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Question: Problem with HDF5 and ncdfFlow
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gravatar for Ulrik Stervbo
2.2 years ago by
Germany
Ulrik Stervbo30 wrote:

Hello,

I am trying to install ncdfFlow on my Kubuntu 15.04 but it fails because the hdf5.h cannot be found

R CMD INSTALL ncdfFlow_2.14.0.tar.gz 
* installing to library ‘/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2’
* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -DNDEBUG -I/usr/include   -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include
" -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/RcppArmadillo/include" -I"/home/ulrik/R/x86_64-pc-linux-gnu-lib
rary/3.2/BH/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
-g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I/usr/include   -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include
" -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/RcppArmadillo/include" -I"/home/ulrik/R/x86_64-pc-linux-gnu-lib
rary/3.2/BH/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
-g  -c bitOps.cpp -o bitOps.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include   -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/R
cpp/include" -I"/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2/RcppArmadillo/include" -I"/home/ulrik/R/x86_64-pc-li
nux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTI
FY_SOURCE=2 -g  -c hdfFlow.c -o hdfFlow.o
In file included from hdfFlow.c:1:0:
hdfFlow.h:4:18: fatal error: hdf5.h: No such file or directory
#include "hdf5.h"
                 ^
compilation terminated.
/usr/lib/R/etc/Makeconf:134: recipe for target 'hdfFlow.o' failed
make: *** [hdfFlow.o] Error 1
ERROR: compilation failed for package ‘ncdfFlow’

I have installed libhdf5-dev, which placed the hdf5.h in

/usr/include/hdf5/serial/hdf5.h

but using this with --configure-args also fails

R CMD INSTALL ncdfFlow_2.14.0.tar.gz --configure-args="--with-hdf5='/usr/inc
lude/serial'"
* installing to library ‘/home/ulrik/R/x86_64-pc-linux-gnu-library/3.2’
* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/include/serial/lib
configure: search for hdf5 library in: /usr/include/serial/lib64
configure: error: hdf5 library not found in "/usr/include/serial"
ERROR: configuration failed for package ‘ncdfFlow’

Any suggestions how I get to install ncdfFlow?

Cheers,

Ulrik

A little system info:

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.04

and all the hdf5 I have installed:

apt --installed list | grep hdf5     

WARNING: apt does not have a stable CLI interface yet. Use with caution in scripts.

hdf5-helpers/vivid,now 1.8.13+docs-15 amd64 [installed,automatic]
libhdf5-8/vivid,now 1.8.13+docs-15 amd64 [installed,automatic]
libhdf5-cpp-8/vivid,now 1.8.13+docs-15 amd64 [installed,automatic]
libhdf5-dev/vivid,now 1.8.13+docs-15 amd64 [installed]
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Ulrik Stervbo30
1
gravatar for SamGG
2.2 years ago by
SamGG90
France
SamGG90 wrote:

Hello,

Look at https://github.com/RGLab/ncdfFlow/issues/39

Best

ADD COMMENTlink written 2.2 years ago by SamGG90
1
gravatar for Ulrik Stervbo
2.2 years ago by
Germany
Ulrik Stervbo30 wrote:

Sorry, didn't help. 

EDIT

I managed by pointing to the correct library:

R CMD INSTALL ncdfFlow_2.14.0.tar.gz --configure-args="--with-hdf5='/usr/lib/x86_64-linux-gnu/hdf5/serial'"

The path was found by

pkg-config --libs hdf5

Although I did initially try to install the package with R 3.2.2, I probably had something messed up which prevented things from working well.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Ulrik Stervbo30
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