[Rd] undefined symbol: cholmod_factorize_p
I am installing R_3.5.1 from source on ubuntu 18.04, and 'config' + 'make' gives me (at the end) Loading required package: Matrix Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/goran/src/R-3.5.1/library/Matrix/libs/Matrix.so': /home/goran/src/R-3.5.1/library/Matrix/libs/Matrix.so: undefined symbol: cholmod_factorize_p Error in eval(exprs[i], envir) : require(Matrix) is not TRUE ERROR: installing package indices failed * removing ‘/home/goran/src/R-3.5.1/library/Matrix’ Makefile:51: recipe for target 'Matrix.ts' failed make[2]: *** [Matrix.ts] Error 1 make[2]: Leaving directory '/home/goran/src/R-3.5.1/src/library/Recommended' Makefile:39: recipe for target 'recommended-packages' failed make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory '/home/goran/src/R-3.5.1/src/library/Recommended' Makefile:77: recipe for target 'stamp-recommended' failed make: *** [stamp-recommended] Error 2 What am I missing? Göran __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] NEWS vs. inst/NEWS
'Writing R Extensions', section 1.1.5, in the part about a package's 'inst'
directory, says that if NEW is in both the top level and in the inst
directory, the in inst will be installed:
Note that with the exceptions of INDEX, LICENSE/LICENCE and NEWS,
information files at the top level of the package will *not* be installed
and so not be known to users of Windows and macOS compiled packages (and
not seen by those who use R CMD INSTALL or install.packages on the
tarball). So any information files you wish an end user to see should be
included in inst. Note that if the named exceptions also occur in inst, the
version in inst will be that seen in the installed package.
However, if I have a package with a NEWS file in both the top-level and in
the inst directory, the top-level one appears in the installed file, not
the one in inst.
Try the following script that makes and installs a package in tempdir():
pkgName <- "junk"
dir.create(tdir <- tempfile())
dir.create(srcPkg <- file.path(tdir, pkgName))
cat(file=file.path(srcPkg, "DESCRIPTION"), sep="\n",
paste("Package:", pkgName),
paste("Title: NEWS vs. inst/NEWS"),
paste("Description: Which is installed, NEWS or inst/NEWS?"),
paste("Version: 0.1"))
file.create(file.path(srcPkg, "NAMESPACE"))
dir.create(inst <- file.path(srcPkg, "inst"))
instFiles <- c("NEWS", "CITATION") # these both at top-level and in inst
directory
for(instFile in instFiles) {
cat(file=file.path(srcPkg, instFile), sep="\n",
paste0("The original top-level ", instFile, " file"))
cat(file=file.path(inst, instFile), sep="\n",
paste0("inst/", instFile, " - the ", instFile, " file from the
source package's inst directory"))
}
dir.create(lib <- file.path(tdir, "lib"))
install.packages(lib=lib, srcPkg, repos=NULL, type="source")
sapply(instFiles, function(instFile) readLines(system.file(package=pkgName,
lib.loc=lib, mustWork=TRUE, instFile)))
# unlink(recursive=TRUE, tdir) # to clean up
The final sapply() gives me
> sapply(instFiles, function(instFile)
readLines(system.file(package=pkgName, lib.loc=lib, mustWork=TRUE,
instFile)))
NEWS
"The original top-level NEWS file"
CITATION
"inst/CITATION - the CITATION file from the source package's inst directory"
Several CRAN packages have both NEWS and inst/NEWS (gdata, genetics,
gplots, mcgibbsit, modeltools, nimble, RRF, session, SII). In most the two
files are identical but in RRF and nimble they differ.
Is the manual wrong is the code wrong?
Bill Dunlap
TIBCO Software
wdunlap tibco.com
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[R-pkg-devel] S4 generics package?
Greetings, I know in Bioconductor there is the BiocGenerics package ( https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html). I have not been able to find any similar package on CRAN. I use S4 methods quite often and a package like this would be very useful for future packages I am developing. My question generally is, should I consider using BiocGenerics as a dependency if I normally submit to CRAN? My understanding is that I would need to submit any package which uses BiocGenerics to Bioconductor to meet dependency requirements. I have no issue with Bioconductor, I even have another package published on there. However, the packages I am developing are not specific to bioinformatics. That said, if no such 'generics' package exists on CRAN I am curious what people would think of me possibly developing a 'peer' package similar to BiocGenerics for CRAN packages. Regards, Charles [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[Rd] CRAN: Update protocol buffers on macOS? (for RProtoBuf)
Hi, I notice that the CRAN binary for the macOS version of RProtoBuf is built against quite an old version of protocol buffers (from 2014, before v3 format support was added). the windows version is (blessedly) kept up-to-date, but I'd like to float the suggestion that the macOS version get an update too. with thanks jonathon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
