fatal error: fftw3.h: No such file or directory

[pips...@gmail.com]

Hi you,

need some help while using Cardinal on Conda Env. When we try to install Cardinal we recieve the error:

fftwtools.c:28:9: fatal error: fftw3.h: No such file or directory
 #include<fftw3.h>

we already tried

sudo apt-get install libfftw3-dev

Does anyone had the same and some advice how to do better?

Thanks!

Best, Pia

[kbemis]

Hi Pia,

For issues involving installation via conda, I would ask on the conda support group.

-Kylie

[pia Hoenscheid]

Hi Kylie, 

thanks for the hint. We solved the problem but another one appeared.. all including directory/library access issues. Lets see how far we get, when this is solved and we finally get to start Cardinal in conda ;). Thank you! Best, Pia

[Biju Saha]

Hi Pia,

Can you elaborate how you resolved the issue

[Jimmy Muldoon]

Hi all

Had a similar issue, Cardinal installation failing on linux with

cc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c fftwtools.c -o fftwtools.o

fftwtools.c:28:9: fatal error: fftw3.h: No such file or directory

  28 | #include<fftw3.h>
     |         ^~~~~~~~~
compilation terminated.

>>>>

and also

>>>>>

Warning messages:
1: In install.packages(...) :
 installation of package ‘tiff’ had non-zero exit status
2: In install.packages(...) :
 installation of package ‘fftwtools’ had non-zero exit status
3: In install.packages(...) :
 installation of package ‘RCurl’ had non-zero exit status
4: In install.packages(...) :
 installation of package ‘EBImage’ had non-zero exit status
5: In install.packages(...) :
 installation of package ‘Cardinal’ had non-zero exit status
> BiocManager::install("EBImage")                     
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
   CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Installing package(s) 'EBImage'
also installing the dependencies ‘tiff’, ‘fftwtools’, ‘RCurl’
>>>>>>>>>>>

Looks like os-level dependencies, using sudo apt-get install  for the packages libfftw3-dev,
libtiff-dev and libcurl4-openssl-dev followed by reattempting Cardinal installation was successful.
This was on Kubuntu 22.04.

Kind regards
Jimmy