Re: [Bioc-devel] RMarkdown for vignettes (builder issues)
Sorry to re-open this thread, but it appears that this configuration
works with some builders but not others. There appear to be two
different failure modes:
Works with: oaxaca, perceval (OSX 10.6, 10.9)
Fails with: moscato1 (windows 2008)
InvalidUrlException
D:%5Cpackagebuilder%5Cjobs%5CSTATegRa_20141007024617%5CR-libs%5CBiocStyle%5Cresources%5Chtml%5Cbioconductor.css
Invalid scheme
This appears to be an error in specific pandoc versions where it
interprets a windows drive letter as a URL scheme - see
https://github.com/jgm/pandoc/issues/1558
Fails with: zin1 (linux ubuntu 12.04)
pandoc: Error running filter pandoc-citeproc
pandoc-citeproc not found in path
The filter for processing references doesn't seem to be available. In
14.04 this is the package `pandoc-citeproc`, but it doesn't appear to be
available for 12.04. I assume this is only an issue if the Rmd document
includes a `bibliography:` field in the header.
Are these issues likely to be addressable for this release? If not, can
we get away with shipping a static vignette to avoid these problems?
(The build log in question is
http://bioconductor.org/spb_reports/STATegRa_0.99.3_buildreport_20141007025338.html
)
Thanks
Gordon Ball
On 04/10/14 00:02, Andrzej Oleś wrote:
Hi Gordon, James,
thank you for pointing this out! At the time BiocStyle for markdown
documents was developed 'rmarkdown' was not yet on CRAN and couldn't
be used as a vignette builder engine.
As things changed in the meantime, the approach described by Gordon
should be just fine. I will update the BiocStyle vignette accordingly.
Best,
Andrzej
On Fri, Oct 3, 2014 at 4:51 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Henrik Bengtsson h...@biostat.ucsf.edu
To: jmac...@u.washington.edu
Cc: bioc-devel@r-project.org
Sent: Friday, October 3, 2014 6:56:59 AM
Subject: Re: [Bioc-devel] RMarkdown for vignettes
I think it requires Bioc core to make a statement that pandoc will be
added
to the list of external software that can be assume to exist on the
servers.
Pandoc is installed on the build servers. Several packages use it.
If it is also expected that users should be able to rebuild all
vignettes/documents themselves, then that assumption has to be
extended to
the users as well. BTW, is there such an assumption on
LaTeX-dependent
packages today?
Users only need LaTeX (or pandoc) if they are going to build package
vignettes from svn. Source packages (as well as binary packages of course)
already contain built vignettes.
Dan
Installing pandoc is not that hard and lightweight (much smaller than
LaTeX), but it does add one more installation. On the other hand, it
opens
up for doing lots of other neat things.
Henrik
On Oct 3, 2014 6:40 AM, James W. MacDonald jmac...@uw.edu wrote:
Hi Gordon,
Sean Davis has something about this on his blog:
http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/
Best,
Jim
On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball gordon.b...@ki.se
wrote:
Hello
Is it possible to use (RStudio's) rmarkdown package as a vignette
builder for the upcoming release?
ie, with the (at least locally working) configuration
DESCRIPTION
Suggests: knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
vignette/vignette.Rmd
---
title: ...
output: BiocStyle::html_document
vignette:
%% \VignetteEngine{knitr::rmarkdown}
%% \VignetteIndexEntry{...}
I couldn't find any explicit reference to markdown vs rmarkdown
in the
package guidelines. The documentation for [BiocStyle] indicates
that it
isn't possible to build package vignettes with the newer
rmarkdown - is
that still correct?
I note that the newer [rmarkdown] is now in CRAN, so presumably
can be
used by the builders - but do they have the non-R dependency
(pandoc)
available?
The rationale for wanting rmarkdown instead markdown is support
for a
few extended features, particularly being able to cite from a
bibtex
file (which as far as I know isn't possible with the older
markdown).
