Re: [Rd] wrong matrix dimension in sparseQR
I have found explanation in the comments to original cs_qr() matlab function http://users.encs.concordia.ca/~krzyzak/R%20Code-Communications%20in%20Statistics%20and%20Simulation%202014/Zubeh%F6r/SuiteSparse/CSparse3/MATLAB/CSparse/cs_qr.m "If A is structurally rank deficient, additional empty rows may have been added to V and R." To my mind, it could be useful to mention it in the manual of Matrix::qr and/or sparseQR-class too. Because in case of augmented nrow we cannot do anymore A[p+1,] as cited in example in ?"sparseQR-class". My 2 cents. Serguei. Le 18/01/2018 à 16:13, Serguei Sokol a écrit : Hi, I came across a case when the dimensions of matrices returned by qr() operated on a sparse matrix does not coincide with the initial matrix. If A is structurally rank deficient, additional empty % rows may have been added to V and R. Here is a spinet code that should produce an example (one of many that I could provide): m=205 n=199 set.seed(7); a=matrix(rnorm(m*n), m, n) a[sample(seq(m*n), m*(n-4))]=0 a=as(a, "Matrix") qa=qr(a); stopifnot(nrow(qa@R) == m) # On my box I have nrow(qa@R):=207 while should be 205 as m is) Note that for m=203 and n=197, the same code produce right (i.e. coinciding) dimensions. Have I missed something? Serguei. > R.version platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 3 minor 4.3 year 2017 month 11 day 30 svn rev 73796 language R version.string R version 3.4.3 (2017-11-30) nickname Kite-Eating Tree -- Serguei Sokol Ingenieur de recherche INRA Cellule mathématique LISBP, INSA/INRA UMR 792, INSA/CNRS UMR 5504 135 Avenue de Rangueil 31077 Toulouse Cedex 04 tel: +33 5 6155 9849 email: so...@insa-toulouse.fr http://www.lisbp.fr __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] bug fix integer overflow in medpolish function
Dear R team I noticed a bug in the "medpolish" function in the "stats" package. When I run medpolish(x), with "x" the matrix in the attached .rda file, I get this rather cryptic error: "Error in if (converged) break : missing value where TRUE/FALSE needed In addition: Warning message: In sum(abs(z), na.rm = na.rm) : integer overflow - use sum(as.numeric(.))" I traced this down to the line: newsum <- sum(abs(z), na.rm = na.rm) I think this "overflow" could be easily fixed by changing this line to: newsum <- sum(as.numeric(abs(z)), na.rm = na.rm) With kind regards Ludger Goeminne ¯ Ludger Goeminne - Ph.D. Student VIB-UGent Center for Medical Biotechnology Albert Baertsoenkaai 3 - 9000 Gent - Belgium Tel: +32 (0)9 264 9360 mbc.vib-ugent.be matrix.rda Description: GNU Zip compressed data __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] bug fix integer overflow in medpolish function
On 19/01/2018 9:33 AM, Ludger Goeminne wrote: Dear R team I noticed a bug in the "medpolish" function in the "stats" package. When I run medpolish(x), with "x" the matrix in the attached .rda file, I get this rather cryptic error: "Error in if (converged) break : missing value where TRUE/FALSE needed In addition: Warning message: In sum(abs(z), na.rm = na.rm) : integer overflow - use sum(as.numeric(.))" I traced this down to the line: newsum <- sum(abs(z), na.rm = na.rm) I think this "overflow" could be easily fixed by changing this line to: newsum <- sum(as.numeric(abs(z)), na.rm = na.rm) Alternatively, you could use medpolish(as.numeric(x)). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Buffer overflow in cairoBM.c line 402
Hi, all. Testing a change to that line to strncpy(xd->filename, filename,PATH_MAX); right now. The bug itself I've yet to reproduce in anything that doesn't involve my employer's proprietary code, but strcpy is strcpy, after all. -- *Omri Schwarz* Engineer REsurety, Inc. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Buffer overflow in cairoBM.c line 402
Thanks for reporting - there is no need to reproduce this, it is an obvious error. I'll probably fix by throwing an error - like it is done in devX11.c when the file names are too long. Tomas On 01/19/2018 09:41 PM, Omri Schwarz wrote: Hi, all. Testing a change to that line to strncpy(xd->filename, filename,PATH_MAX); right now. The bug itself I've yet to reproduce in anything that doesn't involve my employer's proprietary code, but strcpy is strcpy, after all. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
