Different size assigned
I am trying to install graphite package from Bioconductor. However I keep getting cannot allocate vector of size XXX, despite being able to create an object of a bigger size.
> BiocManager::install("graphite") Bioconductor version 3.8 (BiocManager 1.30.3), R 3.5.1 (2018-07-02) Installing package(s) 'graphite' trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/graphite_1.28.0.tar.gz' Content type 'application/x-gzip' length 4937193 bytes (4.7 MB) ================================================== downloaded 4.7 MB * installing *source* package ‘graphite’ ... ** R Error : cannot allocate vector of size 844.3 Mb ERROR: unable to build sysdata DB for package ‘graphite’ * removing ‘/usr/lib/R/site-library/graphite’ The downloaded source packages are in ‘/tmp/RtmpeRdRny/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘graphite’ had non-zero exit status > print(object.size(runif(129999999)), units = "Mb") 991.8 Mb
It doesn't work even if I start a new session with
R --vanilla. The problem might be related to building the sysdata DB for the package. But I don't know how to solve it (as a user). How can I install it?
1 Answers Different size assigned
The problem seems to be on while making the package. I posted another error I got into the support site of Bioconductor and the author answered fixing the bug on version 1.29.1 (devel version of the package). So the solution is to install the latest version of the package:
remotes::install_git("https://git.bioconductor.org/packages/graphite", ref = "master")