Install Rsubread in R

[Bradzhang]

I am a beginner for Linux. When I installed Rsubread I had the following error message:
Anything is wrong with the Renviron file?

biocLite("Rsubread")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘Rsubread’
trying URL 'https://bioconductor.org/packages/3.5/b ... 6.1.tar.gz'
Content type 'application/x-gzip' length 9297322 bytes (8.9 MB)
==================================================
downloaded 8.9 MB

/home/brad/R-3.4.1/bin/Rcmd: 45: /home/brad/R-3.4.1/etc/Renviron: Syntax error: word unexpected (expecting ")")



This is my Renviron file:

### etc/Renviron. Generated from Renviron.in by configure.
###
### ${R_HOME}/etc/Renviron
###
### Record R system environment variables.

R_PLATFORM=${R_PLATFORM-'x86_64-pc-linux-gnu'}
## Default printer paper size: first record if user set R_PAPERSIZE
R_PAPERSIZE_USER=${R_PAPERSIZE}
R_PAPERSIZE=${R_PAPERSIZE-'a4'}
## Default print command
R_PRINTCMD=${R_PRINTCMD-'lpr'}
# for Rd2pdf, reference manual
R_RD4PDF=${R_RD4PDF-'times,hyper'}
## used for options("texi2dvi")
R_TEXI2DVICMD=${R_TEXI2DVICMD-${TEXI2DVI-'/usr/bin/texi2dvi'}}
## used by INSTALL, untar() and installing grDevices
R_GZIPCMD=${R_GZIPCMD-'/bin/gzip'}
## Default zip/unzip commands
R_UNZIPCMD=${R_UNZIPCMD-'/usr/bin/unzip'}
R_ZIPCMD=${R_ZIPCMD-'/usr/bin/zip'}
R_BZIPCMD=${R_BZIPCMD-'/bin/bzip2'}
## Default browser
R_BROWSER=${R_BROWSER-'/usr/bin/firefox'}
## Default editor
EDITOR=${EDITOR-${VISUAL-vi}}
## Default pager
PAGER=${PAGER-'/usr/bin/less'}
## Default PDF viewer
R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xdg-open'}
## Used by libtool
LN_S='ln -s'
MAKE=${MAKE-'make'}
## Prefer a POSIX-compliant sed on e.g. Solaris
SED=${SED-'/bin/sed'}
## Prefer a tar that can automagically read compressed archives
## Used in R CMD INSTALL for binary packages
TAR=${TAR-'/bin/tar'}

## System and compiler types.
R_SYSTEM_ABI='linux,gcc,gxx,gfortran,?'

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.4'}
#R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.4/library'}
setHook(packageEvent("grDevices", "onLoad"),

function(...) grDevices::X11.options(type='cairo'))
options(device='x11')
### Local Variables: ***
### mode: sh ***
### sh-indentation: 2 ***
### End: ***

setHook(packageEvent("grDevices", "onLoad"),
function(...) grDevices::X11.options(type='cairo'))
options(device='x11')

[catweazel]

Anything is wrong with the Renviron file?

You might have better luck on the bioconductor forums https://support.bioconductor.org/

[killer de bug]

Code: Select all

setHook(packageEvent("grDevices", "onLoad"),

function(...) grDevices::X11.options(type='cairo'))

I expect that the blank line is problematic.
It should looks like this:

Code: Select all

setHook(packageEvent("grDevices", "onLoad"),
function(...) grDevices::X11.options(type='cairo'))