Error during EBImage installation
2
1
Entering edit mode
@slagtermaarten-13133
Last seen 4.2 years ago

Hi all

In trying to install the ggtree package, I encountered a problem with one of its dependencies: fftwtools.

Thanks for your help!

Maarten

 

> biocLite("fftwtools")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘fftwtools’
trying URL 'http://cran-mirror.cs.uu.nl/src/contrib/fftwtools_0.9-8.tar.gz'
Content type 'application/x-gzip' length 142268 bytes (138 KB)
==================================================
downloaded 138 KB

Loading required package: colorout
Loading required package: pacman
* installing *source* package ‘fftwtools’ ...
** package ‘fftwtools’ successfully unpacked and MD5 sums checked
** libs
clang -I/usr/local/Cellar/r/3.3.1_3/R.framework/Resources/include -DNDEBUG  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include    -fPIC  -g -O2  -c fftwtools.c -o fftwtools.o
fftwtools.c:28:9: fatal error: 'fftw3.h' file not found
#include<fftw3.h>
        ^
1 error generated.
make: *** [fftwtools.o] Error 1
ERROR: compilation failed for package ‘fftwtools’
* removing ‘/usr/local/lib/R/site-library/fftwtools’

The downloaded source packages are in
        ‘/private/var/folders/fh/6dsbkfmj3jq41nj8vj9x0z600000gn/T/RtmpmzXIgH/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘fftwtools’ had non-zero exit status

 

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin16.0.0 (64-bit)
Running under: OS X 10.12.4 (Sierra)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.20.3 nvimcom_0.9-27       pacman_0.4.6
[4] colorout_1.1-1

loaded via a namespace (and not attached):
[1] tools_3.3.1

 

ebimage ggtree package installation • 3.2k views
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Entering edit mode
Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 8 months ago
Heidelberg, Germany

Dear Maarten,

the output of your sessionInfo indicates that you are running R under OS X Sierra, but attempt to install packages from sources. Is there any particular reason why you don't use mac binaries? Platform-specific binary packages typically include the necessary dependencies, so you should be able to install fftwtools with

install.packages("fftwtools", type="mac.binary.el-capitan")

If you still want to compile from sources, you could first install the fftw system library from the command line

brew install fftw

and then run install.packages("fftwtools").

Cheers,

Andrzej

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@martin-morgan-1513
Last seen 15 days ago
United States

It has an operating system dependency, on the libfftw3 library; you'll have install (the 'devel' version) of it. On my linux machine this is sudo apt-get install libfftw3-dev.

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Entering edit mode

For the record, Martin's solution applies to Debian based Linux distributions such as Ubuntu. On Red Hat Linux (e.g. Fedora) the system dependency can be obtained by yum install fftw-devel.
 

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