Re: [Rd] R Language Definition: Subsetting matrices with negative indices is *not* an error
Ah, the woes of English word order -- even this native English speaker frequently gets messed up! (but maybe I'm just a bear of little brain). Best, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. Clifford Stoll On Sat, May 9, 2015 at 1:33 PM, Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: On Sat, May 9, 2015 at 12:55 AM, peter dalgaard pda...@gmail.com wrote: On 09 May 2015, at 02:53 , Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: Hi, I spotted what looks like another(*) mistake in 'R Language Definition' on how subsetting should work. In Section 'Indexing matrices and arrays' [http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Indexing-matrices-and-arrays] one can read Negative indices are not allowed in indexing matrices. Parse error: I believe that this is intended to mean Indexing matrices may not contain negative indices not You cannot use negative indices when indexing matrices. This is consistent with the help page: A third form of indexing is via a numeric matrix with the one column for each dimension: each row of the index matrix then selects a single element of the array, and the result is a vector. Negative indices are not allowed in the index matrix. Rephrasing would seem to be in order Ah... definitely a parse error (I read it as a new paragraph). I second rephrasing this; your Indexing matrices may not contain negative indices is non-ambiguous. Thanks Peter /Henrik -pd but this is not true, e.g. x - matrix(1:12, nrow=4) x [,1] [,2] [,3] [1,]159 [2,]26 10 [3,]37 11 [4,]48 12 x[c(-2,-4),] [,1] [,2] [,3] [1,]159 [2,]37 11 /Henrik (*) https://stat.ethz.ch/pipermail/r-devel/2015-May/071091.html [docs have been fixed] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R Language Definition: Subsetting matrices with negative indices is *not* an error
On 09 May 2015, at 22:33 , Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: On Sat, May 9, 2015 at 12:55 AM, peter dalgaard pda...@gmail.com wrote: Rephrasing would seem to be in order Ah... definitely a parse error (I read it as a new paragraph). I second rephrasing this; your Indexing matrices may not contain negative indices is non-ambiguous. Now in R-devel. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] PATCH: library(..., quietly=TRUE) still outputs Loading required package: ... (forgot to pass down 'quietly')
Calling library(..., quietly=TRUE) may still output:
Loading required package: other pkg
in some cases, e.g.
library(R.utils, quietly=TRUE)
Loading required package: R.methodsS3
[...]
I traced this to base:::.getRequiredPackages2(), which forgets to pass
'quietly' to an internal library() call:
if (!attached) {
if (!quietly)
packageStartupMessage(gettextf(Loading required package: %s,
pkg), domain = NA)
library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) || stop(gettextf(package %s could not be loaded,
sQuote(pkg)), call. = FALSE, domain = NA)
}
It's from that library() call the message is generated.
Here's a patch:
$ svn diff src\library\base\R\library.R
Index: src/library/base/R/library.R
===
--- src/library/base/R/library.R(revision 68345)
+++ src/library/base/R/library.R(working copy)
@@ -871,7 +871,7 @@
packageStartupMessage(gettextf(Loading required package: %s,
pkg), domain = NA)
library(pkg, character.only = TRUE, logical.return = TRUE,
-lib.loc = lib.loc) ||
+lib.loc = lib.loc, quietly = quietly) ||
stop(gettextf(package %s could not be loaded, sQuote(pkg)),
call. = FALSE, domain = NA)
}
I can submit it via http://bugs.r-project.org/ if preferred.
Thanks,
Henrik
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Re: [Rd] R Language Definition: Subsetting matrices with negative indices is *not* an error
On Sat, May 9, 2015 at 12:55 AM, peter dalgaard pda...@gmail.com wrote: On 09 May 2015, at 02:53 , Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: Hi, I spotted what looks like another(*) mistake in 'R Language Definition' on how subsetting should work. In Section 'Indexing matrices and arrays' [http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Indexing-matrices-and-arrays] one can read Negative indices are not allowed in indexing matrices. Parse error: I believe that this is intended to mean Indexing matrices may not contain negative indices not You cannot use negative indices when indexing matrices. This is consistent with the help page: A third form of indexing is via a numeric matrix with the one column for each dimension: each row of the index matrix then selects a single element of the array, and the result is a vector. Negative indices are not allowed in the index matrix. Rephrasing would seem to be in order Ah... definitely a parse error (I read it as a new paragraph). I second rephrasing this; your Indexing matrices may not contain negative indices is non-ambiguous. Thanks Peter /Henrik -pd but this is not true, e.g. x - matrix(1:12, nrow=4) x [,1] [,2] [,3] [1,]159 [2,]26 10 [3,]37 11 [4,]48 12 x[c(-2,-4),] [,1] [,2] [,3] [1,]159 [2,]37 11 /Henrik (*) https://stat.ethz.ch/pipermail/r-devel/2015-May/071091.html [docs have been fixed] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R Language Definition: Subsetting matrices with negative indices is *not* an error
On 09 May 2015, at 02:53 , Henrik Bengtsson henrik.bengts...@ucsf.edu wrote: Hi, I spotted what looks like another(*) mistake in 'R Language Definition' on how subsetting should work. In Section 'Indexing matrices and arrays' [http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Indexing-matrices-and-arrays] one can read Negative indices are not allowed in indexing matrices. Parse error: I believe that this is intended to mean Indexing matrices may not contain negative indices not You cannot use negative indices when indexing matrices. This is consistent with the help page: A third form of indexing is via a numeric matrix with the one column for each dimension: each row of the index matrix then selects a single element of the array, and the result is a vector. Negative indices are not allowed in the index matrix. Rephrasing would seem to be in order -pd but this is not true, e.g. x - matrix(1:12, nrow=4) x [,1] [,2] [,3] [1,]159 [2,]26 10 [3,]37 11 [4,]48 12 x[c(-2,-4),] [,1] [,2] [,3] [1,]159 [2,]37 11 /Henrik (*) https://stat.ethz.ch/pipermail/r-devel/2015-May/071091.html [docs have been fixed] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] Use and Usability metrics / shields
Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
