similar to: Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu

Testing for an NFS effect on the failure of 'make check': Try first on /usr/local/ 9:42 cd /usr/local/src/ 9:42 sudo mkdir R 9:43 sudo chown mdalphin:mdalphin R 9:43 cd R 9:43 gunzip -c /opt/apps/x86_64/R/Archive/R-3.2.5.tar.gz | tar xf - 9:43 cd R-3.2.5/ 9:44 ./configure --prefix=/opt/apps/x86_64/R/R-3.2.5 LIBnn=lib 9:44 make 9:57 make check

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

I am trying to build the latest version of R (3.6.2) on a CentOS system running 7.7.1908. I have been able to build previous versions of R up to and including 3.5.3 successfully. Starting with 3.6.0 the "make check" step fails with errors relating to "pdflatex" being missing. So, I installed texlive-latex (and the 100 other rpm dependencies) then tried rebuilding R.

Hello, I'm trying to install R from sources on two Linux machines (both with Suse 12.2): 1. > uname -a Linux cs-wsok 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux 2. > uname -a Linux csltok.swansea.ac.uk 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux I am trying version

Dear R User's Please help me to debug this issue. I am trying to write some data ( i= 6) to PostgreSQL database, but it not writing. Is there any issue in the way I use "dbWriteTable"? ++++++++++++++++++ Source Code ++++++++++++++++++++++++ library("DBI") library("RPostgreSQL") drv1 <- dbDriver("PostgreSQL") i=6 connAE1 <- dbConnect(drv1,host

I'm trying to find a clever way to re-map data from a database query into a data.frame. Querying a database often returns a table (data.frame) like this: GeneID MethodID Value 6 1 123 6 2 456 6 3 987 7 1 234 7 3 432 8 2 190 8 3 34 8 1 864 Note that GeneID=7 doesn't have a value for MethodID=2. Note that GeneID=8 doesn't have the

hi there, does anyone know how to calculate the amount of daylight on every day of the year in R? I mean the time between sunrise and sunset. thanks -- View this message in context: http://r.789695.n4.nabble.com/daylight-tp4647213.html Sent from the R help mailing list archive at Nabble.com.

Hi, I am getting an error from one of the test files tests/reg-tests-1.R using the unstable version (r50179). (i've learned my lessons; this is a clean build.) The tail of reg-tests-1.Rout.fail is Loading required package: myTst building package pkgA ... installing package pkgA using file pkgA_1.0.tar.gz ... Error in as.octmode(mode) : invalid digits Error in install.packages(r, lib =

Hello. I have successfully built R on windows scores of times, and have never come across this problem. For this build, I am using the current 4.6.3 prerelease version of Rtools, Windows7 64 bit, and R-devel_2015-09-14.tar.gz When running make check, I get the following error: running code in 'reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1 make[2]: *** [test-Reg] Error 2

Hi, I have some very noisy, relatively sparse data; a biological response of roughly ~8 subjects at ~8 times points). I've been following the data trend using a lowess line, over-plotted with several values of bandwidth, 'f <- seq(0.3, 0.9, by=0.1)'. At this point, we have no models for these data. I wonder if there is any way under R to assign some sort of confidence interval to

Suppose I have a function funcA() in package pkgA that requires function funcB() from another package pkgB under certain circumstances. Those circumstances are rare though, so I put package pkgB under 'Suggests', and use this in funcA() when those circumstances do arise: if (require("pkgB", quietly=TRUE)) { pkgB::funcB(...) } else { stop("Please install package

Hi, SETUP: Consider three packages PkgA, PkgB and PkgC. PkgA defines a generic function foo() and exports it; export(foo) PkgB imports PkgA::foo() and re-exports it; importFrom(PkgA, foo) export(foo) PkgC imports everything from PkgA and PkgB: imports(PkgA, PkgB) PROBLEM: Loading or attaching the namespace of PkgC will generate a warning: replacing previous import by

I was wondering: are the downstream dependencies of a package rebuilt when a package is updated on CRAN? (I'm referring to the binary packages, of course.) The reason I ask is because there are cases where this can cause problems. Suppose that when pkgB is built, it calls pkgA::makeClosure(), which returns a closure that refers to a function in pkgA. Suppose this code is in pkgA 1.0:

Hi, This strange warning happen sometimes when running 'R CMD check': * checking whether the package can be loaded with stated dependencies ... WARNING Error : .onLoad failed in loadNamespace() for ?pkgB?, details: call: length(new("A")) error: could not find function "loadMethod" Error: package/namespace load failed for ?pkgB? Execution halted

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and exporting a generic in the namespace will also export its methods. and Note that importMethodsFrom will also import any generics defined in

Hi, I'd like to list all package PkgA functions that another package PkgB use via Depends or Imports (ignoring Suggests for simplicity). As long as PkgB uses importFrom("PkgA", ...) it's just a matter of parsing the NAMESPACE file or inspecting asNamespace("PkgB")$.__NAMESPACE__.$imports. However, what can be done in case PkgB uses import("PkgA")? Is there

I am using the .Call interface to call c++ code from R. For that, I am trying to create a dynamic library (mylib.so) using "R CMD SHLIB" by linking my own c++ code and an external c++ library (blitz++). The makefile works fine on my Mac, produces mylib.so and I am able to call .Call() from R, but on a linux server (I think Debian), I got the following error: ---------- /usr/bin/ld:

I am using the .Call interface to call c++ code from R. For that, I am trying to create a dynamic library (mylib.so) using "R CMD SHLIB" by linking my own c++ code and an external c++ library (blitz++). The makefile works fine on my Mac, produces mylib.so and I am able to call .Call() from R, but on a linux server (I think Debian), I got the following error: ---------- /usr/bin/ld:

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would