Thanks
Gordon Ball
Computational Medicine Group
Karolinska Institute
[BiocStyle]:
http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
[rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/
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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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[Bioc-devel] GOexpress: new package to visualise microarray and RNAseq data using gene ontology annotations
Dear all, I would like to introduce a recent addition to Bioconductor. I hope those of you working with transcriptomics data will find it useful for their own work. *GOexpress *is a package taking an *ExpressionSet *object minimally including *assayData *and *phenoData* corresponding to either microarray or RNA-Sequencing data, and enables rapid plotting of the expression profile of any given gene in the different experimental groups. The package also initially fetches gene ontology annotations from the *Ensembl BioMart* to display the expression level of genes associated with each ontology in a heatmap. Consequently, all species and microarray present in the *Ensembl BioMart* should be supported by *GOexpress* (only a few were tested during the development of the package). We included two scoring methods (random-forest and ANOVA) to rank genes and gene ontologies best clustering predefined groups of samples (e.g. treatment groups). Note that we do not intend to compete with packages such as GOstats and topGO for hypothesis testing, but rather to complement such packages with means of accompanying their result statistics with plots showing group-wise and sample-wise expression levels. I have a few more ideas of my own to extend the package when time allows, but I do also welcome feedback and suggestions from testers that could benefit the community. Link: http://bioconductor.org/packages/devel/bioc/html/GOexpress.html Yours sincerely, Kevin -- Kévin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] NAMESPACE question
Does that happen with the other methods or just [? As a last resort, you could just drop the import (because [ is a primitive, it should just work). On Tue, Oct 7, 2014 at 3:08 AM, Robert Castelo robert.cast...@upf.edu wrote: hi Martin, On 10/06/2014 07:24 PM, Martin Morgan wrote: [...] There are two 'as.vector' generics, one defined in Matrix and one in BiocGenerics (and made available via IRanges). These generics have different methods showMethods(Matrix::as.vector) Function: as.vector (package base) x=abIndex, mode=ANY x=abIndex, mode=character x=ANY, mode=ANY x=dgCMatrix, mode=missing x=dgeMatrix, mode=missing x=diagonalMatrix, mode=missing x=dsCMatrix, mode=missing x=ldenseMatrix, mode=missing x=Matrix, mode=missing x=ndenseMatrix, mode=missing x=sparseVector, mode=character x=sparseVector, mode=missing showMethods(BiocGenerics::as.vector) Function: as.vector (package BiocGenerics) x=ANY x=AtomicList x=Rle x=XDouble x=XInteger x=XRaw x=XString x=XStringSet so it's important that your code clearly distinguish between generics. One possibility is to remove importMethodsFrom(IRanges, as.vector) from the NAMESPACE, and explicitly use IRanges::as.vector(...) in your code. ok, i've done this as it is the easiest at the moment to meet the release schedule. i guess that in the future i should try to avoid using the '::' operator by importing exclusively what is needed from each package. codetoolsBioC::writeNamespaceImports(qpgraph) might provide you with some guidance (it's not 100% reliable; available via svn at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC ) about what functionality is being imported. thanks for the heads up about codetoolsBioC, i've tried it out and seen that some of the suggested imports are not necessary but some others i was really missing them (which makes me wonder how was it possible that he package did not break at those points). one further question related to NAMESPACE. i subset GRanges objects in the package via the '[' operator, i've included this into the NAMESPACE file as: importMethodsFrom(GenomicRanges, c, cbind, rbind, mcols-, start, end, strand, sort, [, [-, [[, [[-, $, $-) however, when the package reaches a subset operation x[i] with x being a GRanges object, an entire package loading sequence starts: Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ [... etc ...] which may look a bit odd to the user. for every other imported method the package uses them silently without loading the corresponding package, am i importing '[' for GRanges objects from the wrong package? is there a way to import '[' so that my package can use it without triggering that package loading sequence? thanks again! robert. ___ 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
Re: [Bioc-devel] NAMESPACE question
