would be 
available by the time the next bioconductor release occurs? In that case 
I can just plan to re-enable that function at release time. Otherwise I 
will have to find another workaround for it. Thanks.



Kevin


On 02/13/2018 05:24 PM, Hervé Pagès wrote:

Hi Kevin,

As Val said, some CRAN packages with native code won't compile
on our Windows or Mac builders because of missing components,
and rsvg is one of them. Please keep in mind that we already
install many external components required for the compilation
of Bioconductor packages. The process of doing so on a fresh
Mac El Capitan system is documented here:


https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-MacOSX-El-Capitan-HOWTO.TXT 



Installing these components is time consuming and there is always
the risk to introduce some conflicts/instabilities when installing
new components. Given that our resources are limited, it wouldn't
make much sense that we do this for those CRAN packages for which
the binaries are only temporarily unavailable.

Cheers,
H.


On 02/13/2018 12:56 PM, Kevin Horan wrote:

Valerie,

  Ok, I understand the difference now. Would it be possible to
install the system requirement for rsvg ( just on devel)?

  I'm trying to generate plots in either PNG or SVG with OpenBabel.
For PNG, OpenBabel requires it's own Cario library be installed on the
system (doesn't seem to work with what is built into R, as it needs to
be linked with OpenBabel). I've not been successful getting the Cairo
lib installed on windows, but using SVG with OpenBabel, and then reading
that back into R with rsvg, works fine. So it seems I'll need a extra
system library either way ( either Cairo, or librsvg2).

Thanks.

Kevin


On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:

Hi,

By default, the build system installs CRAN dependencies on the Mac and
Windows builders with 'type=both':

   install.packages("mypackage", type="both")

This means it first tries to install the binary and if that fails, it
tries to install from source. Packages without native code or
SystemRequirements usually install fine from source. This is the case
for DiagrammeR which can be installed on the build machines. rsvg is
in the Suggests field of DiagrammeR so rsvg is not needed to install
or load the package.

The rsvg package is different in that it has 'librsvg2' as a
SystemRequirement which is not installed on the Mac (or Windows) build
machine:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w= 



We do install all SystemRequirements for Bioconductor packages on the
Mac and Windows builders but not for CRAN packages. Installing all
third party requirements of CRAN dependencies would add significantly
to the build system maintenance and really only serves a purpose in
this window of time where binaries are not available for devel.

cc'ing Herve in case he has more to add.


Valerie




On 02/12/2018 12:25 PM, Kevin Horan wrote:

Valerie,
 I'm not sure I understand. I looked at another package that is
currently installed on the mac devel machine, DiagrammeR
(https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_package-3DDiagrammeR=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE=), 
and it has the same

set of links on the CRAN site as rsvg does. In particular, it does
not show a  r-devel version for El Capitan.
 Also, rsvg is not installed on the release mac build machine
either, which it should have a version for.

Kevin

On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:

Hi Kevin,

CRAN binaries for El Capitan in devel aren't available. You can see
this on the rsvg landing page:

https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w= 



Nothing we can do until CRAN makes them available.

Valerie


On 02/07/2018 08:29 AM, Kevin Horan wrote:
The ChemmineR build is failing on the mac due to a new dependency 
not

being available, the package "rsvg". Would it be possible to install
that on the mac build machine? Thanks.

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineR_merida2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU= 




Kevin

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Re: [Bioc-devel] ShortRead::countLines integer overflow with large fastq files

[Thomas Girke]

Great thanks!

Thomas

On Wed, Feb 21, 2018 at 3:11 AM Martin Morgan 
wrote:

> Thanks Thomas, countLines() in ShortRead 1.37.3 and later) will return
> numeric() rather than integer() and hence support large files.
>
> Martin
>
> On 02/20/2018 10:08 PM, Thomas Girke wrote:
> > Dear Martin,
> >
> > countLines in ShrotRead returns the line counts as integers which appears
> > to create problems with large FASTQ files (>536.8 Mio lines) due to R's
> > integer limit (2^31-1). When the integer limit is reached/exceeded it
> seems
> > that countLines returns negative values not reflecting the number of
> lines
> > in a file anymore. At least this is what I learned after several users
> > reported this problem and then running some tests myself on large FASTQ
> > files with variable line numbers around the integer limit. If my
> conclusion
> > is correct and there aren' t any strong reasons against it, would it be
> > possible to consider returning numeric values instead either by default
> or
> > conditionally (e.g. when the count is >= .Machine$integer.max) to lift
> this
> > limit. If this is not possible then returning NAs instead of negative
> > values would be a sensible compromise.
> >
> > Thanks,
> >
> > Thomas
> >
> >> sessionInfo()
> > R version 3.4.2 (2017-09-28)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: CentOS Linux 7 (Core)
> >
> > Matrix products: default
> > BLAS: /usr/lib64/libblas.so.3.4.2
> > LAPACK: /usr/lib64/liblapack.so.3.4.2
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats4parallel  stats graphics  utils datasets  grDevices
> > methods   base
> >
> > other attached packages:
> >   [1] ShortRead_1.36.0   GenomicAlignments_1.14.1
> >   SummarizedExperiment_1.8.0 DelayedArray_0.4.1
>  matrixStats_0.52.2
> > Biobase_2.38.0 Rsamtools_1.30.0
> >   GenomicRanges_1.30.0   GenomeInfoDb_1.14.0Biostrings_2.46.0
> >XVector_0.18.0 IRanges_2.12.0
> >   S4Vectors_0.16.0
> > [14] BiocParallel_1.12.0BiocGenerics_0.24.0setwidth_1.0-4
> > colorout_1.1-3
> >
> > loaded via a namespace (and not attached):
> >   [1] zlibbioc_1.24.0 lattice_0.20-35 hwriter_1.3.2
> >   tools_3.4.2 grid_3.4.2  latticeExtra_0.6-28
> >   Matrix_1.2-12   GenomeInfoDbData_0.99.1 RColorBrewer_1.1-2
> > bitops_1.0-6RCurl_1.95-4.8  compiler_3.4.2
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
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> >
>
>
> 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.
>

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[Bioc-devel] Update existing packages and change name

[Sokratis Kariotis]

Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData) with
considerably more data and a few code updates. I also want to change the
name of the data package to reflect the new content. Can the package name
be changed or do I have to create new sub-packages? Thanks in advance.

Cheers
-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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Re: [Bioc-devel] ShortRead::countLines integer overflow with large fastq files

[Martin Morgan]

Thanks Thomas, countLines() in ShortRead 1.37.3 and later) will return 
numeric() rather than integer() and hence support large files.


Martin

On 02/20/2018 10:08 PM, Thomas Girke wrote:

Dear Martin,

countLines in ShrotRead returns the line counts as integers which appears
to create problems with large FASTQ files (>536.8 Mio lines) due to R's
integer limit (2^31-1). When the integer limit is reached/exceeded it seems
that countLines returns negative values not reflecting the number of lines
in a file anymore. At least this is what I learned after several users
reported this problem and then running some tests myself on large FASTQ
files with variable line numbers around the integer limit. If my conclusion
is correct and there aren' t any strong reasons against it, would it be
possible to consider returning numeric values instead either by default or
conditionally (e.g. when the count is >= .Machine$integer.max) to lift this
limit. If this is not possible then returning NAs instead of negative
values would be a sensible compromise.

Thanks,

Thomas


sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

locale:
[1] C

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

other attached packages:
  [1] ShortRead_1.36.0   GenomicAlignments_1.14.1
  SummarizedExperiment_1.8.0 DelayedArray_0.4.1 matrixStats_0.52.2
Biobase_2.38.0 Rsamtools_1.30.0
  GenomicRanges_1.30.0   GenomeInfoDb_1.14.0Biostrings_2.46.0
   XVector_0.18.0 IRanges_2.12.0
  S4Vectors_0.16.0
[14] BiocParallel_1.12.0BiocGenerics_0.24.0setwidth_1.0-4
colorout_1.1-3

loaded via a namespace (and not attached):
  [1] zlibbioc_1.24.0 lattice_0.20-35 hwriter_1.3.2
  tools_3.4.2 grid_3.4.2  latticeExtra_0.6-28
  Matrix_1.2-12   GenomeInfoDbData_0.99.1 RColorBrewer_1.1-2
bitops_1.0-6RCurl_1.95-4.8  compiler_3.4.2

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