Hello. I am trying to install openCyo on GNU/Linux Debian 8.0 (stable version). I have non-zero exit due to compilation failure of ncdfFlow package. It seems hdf5 file or directory are not found. Following, the console output:
In file included from hdfFlow.c:1:0:
hdfFlow.h:4:18: fatal error: hdf5.h: No existe el fichero o el directorio
/usr/lib/R/etc/Makeconf:134: recipe for target 'hdfFlow.o' failed
make: *** [hdfFlow.o] Error 1
ERROR: compilation failed for package ‘ncdfFlow’
* removing ‘/home/germ/R/x86_64-pc-linux-gnu-library/3.2/ncdfFlow’
ERROR: dependency ‘ncdfFlow’ is not available for package ‘flowWorkspace’
* removing ‘/home/germ/R/x86_64-pc-linux-gnu-library/3.2/flowWorkspace’
ERROR: dependency ‘flowWorkspace’ is not available for package ‘flowStats’
* removing ‘/home/germ/R/x86_64-pc-linux-gnu-library/3.2/flowStats’
ERROR: dependencies ‘flowWorkspace’, ‘ncdfFlow’, ‘flowStats’ are not available for package ‘openCyto’
* removing ‘/home/germ/R/x86_64-pc-linux-gnu-library/3.2/openCyto’
During compilation the following messages show up:
* installing *source* package ‘ncdfFlow’ ...
configure: No directory was specified for --with-hdf5. Trying to find hdf5 using pkg-config.
checking for pkg-config... no
configure: pkg-config was not able to find the hdf5 library.
configure: Trying some common locations."
configure: search for hdf5 library in: /usr/local/lib
configure: search for hdf5 library in: /usr/local/lib64
configure: search for hdf5 library in: /usr/local/lib/x86_64-linux-gnu
configure: search for hdf5 library in: /usr/local/lib64/x86_64-linux-gnu
checking for h5cc... /usr/bin/h5cc
It looks like hdf5 library can't be found in the system during compilation. Am I right?
I thought it was because I hadn't installed rhdf5, which I did after the first failure. But the problem persists after rhdf5 installation.
Then, I checked all hdf5-related packages for my GNU/Linux distribution. These are:
I can see both hdf5-utils and r-cran-hdf5 both differ in version number from what is suggested (>=1.8). May be this is the problem?
My sessionInfo() follows:
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
 LC_CTYPE=es_AR.utf8 LC_NUMERIC=C
 LC_TIME=es_AR.utf8 LC_COLLATE=es_AR.utf8
 LC_MONETARY=es_AR.utf8 LC_MESSAGES=es_AR.utf8
 LC_PAPER=es_AR.utf8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=es_AR.utf8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
 tools_3.2.3 tcltk_3.2.3
I would apprec¡ate your help to solve this issue. Thank you in advance. Best regards,