On 10/07/2014 08:15 AM, Robert Castelo wrote: hi, it happens only with [, that's why i'm puzzled. it behaves as if you load a GRanges object 'x' and try to subset it x[1] without loading 'GenomicRanges' first. Is there a reproducible example? I see in your code there are several places where you require() or library() various packages. I think one of these Depends: on GenomicRanges, and the messages you see are the effect of moving GenomicRanges from 'loaded' to 'attached'. You can see the effect with library(qpgraph) sessionInfo() ## GenomicRanges loaded but not attached library(GenomicRanges) ## information about the package being attached Probably in your code you do not actually want to require() ad hoc packages and influence the user search path (and implicitly rely on search path order for correct functionality), but rather to requireNamespace(foo); foo::fun(...) (or possibly loadNamespace()). Complicated! Martin robert. On 10/07/2014 05:05 PM, Michael Lawrence wrote: Does that happen with the other methods or just [? As a last resort, you could just drop the import (because [ is a primitive, it should just work). On Tue, Oct 7, 2014 at 3:08 AM, Robert Castelo robert.cast...@upf.edu mailto:robert.cast...@upf.edu wrote: hi Martin, On 10/06/2014 07:24 PM, Martin Morgan wrote: [...] There are two 'as.vector' generics, one defined in Matrix and one in BiocGenerics (and made available via IRanges). These generics have different methods showMethods(Matrix::as.vector) Function: as.vector (package base) x=abIndex, mode=ANY x=abIndex, mode=character x=ANY, mode=ANY x=dgCMatrix, mode=missing x=dgeMatrix, mode=missing x=diagonalMatrix, mode=missing x=dsCMatrix, mode=missing x=ldenseMatrix, mode=missing x=Matrix, mode=missing x=ndenseMatrix, mode=missing x=sparseVector, mode=character x=sparseVector, mode=missing showMethods(BiocGenerics::as.__vector) Function: as.vector (package BiocGenerics) x=ANY x=AtomicList x=Rle x=XDouble x=XInteger x=XRaw x=XString x=XStringSet so it's important that your code clearly distinguish between generics. One possibility is to remove importMethodsFrom(IRanges, as.vector) from the NAMESPACE, and explicitly use IRanges::as.vector(...) in your code. ok, i've done this as it is the easiest at the moment to meet the release schedule. i guess that in the future i should try to avoid using the '::' operator by importing exclusively what is needed from each package. codetoolsBioC::__writeNamespaceImports(__qpgraph) might provide you with some guidance (it's not 100% reliable; available via svn at https://hedgehog.fhcrc.org/__bioconductor/trunk/madman/__Rpacks/codetoolsBioC https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC) about what functionality is being imported. thanks for the heads up about codetoolsBioC, i've tried it out and seen that some of the suggested imports are not necessary but some others i was really missing them (which makes me wonder how was it possible that he package did not break at those points). one further question related to NAMESPACE. i subset GRanges objects in the package via the '[' operator, i've included this into the NAMESPACE file as: importMethodsFrom(__GenomicRanges, c, cbind, rbind, mcols-, start, end, strand, sort, [, [-, [[, [[-, $, $-) however, when the package reaches a subset operation x[i] with x being a GRanges object, an entire package loading sequence starts: Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ [... etc ...] which may look a bit odd to the user. for every other imported method the package uses them silently without loading the corresponding package, am i importing '[' for GRanges objects from the wrong package? is there a way to import '[' so that my package can use it without triggering that package loading sequence? thanks again! robert. _ Bioc-devel@r-project.org mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] RMarkdown for vignettes (builder issues)
This is fixed now.
http://bioconductor.org/spb_reports/STATegRa_0.99.4_buildreport_20141007100210.html
Dan
- Original Message -
From: Gordon Ball gordon.b...@ki.se
To: Andrzej Oleś andrzej.o...@gmail.com, Dan Tenenbaum
dtene...@fhcrc.org
Cc: jmac...@u.washington.edu, bioc-devel@r-project.org, david Gomez-Cabrero
david.gomezcabr...@ki.se
Sent: Tuesday, October 7, 2014 3:53:40 AM
Subject: Re: [Bioc-devel] RMarkdown for vignettes (builder issues)
Sorry to re-open this thread, but it appears that this configuration
works with some builders but not others. There appear to be two
different failure modes:
Works with: oaxaca, perceval (OSX 10.6, 10.9)
Fails with: moscato1 (windows 2008)
InvalidUrlException
D:%5Cpackagebuilder%5Cjobs%5CSTATegRa_20141007024617%5CR-libs%5CBiocStyle%5Cresources%5Chtml%5Cbioconductor.css
Invalid scheme
This appears to be an error in specific pandoc versions where it
interprets a windows drive letter as a URL scheme - see
https://github.com/jgm/pandoc/issues/1558
Fails with: zin1 (linux ubuntu 12.04)
pandoc: Error running filter pandoc-citeproc
pandoc-citeproc not found in path
The filter for processing references doesn't seem to be available. In
14.04 this is the package `pandoc-citeproc`, but it doesn't appear to
be
available for 12.04. I assume this is only an issue if the Rmd
document
includes a `bibliography:` field in the header.
Are these issues likely to be addressable for this release? If not,
can
we get away with shipping a static vignette to avoid these problems?
(The build log in question is
http://bioconductor.org/spb_reports/STATegRa_0.99.3_buildreport_20141007025338.html
)
Thanks
Gordon Ball
On 04/10/14 00:02, Andrzej Oleś wrote:
Hi Gordon, James,
thank you for pointing this out! At the time BiocStyle for markdown
documents was developed 'rmarkdown' was not yet on CRAN and
couldn't
be used as a vignette builder engine.
