Question: Error installing graphite
0
gravatar for Lluís Revilla Sancho
12 months ago by
European Union
Lluís Revilla Sancho530 wrote:

I have some problems installing graphite since the new release of Bioconductor.

Initially I had trouble allocating a vector of certain size. However, on the last try I got a new error, related to graphite.ts before getting the same error message:

> BiocManager::install("graphite")
Bioconductor version 3.8 (BiocManager 1.30.4), 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

begin installing package ‘graphite’
Makefile:3: recipe for target 'graphite.ts' failed
make: *** [graphite.ts] Error 1
make: Target 'all' not remade because of errors.
* 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’

I am using a Ubuntu distribution (16.04) of 32 bytes. I see that the building of the package in windows is also having some problems I don't know if these problems are related or not. Any advice how can I install it? Or does someone else have the same problem?

Starting from an R --vanilla session

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library("BiocManager")
Bioconductor version 3.8 (BiocManager 1.30.4), ?BiocManager::install for help  
> install("graphite", lib = "/usr/lib/R/site-library")
Bioconductor version 3.8 (BiocManager 1.30.4), 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/RtmpN2CoOB/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(117999999)), units = "Mb")
900.3 Mb
graphite • 250 views
ADD COMMENTlink modified 12 months ago by gabriele.sales100 • written 12 months ago by Lluís Revilla Sancho530
Answer: Error installing graphite
3
gravatar for gabriele.sales
12 months ago by
European Union
gabriele.sales100 wrote:

Dear Lluís,

I've been able to reproduce the issue you mentioned on a 32 bit system. I developed a fix; it is already available in the development version of graphite (http://bioconductor.org/packages/3.9/bioc/html/graphite.html).

I will also backport the change to the stable release. It should be available as soon as the package is rebuilt; hopefully, early next week.

Gabriele

ADD COMMENTlink written 12 months ago by gabriele.sales100

Many thanks Gabriele! The fix worked in my machine too and I could install other packages that depend on graphite.

I hope it wasn't hard to traceback. Many thanks for fixing it.

ADD REPLYlink written 12 months ago by Lluís Revilla Sancho530
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