Re: [Bioc-devel] dimnames of multidimensional assays in SummarizedExperiment
Hi Pete, I'll look into this. Thanks! H. On 02/10/2016 12:33 PM, Peter Hickey wrote: The assays slot in a SummarizedExperiment object supports elements with up to 4 dimensions [*] library(SummarizedExperiment) makeSE <- function(n) { assay <- array(1:2^n, dim = rep(2, n), dimnames = split(letters[1:(2 * n)], seq_len(n))) SummarizedExperiment(assay) } x <- makeSE(4) However, the "higher-order" dimnames of the assays aren't preserved when calling the `assays` or `assay` getters: dimnames(assay(x, withDimnames = TRUE)) [[1]] [1] "a" "e" [[2]] [1] "b" "f" [[3]] NULL [[4]] NULL This is despite the data still being available in the assays slot: dimnames(x@assays[[1]]) 1` [1] "a" "e" 2` [1] "b" "f" 3` [1] "c" "g" 4` [1] "d" "h" The following patch fixes this by only touching the rownames and colnames and not touching the "higher-order" dimnames. Seem reasonable? Index: R/SummarizedExperiment-class.R === --- R/SummarizedExperiment-class.R (revision 113505) +++ R/SummarizedExperiment-class.R (working copy) @@ -174,7 +174,10 @@ { assays <- as(x@assays, "SimpleList") if (withDimnames) -endoapply(assays, "dimnames<-", dimnames(x)) + endoapply(assays, function(assay) { +dimnames(assay)[1:2] <- dimnames(x) +assay +}) else assays }) [*] In fact, the assay elements can have more than 4 dimensions when constructed, although subsetting with `[` isn't supported (possibly things other than subsetting break as well in this case). # No error y <- makeSE(5) y # Error y[1, ] Perhaps there should be a check in the constructor that all assay elements have < 5 dimensions? Cheers, Pete ___ 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...@fredhutch.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 citation and version is not updated
OK, I looked into this a bit. The citation is there now and I will continue to look into this. Dan - Original Message - > From: "Michael Love" > To: "Dan Tenenbaum" > Cc: "bioc-devel" > Sent: Monday, February 15, 2016 7:36:14 AM > Subject: Re: [Bioc-devel] package citation and version is not updated > hi Dan, > > I'm having the same issue with tximport: > > http://bioconductor.org/packages/devel/bioc/html/tximport.html > > The CITATION file has been in there since the package was added to devel > last week > > https://github.com/Bioconductor-mirror/tximport/blob/master/inst/CITATION > > citation("tximport") works > > thanks, > Mike > > On Fri, Jan 29, 2016 at 5:56 PM, Dan Tenenbaum > wrote: > >> This is fixed now. Thanks for the report. >> Dan >> >> >> - Original Message - >> > From: "Ludwig Geistlinger" >> > To: "bioc-devel" >> > Sent: Friday, January 29, 2016 2:06:37 AM >> > Subject: [Bioc-devel] package citation and version is not updated >> >> > Dear Dan, >> > >> > For some reason the citation on my package's landing page >> > >> > http://bioconductor.org/packages/EnrichmentBrowser.html >> > >> > is not displayed in agreement with my inst/CITATION file. >> > >> > Furthermore, the version number is also not up to date here, although >> > displayed correctly at the bottom of the page (--> Package Archives). >> > >> > How to resolve this? >> > >> > Thx, >> > Ludwig >> > >> > -- >> > Dipl.-Bioinf. Ludwig Geistlinger >> > >> > Lehr- und Forschungseinheit für Bioinformatik >> > Institut für Informatik >> > Ludwig-Maximilians-Universität München >> > Amalienstrasse 17, 2. Stock, Büro A201 >> > 80333 München >> > >> > Tel.: 089-2180-4067 >> > eMail: ludwig.geistlin...@bio.ifi.lmu.de >> > >> > ___ >> > 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Michael, Thanks for the reply. I created a minimal reproducible package with the issue. As it seems the warning comes because I have a 'data' folder where I have stored some example data, and one of the data is stored in GRanges format. If I delete the GRanges example data and keep any other data, I get no warning. So the issue is only when I import the 'methods' package and I have data locally stored as GRanges objects in the 'data' folder. You can download and install the simple example package by typing: devtools::install_github("andreaskapou/simplePackage") Or you can see the code in the following link, which just contains a simple function to call the methods::is() function and create a GRanges object. https://github.com/andreaskapou/simplePackage Thanks, Andreas -- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh e-mail : c.a.kapour...@sms.ed.ac.uk : kapouranis.andr...