As things changed in the meantime, the approach described by Gordon
should be just fine. I will update the BiocStyle vignette
accordingly.
Best,
Andrzej
On Fri, Oct 3, 2014 at 4:51 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
- Original Message -
From: Henrik Bengtsson h...@biostat.ucsf.edu
To: jmac...@u.washington.edu
Cc: bioc-devel@r-project.org
Sent: Friday, October 3, 2014 6:56:59 AM
Subject: Re: [Bioc-devel] RMarkdown for vignettes
I think it requires Bioc core to make a statement that pandoc
will be
added
to the list of external software that can be assume to exist on
the
servers.
Pandoc is installed on the build servers. Several packages use it.
If it is also expected that users should be able to rebuild all
vignettes/documents themselves, then that assumption has to be
extended to
the users as well. BTW, is there such an assumption on
LaTeX-dependent
packages today?
Users only need LaTeX (or pandoc) if they are going to build
package vignettes from svn. Source packages (as well as binary
packages of course) already contain built vignettes.
Dan
Installing pandoc is not that hard and lightweight (much smaller
than
LaTeX), but it does add one more installation. On the other hand,
it
opens
up for doing lots of other neat things.
Henrik
On Oct 3, 2014 6:40 AM, James W. MacDonald jmac...@uw.edu
wrote:
Hi Gordon,
Sean Davis has something about this on his blog:
http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/
Best,
Jim
On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball gordon.b...@ki.se
wrote:
Hello
Is it possible to use (RStudio's) rmarkdown package as a
vignette
builder for the upcoming release?
ie, with the (at least locally working) configuration
DESCRIPTION
Suggests: knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
vignette/vignette.Rmd
---
title: ...
output: BiocStyle::html_document
vignette:
%% \VignetteEngine{knitr::rmarkdown}
%% \VignetteIndexEntry{...}
I couldn't find any explicit reference to markdown vs rmarkdown
in the
package guidelines. The documentation for [BiocStyle] indicates
that it
isn't possible to build package vignettes with the newer
rmarkdown - is
that still correct?
I note that the newer [rmarkdown] is now in CRAN, so presumably
can be
used by the builders - but do they have the non-R dependency
(pandoc)
available?
The rationale for wanting rmarkdown instead markdown is support
for a
few extended features, particularly being able to cite from a
bibtex
file (which as far as I know isn't possible with the older
markdown).
Thanks
Gordon Ball
Computational Medicine Group
Karolinska Institute
[BiocStyle]:
Re: [Bioc-devel] S4Vectors unit tests
On 10/07/2014 10:35 AM, Michael Lawrence wrote: Looks like we still have to move over the DataFrame, etc tests from IRanges? Yes this and other leftovers. H. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] droplevels method for DataFrame?
Cool. We should consider moving some of the infrastructure pieces to the github bridge. I added a droplevels method for List that should take care of things. On Mon, Oct 6, 2014 at 6:11 PM, Ryan C. Thompson r...@thompsonclan.org wrote: Hi, Yes, if something is on Github (or just any git/hg repo that I can clone) then I'm much more likely to try to fix simple bugs that I discover and submit patches or pull requests rather than report them as bugs. It doesn't hurt that Github provides tools to submit pull requests from the terminal. I've never learned cvs or svn because I mostly haven't had the need in the past (haven't been working on projects that use cvs/svn). So in my case, yes, if S4Vectors was on Github I probably would have cloned it and tried to fix it before reporting the issue here, and I would have either reported it with a patch or explained what I tried and where I got stuck. -Ryan On Mon 06 Oct 2014 05:55:02 PM PDT, Michael Lawrence wrote: Makes sense to me. Just wondering: if S4Vectors were say on github, would this be something that you would be comfortable resolving via a pull request? Would social coding increase external contributions to the infrastructure? On Mon, Oct 6, 2014 at 5:13 PM, Ryan C. Thompson r...@thompsonclan.org mailto:r...