similar to: R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()

On 21/04/2019 4:56 p.m., Benjamin Tyner wrote: > Hello, > > Most likely I'm doing something wrong, but am at a loss as to what the > issue is. I have a clean checkout of trunk here: > > ?? ~/svn/r-devel/R$ svn info > ?? Path: . > ?? Working Copy Root Path: /home/btyner/svn/r-devel/R > ?? URL: https://svn.r-project.org/R/trunk > ?? Relative URL: ^/trunk

Duncan that does indeed look to be the case. Many thanks! In particular, tests/reg-tests-1d.R optionally loads the Matrix namespace which allows the test to succeed. Compare: ~/R-rc_2019-04-21_r76409/bin/Rscript -e "options(warn=2); library(Matrix); res <- findMethods('isSymmetric'); print('success')" [1] "success" versus

Full_Name: Mike Danilov Version: 2.9.0 OS: Fedora Core 9 Submission from: (NULL) (142.103.121.198) When checking for the symmetry of a matrix, function isSymmetric.matrix() gets confused by the discrepancy of colnames/rownames if its argument. See the code snippet below. Perhaps it's a problem of the matrix product which copies colnames of the first argument but not the rownames of the

Hello everyone. R-2.12.0, suse linux 11.3. I am debugging a package that uses S4 methods and R CMD check gives the following warning: > Warning in methods::findMethods(g, env) : > non-generic function 'mdm' given to findMethods() > See the information on DESCRIPTION files in the chapter 'Creating R > packages' of the 'Writing R Extensions' manual. I

Hi, I have this symmetric matrix, at least I think so. col1 col2 col3 [1,] 0.20 0.05 0.06 [2,] 0.05 0.10 0.03 [3,] 0.06 0.03 0.08 or structure(c(0.2, 0.05, 0.06, 0.05, 0.1, 0.03, 0.06, 0.03, 0.08 ), .Dim = c(3L, 3L), .Dimnames = list(NULL, c("var1", "var2", "var3"))) But isSymmetric() doesn't agree. Any comment? I am on R 2.10.1 Thanks. Jun

Dear R developers, I am having a slightly weird issue with a S4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far. The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's

In a newly downloaded version (today) of R-2-4-0alpha, with all packages from CRAN also installed today, I get: > library(Matrix) Erro en loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'Matrix' methods specified for export, but none defined: BIC, anova, coef, confint, deviance, fitted, fixef, formula, head, lmer, logLik, mcmcsamp, plot,

From the first page of the NEWS file: (2016-04-29 r70564) isSymmetrix(m) is much faster for large asymmetric matrices m via pre-tests and a new option tol1 (with which strict back compatibility is possible but not the default). It probably should be isSymmetric -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size:

I represent a graph as an adjacency matrix of class "dgCMatrix" (from the Matrix package). > xx 5 x 5 sparse Matrix of class "dgCMatrix" a b c d e a . 1 1 . . b 1 . 1 . . c 1 1 . 1 1 d . . 1 . 1 e . . 1 1 . To check if the matrix defines and undirected graph, I have made the following functions/methods: is.UG <- function (object) { UseMethod("is.UG") }

Hi, Using latest R 2.5.0 Patched, I'm unable to install the Matrix package from cran.fhcrc.org. I get: Creating a new generic function for "isSymmetric" in "Matrix" Creating a new generic function for "unname" in "Matrix" Error in conformMethod(signature, mnames, fnames, f) : In method for function "!": formal arguments omitted in

I am only reporting this because it is the current release branch and not devel. R-2.13 from svn revision 55957 builds fine, but fails make check. This happened with a fresh svn checkout 12 hours ago and it still happens as of now. Two days ago I could build R-2.13 and it passed make check on the same system, so I doubt it is a system problem. But just in case my system details are a fresh

Hello, When building R from source, during the part where the 'tools' package is built, I get: make[6]: Entering directory `/home/btyner/R-3.1.1/src/library/tools/src' make[6]: Leaving directory `/home/btyner/R-3.1.1/src/library/tools/src' make[5]: Leaving directory `/home/btyner/R-3.1.1/src/library/tools/src' make[4]: Leaving directory

1. Martin Maechler's comments should be taken as replacements for anything I wrote where appropriate. Any apparent conflict is a result of his superior knowledge. 2. 'eigen' returns the eigenvalue decomposition assuming the matrix is symmetric, ignoring anything in m[upper.tri(m)]. 3. The basic idea behind both posdefify and nearPD is to compute the

The package 'graph' defines classes graph and graphNEL (extending graph) and a union,graph,graph-method. These are all exported and fully documented. The package 'GSEABase' Imports: graph and importClassesFrom(graph, graphNEL). GSEABase defines methods on union for its own classes (not graph / graphNEL), and has exportMethods(union). union,graph,graph-method is not used in

quote(expr) will make no changes in expr, it just returns its one argument, unevaluated. substitute could be used in your lapply(..., library) example to give library a name instead of a character string for an input (which might be necessary if the character.only argument were not available) lapply(c("MASS", "splines"), function(pkg) eval(substitute(library(pkg),

A kind member of R-core suggested this is due to a misconfiguration on my system, and to post it to the mailing list for troubleshooting. When trying to build R version 4.3.3, in at least two places during the process it gives LaTeX errors of the form: (example 1) you should 'make docs' now ... make[1]: Entering directory '/home/btyner/R-4.3.3/doc' creating

True or False: when USE_OPENMP=1 is not used, then race conditions are not unexpected. If True, and we wish to avoid race conditions, then sources such as the conda channel and ubuntu would need to add this enhancement. If False, then what is the next step (i.e. forum) for debugging the race condition? On 01/11/2018 07:56 AM, Ista Zahn wrote: > > > On Jan 10, 2018 8:24 PM,

Andreas, How right you are! Still, I find it curious that in the context of the while(TRUE) loop, I am allowed to do this 653 times, with failure on the 654th attempt. Perhaps there is something asynchronous going on? If I eliminate the looping, it does indeed fail (as expected) on the first attempt to close the pipe. Regards Ben On 12/6/19 2:04 AM, Andreas Kersting wrote: > Hi

Hi Benjamin, you cannot pipe to echo, since it does not read from stdin. echo just echos is first arg, i.e. echo /dev/stdin > /dev/null will echo the string "/dev/stdin"to /dev/stdout, which is redirected to /dev/null. Try p <- pipe("cat > /dev/null", open = "w") instead. Regards, Andreas 2019-12-06 02:46 GMT+01:00 Benjamin Tyner<btyner at

Not sure if this is a bug, so posting here first. If I run: ?? cnt <- 0L ?? while (TRUE) { ? ? ?? cnt <- cnt + 1L ? ? ?? p <- pipe("echo /dev/stdin > /dev/null", open = "w") ? ? ?? writeLines("foobar", p) ? ? ?? tryCatch(close(p), error = function(e) { print(cnt); stop(e)}) ?? } then once cnt gets to around 650, it fails with: ?? [1] 654 ??