Question: (Closed) failed to install RBGL using Bioconductor 3.10
0
gravatar for Ming Wang
5 weeks ago by
Ming Wang0
United States
Ming Wang0 wrote:

Failed to install package RGBL using Bioconductor 3.10. (But it is ok for Bioconductor 3.9)

Error, a typo?

Error: unexpected ')' in "cat(system.file(package="BH", "include")))"

I am working on ubuntu 18.04.

The full log:

> BiocManager::install("RBGL")
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'RBGL'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/RBGL_1.62.0.tar.gz'
Content type 'application/x-gzip' length 2303426 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘RBGL’ ...
** using staged installation
checking R package BH ... yes
Error: unexpected ')' in "cat(system.file(package="BH", "include")))"
Execution halted
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I  -I"/data/yulab/zhangjiao/Library/R/3.6/library/BH/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bbc.cpp -o bbc.o
In file included from bbc.cpp:1:0:
RBGL.hpp:15:10: fatal error: boost/config.hpp: No such file or directory
 #include <boost config.hpp="">
          ^~~~~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:176: recipe for target 'bbc.o' failed
make: *** [bbc.o] Error 1
ERROR: compilation failed for package ‘RBGL’
* removing ‘/data/yulab/zhangjiao/Library/R/3.6/library/RBGL’
* restoring previous ‘/data/yulab/zhangjiao/Library/R/3.6/library/RBGL’

The downloaded source packages are in
        ‘/tmp/Rtmp8cGsZ0/downloaded_packages’
installation path not writeable, unable to update packages: class, codetools,
  KernSmooth, lattice, mgcv, nnet, spatial
Update old packages: 'RBGL'

rbgl failed • 52 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Ming Wang0

Hello Ming Wang!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: See https://support.bioconductor.org/p/125984/
ADD REPLYlink written 5 weeks ago by Martin Morgan ♦♦ 24k
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