@thompsonclan.org wrote: Hi, I've just noticed that DataFrame doesn't have a droplevels method, but data.frame does. In fact, droplevels.data.frame seems to work just fine on DataFrame objects. Could this be added? -Ryan sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grDevices datasets parallel graphics stats utils [8] methods base other attached packages: [1] DESeq2_1.4.5 RcppArmadillo_0.4.450.1.0 [3] Rcpp_0.11.2cqn_1.10.0 [5] quantreg_5.05 SparseM_1.05 [7] preprocessCore_1.26.1 nor1mix_1.2-0 [9] mclust_4.4 baySeq_1.18.0 [11] DESeq_1.16.0 lattice_0.20-29 [13] locfit_1.5-9.1 edgeR_3.6.8 [15] limma_3.20.9 arrayQualityMetrics_3.20.0 [17] partitions_1.9-15 biomaRt_2.20.0 [19] functional_0.6 sqldf_0.4-7.1 [21] RSQLite.extfuns_0.0.1 RSQLite_0.11.4 [23] DBI_0.3.1 gsubfn_0.6-6 [25] proto_0.3-10 GenomicFeatures_1.16.2 [27] AnnotationDbi_1.26.0 chipseq_1.14.0 [29] inline_0.3.13 affy_1.42.3 [31] Biobase_2.24.0 ShortRead_1.22.0 [33] GenomicAlignments_1.0.6BSgenome_1.32.0 [35] BiocParallel_0.6.1 Rsamtools_1.16.1 [37] Biostrings_2.32.1 XVector_0.4.0 [39] doParallel_1.0.8 iterators_1.0.7 [41] rtracklayer_1.24.2 GenomicRanges_1.16.4 [43] GenomeInfoDb_1.0.2 Matrix_1.1-4 [45] RColorBrewer_1.0-5 foreach_1.4.2 [47] plyr_1.8.1 stringr_0.6.2 [49] ggplot2_1.0.0 IRanges_1.22.10 [51] BiocGenerics_0.10.0BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 affyio_1.32.0affyPLM_1.40.1 [4] annotate_1.42.1 base64_1.2 base64enc_0.1-2 [7] BatchJobs_1.4BBmisc_1.7 beadarray_2.14.1 [10] BeadDataPackR_1.16.0 bitops_1.0-6 brew_1.0-6 [13] Cairo_1.5-6 checkmate_1.4chron_2.3-45 [16] cluster_1.15.3 codetools_0.2-9 colorspace_1.2-4 [19] compiler_3.1.0 digest_0.6.4 fail_1.2 [22] foreign_0.8-61 Formula_1.1-2gcrma_2.36.0 [25] genefilter_1.46.1geneplotter_1.42.0 gmp_0.5-12 [28] grid_3.1.0 gridSVG_1.4-0gtable_0.1.2 [31] Hmisc_3.14-5 hwriter_1.3.2illuminaio_0.6.1 [34] latticeExtra_0.6-26 MASS_7.3-34 munsell_0.4.2 [37] nnet_7.3-8 polynom_1.3-8RCurl_1.96-0 [40] reshape2_1.4 RJSONIO_1.2-0.2 rpart_4.1-8 [43] scales_0.2.4 sendmailR_1.2-1 setRNG_2013.9-1 [46] stats4_3.1.0 survival_2.37-7 SVGAnnotation_0.93-1 [49] tools_3.1.0 vsn_3.32.0 XML_3.98-1.1 [52] xtable_1.7-4 zlibbioc_1.10.0 _ Bioc-devel@r-project.org mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel
[Bioc-devel] Request for Comments on The NIH Software Discovery Index--a system for linking software, publications and users in the research community
On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system. The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your input. In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index, the final document will be used by the NIH Office of the Associate Director (ADDS) to inform a strategy for the development of a Software Discovery Index and a commons ecosystem for data, software, and resources. We need your help to ensure that this critical task is achieved: to guide the development of a community based system that gives credit and acknowledgment to the builder and maintainers of the software we all depend on! We invite all users, software developers, publishers, and software repository administrators to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014. The link to the report is here: http://softwarediscoveryindex.org [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] NAMESPACE question
On 10/07/2014 07:05 PM, Michael Lawrence wrote:
I think the intent there is that if you virtually always need a package to
generate the input or analyze the output of a documented function, it
should be in Depends. If it's a package that is only useful for
demonstration, it should be in Suggests, and one should abide by the same
guidelines (requireNamespace, etc) as Martin contributed.
I adjusted the wording a bit. I was also quite disturbed to find how similar my
Suggests illustration is to the advice in Writing R Extensions,
RShowDoc('R-exts'), section 1.1.3.1.
Martin
On Tue, Oct 7, 2014 at 6:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au
wrote:
The guidelines state :
Depends: is appropriate when a package is used in the example section of a
man page.
I think such packages should be in Suggests. In the example, the package
should be loaded by :
if(require(examplePackage))
{
exampleFunction(data)
}
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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