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
#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’
* 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:
hdf5-utils 1.12.1-2.1+b2
hdf5-helpers 1.8.13+docs-15
hdf5-tools 1.8.13+docs-15
libhdf5-8 1.8.13+docs-15
libhdf5-cpp-8 1.8.13+docs-15
libhdf5-dev 1.8.13+docs-15
r-cran-hdf5 1.6.10-3+b1
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:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
locale:
[1] LC_CTYPE=es_AR.utf8 LC_NUMERIC=C
[3] LC_TIME=es_AR.utf8 LC_COLLATE=es_AR.utf8
[5] LC_MONETARY=es_AR.utf8 LC_MESSAGES=es_AR.utf8
[7] LC_PAPER=es_AR.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_AR.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] tools_3.2.3 tcltk_3.2.3
I would apprec¡ate your help to solve this issue. Thank you in advance. Best regards,
Gerardo
The README of ncdfFlow may be helpful.
Your hdf5 seems to be installed at the non-standard location. Can you try to specify the prefix through `--with-hdf5` as you manually install ncdfFlow package? (refer to the doc for the details as Dan mentioned).