Re: [Bioc-devel] BiocStyle on windows with spaces in path names
On Wed, Oct 8, 2014 at 12:20 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 10/08/2014 11:41 AM, Henrik Bengtsson wrote:
You may want to make those function local to latex(). I haven't
verified it works (won't have time), but I bet a beer that it will
work.
I'll take you up on the bet, at least for some definition of 'work'. For
instance when debugging a vignette or writing a complicated Makefile for
courses I commonly do the equivalent of
R CMD Sweave foo.Rnw
R CMD texi2dvi --pdf foo.tex
Any environment variables set running Sweave are not available running
texi2dvi.
Easy,
Rscript -e R.rsp::rfile foo.Rnw
would Sweave + texi2dvi --pdf in one go. Putting that aside, I'm
happy to buy you a beer :)
Another solution along along lines of using TEXINPUTS would be to do:
R CMD Sweave foo.Rnw
export TEXINPUTS=`Rscript -e BiocStyle::texinputs()`
R CMD texi2dvi --pdf foo.tex
A third different (and obvious) solution, is to copy the files to
the current directory, i.e.
$ svn diff -x --ignore-all-space R/latex.R
Index: R/latex.R
===
--- R/latex.R (revision 95224)
+++ R/latex.R (working copy)
@@ -3,12 +3,14 @@
error=FALSE, use.unsrturl=TRUE)
{
options(..., width=width)
-cat(sprintf(\\RequirePackage{%s}\n\n,
-sub(.sty$, , .bioconductor.sty)))
+sty - .bioconductor.sty
+file.copy(sty, basename(sty), overwrite=TRUE)
+cat(\\RequirePackage{Bioconductor}\n\n)
if (use.unsrturl) {
bst - file.path(system.file(package=BiocStyle, resources,
latex), unsrturl)
+file.copy(bst, basename(bst), overwrite=TRUE)
cat(sprintf(\\AtBeginDocument{\\bibliographystyle{%s}}\n, bst))
}
This works also in your use case and those local copies are
automagically cleaned out by R CMD build. This passes R CMD check
--as-cran on BiocStyle etc. Now one can argue that it will clutter up
your local directory. For the original problem of \usepackage{} et
al. does not support spaces in paths one can also copy to a temporary
directory and use that path instead. (Personally I favor not
specifying paths at all to make even the intermediate *.tex file
portable.)
/Henrik
Martin
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Re: [Bioc-devel] NAMESPACE question
hi Martin, thanks for your recommendations regarding the conditional loading of packages. I think however, that they are not related to the problem I'm referring. Let me put here a reproducible example which works with qpgraph version 0.99.7 that I have just pushed to svn: library(qtl) library(qpgraph) map - sim.map(len=100, n.mar=10, anchor.tel=FALSE, eq.spacing=TRUE, include.x=FALSE) eqtlcross - eQTLcross(map) eqtlcross - addGenes(eqtlcross, 5) eqtlcross - addeQTL(eqtlcross, g1, location=map[[1]][1]) sim.eqtl - reQTLcross(eqtlcross, rho=0.5, a=1) cross - sim.cross(map, sim.eqtl, n.ind=100) gstarts -runif(5, min=range(map[[1]])[1], max=range(map[[1]])[2]) annot - data.frame(chr=rep(names(map)[1], 5), start=gstarts, end=gstarts+1, strand=rep(+, 5), row.names=sim.eqtl$model$Y, stringsAsFactors=FALSE) ## the following is the method that triggers the ## unexpected behavior. Its last but one instruction ## in line 208 of file qpgraph/R/eQTLnetworkEstimationParam-methods.R ## is the following: ## ## geneAnnotation - geneAnnotation[genes] ## ## and should be using the method [ imported from GenomicRanges ## however it starts loading a number of packages to do the job param - eQTLnetworkEstimationParam(cross, geneAnnotation=annot, genome=simulatedGenome) Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: [...etc...] sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8 LC_PAPER=en_US.UTF8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5 qpgraph_1.99.7 qtl_1.33-7 [6] vimcom_0.9-93 setwidth_1.0-3 colorout_1.0-2 loaded via a namespace (and not attached): [1] annotate_1.43.5 AnnotationDbi_1.27.16base64enc_0.1-2 BatchJobs_1.4 [5] BBmisc_1.7 Biobase_2.25.0 BiocParallel_0.99.22 biomaRt_2.21.1 [9] Biostrings_2.33.14 bitops_1.0-6 brew_1.0-6 checkmate_1.4 [13] codetools_0.2-9 DBI_0.3.1digest_0.6.4 fail_1.2 [17] foreach_1.4.2futile.logger_1.3.7 futile.options_1.0.0 GenomeInfoDb_1.1.23 [21] GenomicAlignments_1.1.30 GenomicFeatures_1.17.19 GenomicRanges_1.17.42graph_1.43.0 [25] grid_3.1.0 iterators_1.0.7 lambda.r_1.1.6 lattice_0.20-29 [29] Matrix_1.1-4 mvtnorm_1.0-0RCurl_1.95-4.3 Rgraphviz_2.9.1 [33] Rsamtools_1.17.34RSQLite_0.11.4 rtracklayer_1.25.17 sendmailR_1.2-1 [37] stringr_0.6.2tools_3.1.0 XML_3.98-1.1 xtable_1.7-4 [41] XVector_0.5.8zlibbioc_1.11.1 cheers, robert. On 10/07/2014 05:54 PM, Martin Morgan wrote: 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,
[Bioc-devel] Faculty Position in Computational Systems Biology at UC Riverside