@gmail.com On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence wrote: > It would be helpful to have a reproducible example, i.e., your actual > package or a skeleton of it that reproduces the issue. Btw, you might > be able to debug this behavior by: > > debug(tools::undoc) > tools::undoc(dir=yourPackageDir) > > > > On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis > wrote: > > Hi, > > > > I am developing a package for Bioconductor, and I have a weird issue when > > importing the 'methods' package. Before I add the 'methods' package in > > Imoprts in the DESCRIPTION file, I pass the CMD check without any > warnings. > > > > However, when I add the 'methods' package in the Imports field, I get a > > warning during CMD check. (I need the methods package since I use the > > methods::is() function, and if I call it just as is(), when running the > > package from Rscript will fail since by default it does not load the > > 'methods' package.) > > > > I read a similar issue here: > > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html > > and I updated all my packages from Bioconductor including IRanges and > > GenomicRanges. > > > > This is the warning that I get, which is exactly the same as the previous > > issue in Bioc-Devel, and I understand that for some reason the > BiocGenerics > > is attached only when the 'methods' package is imported. > > > > * checking for missing documentation entries ... WARNING > > > > Attaching package: ‘BiocGenerics’ > > > > The following objects are masked from ‘package:parallel’: > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > > clusterExport, clusterMap, parApply, parCapply, parLapply, > > parLapplyLB, parRapply, parSapply, parSapplyLB > > > > The following objects are masked from ‘package:stats’: > > > > IQR, mad, xtabs > > > > The following objects are masked from ‘package:base’: > > > > Filter, Find, Map, Position, Reduce, anyDuplicated, append, > > as.data.frame, as.vector, cbind, colnames, do.call, duplicated, > > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, > > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, > > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > > tapply, union, unique, unlist, unsplit > > > > All user-level objects in a package should have documentation entries. > > See chapter ‘Writing R documentation files’ in the ‘Writing R > > Extensions’ manual. > > > > > > > > My DESCRIPTION file when I add the 'methods' package is the following: > > ... > > Depends: R (>= 3.2.0) > > LazyData: TRUE > > RoxygenNote: 5.0.1 > > Imports: GenomicRanges, > > IRanges, > > assertthat, > > S4Vectors, > > graphics, > > data.table, > > methods > > Suggests: knitr, > > rmarkdown, > > testthat > > VignetteBuilder: knitr > > > > > > > > Regards, > > Andreas > > > > [[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
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Joris, Apologies for not including the NAMESPACE file, but I have included the methods package also there, although I have used: importFrom(methods,is) since I just need the is() function for the time being. Regards, Andreas -- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh e-mail : c.a.kapour...@sms.ed.ac.uk : kapouranis.andr...@gmail.com On Mon, Feb 15, 2016 at 4:16 PM, Joris Meys wrote: > Hi Andreas, > > for a good understanding: just mentioning the methods package in the > DESCRIPTION file isn't doing a thing if you don't also add > > import(methods) > > to the NAMESPACE file. > > So it looks like the warning occurs when the package indicates that the > methods package is imported when it actually isn't. Do you still get that > warning if you update the NAMESPACE file? > > Cheers > Joris > > On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis < > kapouranis.andr...@gmail.com> wrote: > >> Hi, >> >> I am developing a package for Bioconductor, and I have a weird issue when >> importing the 'methods' package. Before I add the 'methods' package in >> Imoprts in the DESCRIPTION file, I pass the CMD check without any >> warnings. >> >> However, when I add the 'methods' package in the Imports field, I get a >> warning during CMD check. (I need the methods package since I use the >> methods::is() function, and if I call it just as is(), when running the >> package from Rscript will fail since by default it does not load the >> 'methods' package.) >> >> I read a similar issue here: >> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html >> and I updated all my packages from Bioconductor including IRanges and >> GenomicRanges. >> >> This is the warning that I get, which is exactly the same as the previous >> issue in Bioc-Devel, and I understand that for some reason the >> BiocGenerics >> is attached only when the 'methods' package is imported. >> >> * checking for missing documentation entries ... WARNING >> >> Attaching package: ‘BiocGenerics’ >> >> The following objects are masked from ‘package:parallel’: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following objects are masked from ‘package:stats’: >> >> IQR, mad, xtabs >> >> The following objects are masked from ‘package:base’: >> >> Filter, Find, Map, Position, Reduce, anyDuplicated, append, >> as.data.frame, as.vector, cbind, colnames, do.call, duplicated, >> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, >> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, >> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist, unsplit >> >> All user-level objects in a package should have documentation entries. >> See chapter ‘Writing R documentation files’ in the ‘Writing R >> Extensions’ manual. >> >> >> >> My DESCRIPTION file when I add the 'methods' package is the following: >> ... >> Depends: R (>= 3.2.0) >> LazyData: TRUE >> RoxygenNote: 5.0.1 >> Imports: GenomicRanges, >> IRanges, >> assertthat, >> S4Vectors, >> graphics, >> data.table, >> methods >> Suggests: knitr, >> rmarkdown, >> testthat >> VignetteBuilder: knitr >> >> >> >> Regards, >> Andreas >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > Joris Meys > Statistical consultant > > Ghent University > Faculty of Bioscience Engineering > Department of Mathematical Modelling, Statistics and Bio-Informatics > > tel : +32 9 264 59 87 > joris.m...@ugent.be > --- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
It would be helpful to have a reproducible example, i.e., your actual package or a skeleton of it that reproduces the issue. Btw, you might be able to debug this behavior by: debug(tools::undoc) tools::undoc(dir=yourPackageDir) On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis wrote: > Hi, > > I am developing a package for Bioconductor, and I have a weird issue when > importing the 'methods' package. Before I add the 'methods' package in > Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings. > > However, when I add the 'methods' package in the Imports field, I get a > warning during CMD check. (I need the methods package since I use the > methods::is() function, and if I call it just as is(), when running the > package from Rscript will fail since by default it does not load the > 'methods' package.) > > I read a similar issue here: > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html > and I updated all my packages from Bioconductor including IRanges and > GenomicRanges. > > This is the warning that I get, which is exactly the same as the previous > issue in Bioc-Devel, and I understand that for some reason the BiocGenerics > is attached only when the 'methods' package is imported. > > * checking for missing documentation entries ... WARNING > > Attaching package: ‘BiocGenerics’ > > The following objects are masked from ‘package:parallel’: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following objects are masked from ‘package:stats’: > > IQR, mad, xtabs > > The following objects are masked from ‘package:base’: > > Filter, Find, Map, Position, Reduce, anyDuplicated, append, > as.data.frame, as.vector, cbind, colnames, do.call, duplicated, > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist, unsplit > > All user-level objects in a package should have documentation entries. > See chapter ‘Writing R documentation files’ in the ‘Writing R > Extensions’ manual. > > > > My DESCRIPTION file when I add the 'methods' package is the following: > ... > Depends: R (>= 3.2.0) > LazyData: TRUE > RoxygenNote: 5.0.1 > Imports: GenomicRanges, > IRanges, > assertthat, > S4Vectors, > graphics, > data.table, > methods > Suggests: knitr, > rmarkdown, > testthat > VignetteBuilder: knitr > > > > Regards, > Andreas > > [[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
Re: [Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Andreas, for a good understanding: just mentioning the methods package in the DESCRIPTION file isn't doing a thing if you don't also add import(methods) to the NAMESPACE file. So it looks like the warning occurs when the package indicates that the methods package is imported when it actually isn't. Do you still get that warning if you update the NAMESPACE file? Cheers Joris On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis < kapouranis.andr...@gmail.com> wrote: > Hi, > > I am developing a package for Bioconductor, and I have a weird issue when > importing the 'methods' package. Before I add the 'methods' package in > Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings. > > However, when I add the 'methods' package in the Imports field, I get a > warning during CMD check. (I need the methods package since I use the > methods::is() function, and if I call it just as is(), when running the > package from Rscript will fail since by default it does not load the > 'methods' package.) > > I read a similar issue here: > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html > and I updated all my packages from Bioconductor including IRanges and > GenomicRanges. > > This is the warning that I get, which is exactly the same as the previous > issue in Bioc-Devel, and I understand that