Off topic:failed to install RBGL using Bioconductor 3.10
0
0
Entering edit mode
Ming Wang • 0
@ming-wang-8281
Last seen 2.3 years ago
United States

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 • 199 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 973 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6