University of California, Riverside AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230 POSITION We are seeking an Assistant Professor in the field of Computational Systems Biology. Research should be in systems biology, using computational approaches or a combination of both experimental and computational approaches. TITLE/RANK Assistant Professor. Appointment and salary will be competitive and commensurate with accomplishments. LOCATION University of California, Riverside. BACKGROUND The successful candidate will hold an academic appointment in the Department of Botany and Plant Sciences with the option of a secondary cooperating faculty appointment in a quantitative department such as statistics, computer science, engineering or related. The candidate will also join the innovative and multidisciplinary Institute for Integrative Genome Biology (IIGB) which connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of Instrumentation Facilities that serve as a centralized, shareduse resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy, proteomics and genomics. Its bioinformatic component is equipped with a modern highperformance compute (HPC) infrastructure. This position will include an appointment in the Agricultural Experiment Station, which incl udes the responsibility to conduct research and outreach relevant to the mission of the California Agricultural Experiment Station (http://cnas.ucr.edu/about/anr/). QUALIFICATIONS A Ph.D. in a field related to systems biology is required including several years of postdoctoral research. RESPONSIBILITIES Qualified candidates are expected to have excellent publication and research records in computational systems biology or related areas, such as bioinformatics or computational genome biology. The candidate’s research program should be heavily focused on involving modern highthroughput data, especially from next generation sequencing technologies. An additional requirement is a strong commitment to teaching in computational systems biology. TO APPLY Review of applications will begin November 7, 2014 and continue until the position is filled. Interested individuals should: (1) submit a curriculum vitae, (2) provide a statement of research, and (3) three letters of reference. A teaching statement is strongly recommended. Please submit your applications through the AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230 Websites: http://www.genomics.ucr.edu, http://cnas.ucr.edu/, http://www.ucr.edu The University of California is an Equal Opportunity/Affirmative Action Employer/Veterans Employer. In accordance with Federal law, we are making available our Campus Security Report to all prospective employees. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] NAMESPACE question
Hi Robert, Martin, Yes using requireNamespace() internally is much cleaner than using require(). Sorry for that. Just made the change in S4Vectors 0.2.6. FYI the need to load IRanges namespace in a couple of places inside S4Vectors is temporary and will go away soon. Cheers, H. On 10/09/2014 09:33 AM, Martin Morgan wrote: On 10/09/2014 08:00 AM, Robert Castelo wrote: hi Martin, thanks for your recommendations regarding the conditional loading of packages. I think however, that they are not related to the problem I'm referring. Let me put here a reproducible example which works with qpgraph version 0.99.7 that I have just pushed to svn: library(qtl) library(qpgraph) map - sim.map(len=100, n.mar=10, anchor.tel=FALSE, eq.spacing=TRUE, include.x=FALSE) eqtlcross - eQTLcross(map) eqtlcross - addGenes(eqtlcross, 5) eqtlcross - addeQTL(eqtlcross, g1, location=map[[1]][1]) sim.eqtl - reQTLcross(eqtlcross, rho=0.5, a=1) cross - sim.cross(map, sim.eqtl, n.ind=100) gstarts -runif(5, min=range(map[[1]])[1], max=range(map[[1]])[2]) annot - data.frame(chr=rep(names(map)[1], 5), start=gstarts, end=gstarts+1, strand=rep(+, 5), row.names=sim.eqtl$model$Y, stringsAsFactors=FALSE) ## the following is the method that triggers the ## unexpected behavior. Its last but one instruction ## in line 208 of file qpgraph/R/eQTLnetworkEstimationParam-methods.R ## is the following: ## ## geneAnnotation - geneAnnotation[genes] ## ## and should be using the method [ imported from GenomicRanges ## however it starts loading a number of packages to do the job param - eQTLnetworkEstimationParam(cross, geneAnnotation=annot, genome=simulatedGenome) Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: [...etc...] Hmm, I see that the parallel, BiocGenerics, and stats4 packages are being attached. In a new R session I did this: trace(loadNamespace, tracer=recover) Tracing function loadNamespace in package base [1] loadNamespace param - eQTLnetworkEstimationParam(cross, geneAnnotation=annot, genome=simulatedGenome) Loading required package: parallel Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry Enter a frame number, or 0 to exit 1: eQTLnetworkEstimationParam(cross, geneAnnotation = annot, genome = simulat 2: geneAnnotation[genes] 3: geneAnnotation[genes] 4: extractROWS(x, i) 5: extractROWS(x, i) 6: extractROWS(seqnames(x), i) 7: extractROWS(seqnames(x), i) 8: suppressWarnings(require(IRanges, quietly = TRUE)) 9: withCallingHandlers(expr, warning = function(w) invokeRestart(muffleWarnin 10: require(IRanges, quietly = TRUE) ... and it's likely from ./S4Vectors/R/Rle-class.R:if (!suppressWarnings(require(IRanges, quietly=TRUE))) ./S4Vectors/R/Rle-class.R:if (!suppressWarnings(require(IRanges, quietly=TRUE))) could be addressed with suppressPackageStartupMessages() (less-preferred) or requireNamespace(IRanges) followed by IRanges::...; let's see if we can get that fixed... Martin sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8 [5] LC_MONETARY=en_US.UTF8LC_MESSAGES=en_US.UTF8 LC_PAPER=en_US.UTF8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C attached base packages: [1] stats4parallel stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5 qpgraph_1.99.7 qtl_1.33-7 [6] vimcom_0.9-93 setwidth_1.0-3 colorout_1.0-2 loaded via a namespace (and not attached): [1] annotate_1.43.5 AnnotationDbi_1.27.16base64enc_0.1-2 BatchJobs_1.4 [5] BBmisc_1.7 Biobase_2.25.0 BiocParallel_0.99.22 biomaRt_2.21.1 [9] Biostrings_2.33.14 bitops_1.0-6 brew_1.0-6 checkmate_1.4 [13] codetools_0.2-9 DBI_0.3.1digest_0.6.4 fail_1.2 [17] foreach_1.4.2futile.logger_1.3.7 futile.options_1.0.0 GenomeInfoDb_1.1.23 [21] GenomicAlignments_1.1.30 GenomicFeatures_1.17.19 GenomicRanges_1.17.42 graph_1.43.0 [25] grid_3.1.0 iterators_1.0.7 lambda.r_1.1.6 lattice_0.20-29 [29] Matrix_1.1-4 mvtnorm_1.0-0RCurl_1.95-4.3 Rgraphviz_2.9.1 [33] Rsamtools_1.17.34RSQLite_0.11.4 rtracklayer_1.25.17 sendmailR_1.2-1 [37] stringr_0.6.2tools_3.1.0 XML_3.98-1.1 xtable_1.7-4 [41] XVector_0.5.8zlibbioc_1.11.1 cheers, robert. On 10/07/2014 05:54 PM, Martin Morgan wrote: 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.
Re: [Bioc-devel] a warning we may not need any more?
Hi Vince, Good idea. I made that change in GenomeInfoDb 1.1.26: library(GenomeInfoDb) x - Seqinfo(seqnames=c(chr1, chr2, chr3, chrM), seqlengths=c(100, 200, NA, 15), isCircular=c(NA, FALSE, FALSE, TRUE), genome=toy) y - Seqinfo(seqnames=c(chr3, chr4, chrM), seqlengths=c(300, NA, 15)) merge(x, y) # warning genome(y) - genome(x)[[1]] merge(x, y) # no warning Cheers, H. On 10/09/2014 12:04 PM, Vincent Carey wrote: *Warning message:* *In .Seqinfo.mergexy(x, y) :* * Each of the 2 combined objects has sequence levels not in the other:* * - in 'x': chr4, chr16, chr10, chr11, chr18, chr20, chr22* * - in 'y': chrY* * Make sure to always combine/compare objects based on the same reference* * genome (use suppressWarnings() to suppress this warning).* *It seems to me that if we can check equality of the assigned genomes, we should* *not issue this warning.* [[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] package ‘FEM’ is not available (for R version 3.0.2)
- Original Message - From: Yinming Jiao 20907...@zju.edu.cn To: bioc-devel@r-project.org Sent: Thursday, October 9, 2014 7:46:38 PM Subject: [Bioc-devel] package ‘FEM’ is not available (for R version 3.0.2) Dear All, I have a package, FEM, which is published few days ago. The link is :http://www.bioconductor.org/packages/devel/bioc/html/FEM.html But when I try to install it, source(http://bioconductor.org/biocLite.R;) biocLite(FEM) R reports: package ��FEM�� is not available (for R version 3.0.2). So How can I resolve this problem. I also noted that Bioconductor version: Development (3.0) What does this mean? Bioconductor is versioned and Bioconductor versions are meant to work with specific versions of R. Bioconductor 3.0 which will be released next week, and which will contain your package, only works with R-3.1.x. Currently both Bioconductor 2.14 (the current release version) and Bioconductor 3.0 (the devel version, soon to be release) work with this version of R. So if you want to install FEM, you need to install R-3.1.1. If you want to install FEM before the release you need to do the following: source(http://bioconductor.org/biocLite.R;) useDevel() biocLite(FEM) If you wait till after the release, you won't need to do the second line. BTW, as a package developer, it's a good idea to develop your package using the same (devel) version of Bioconductor that your package will be added to (and of course the appropriate version of R). R may change, and other packages that you depend on may change, and you want to make sure your package will work as expected for end users. Dan Thanks very much. Yinming Jiao -- CAS-MPG Partner Institute for Computational Biology 320 Yue Yang Road Shanghai 200031 China Email: 20907...@zju.edu.cn or jiaoyinm...@picb.ac.cn Mob: +86 1852139 6188 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
