Error during EBImage installation
2
1
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@slagtermaarten-13133
Last seen 6.8 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 • 5.2k views
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Entering edit mode
Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 3.3 years 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 4 weeks 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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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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