for some reason the BiocGenerics > is attached only when the 'methods' package is imported. > > * checking for missing documentation entries ... WARNING > > Attaching package: ‘BiocGenerics’ > > The following objects are masked from ‘package:parallel’: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following objects are masked from ‘package:stats’: > > IQR, mad, xtabs > > The following objects are masked from ‘package:base’: > > Filter, Find, Map, Position, Reduce, anyDuplicated, append, > as.data.frame, as.vector, cbind, colnames, do.call, duplicated, > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist, unsplit > > All user-level objects in a package should have documentation entries. > See chapter ‘Writing R documentation files’ in the ‘Writing R > Extensions’ manual. > > > > My DESCRIPTION file when I add the 'methods' package is the following: > ... > Depends: R (>= 3.2.0) > LazyData: TRUE > RoxygenNote: 5.0.1 > Imports: GenomicRanges, > IRanges, > assertthat, > S4Vectors, > graphics, > data.table, > methods > Suggests: knitr, > rmarkdown, > testthat > VignetteBuilder: knitr > > > > Regards, > Andreas > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Mathematical Modelling, Statistics and Bio-Informatics tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocGenerics attaches when methods package is imported
Hi, I am developing a package for Bioconductor, and I have a weird issue when importing the 'methods' package. Before I add the 'methods' package in Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings. However, when I add the 'methods' package in the Imports field, I get a warning during CMD check. (I need the methods package since I use the methods::is() function, and if I call it just as is(), when running the package from Rscript will fail since by default it does not load the 'methods' package.) I read a similar issue here: https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html and I updated all my packages from Bioconductor including IRanges and GenomicRanges. This is the warning that I get, which is exactly the same as the previous issue in Bioc-Devel, and I understand that for some reason the BiocGenerics is attached only when the 'methods' package is imported. * checking for missing documentation entries ... WARNING Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. My DESCRIPTION file when I add the 'methods' package is the following: ... Depends: R (>= 3.2.0) LazyData: TRUE RoxygenNote: 5.0.1 Imports: GenomicRanges, IRanges, assertthat, S4Vectors, graphics, data.table, methods Suggests: knitr, rmarkdown, testthat VignetteBuilder: knitr Regards, Andreas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package citation and version is not updated
hi Dan, I'm having the same issue with tximport: http://bioconductor.org/packages/devel/bioc/html/tximport.html The CITATION file has been in there since the package was added to devel last week https://github.com/Bioconductor-mirror/tximport/blob/master/inst/CITATION citation("tximport") works thanks, Mike On Fri, Jan 29, 2016 at 5:56 PM, Dan Tenenbaum wrote: > This is fixed now. Thanks for the report. > Dan > > > - Original Message - > > From: "Ludwig Geistlinger" > > To: "bioc-devel" > > Sent: Friday, January 29, 2016 2:06:37 AM > > Subject: [Bioc-devel] package citation and version is not updated > > > Dear Dan, > > > > For some reason the citation on my package's landing page > > > > http://bioconductor.org/packages/EnrichmentBrowser.html > > > > is not displayed in agreement with my inst/CITATION file. > > > > Furthermore, the version number is also not up to date here, although > > displayed correctly at the bottom of the page (--> Package Archives). > > > > How to resolve this? > > > > Thx, > > Ludwig > > > > -- > > Dipl.-Bioinf. Ludwig Geistlinger > > > > Lehr- und Forschungseinheit für Bioinformatik > > Institut für Informatik > > Ludwig-Maximilians-Universität München > > Amalienstrasse 17, 2. Stock, Büro A201 > > 80333 München > > > > Tel.: 089-2180-4067 > > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > > > ___ > > 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 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Close connections continuously in fasta.index in Biostrings
Hi (mostly Hervé) I’m running into problems trying to run fasta.index() from Biostrings on a list of 4700 files, as the limit on open files are reached. Is it possible to continuously open and close the connections in the C code to circumvent this? I expect this problem also arises with readXStringSet..? I know dealing with such a high number of files in one chunk is probably an edge case, so I can understand if this is not something you wish to change the code for... with best wishes Thomas Lin Pedersen ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel