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Question: openCyto: compilation failure during installation
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gravatar for gmirkin
23 months ago by
gmirkin0
Argentina,/Buenos Aires/Facultad de Medicina (UBA)
gmirkin0 wrote:

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

 

ADD COMMENTlink modified 22 months ago • written 23 months ago by gmirkin0

The README of ncdfFlow may be helpful.

 

ADD REPLYlink written 23 months ago by Dan Tenenbaum ♦♦ 8.2k

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).

ADD REPLYlink written 23 months ago by Jiang, Mike1.0k
0
gravatar for gmirkin
22 months ago by
gmirkin0
Argentina,/Buenos Aires/Facultad de Medicina (UBA)
gmirkin0 wrote:
Hello. I succeeded installing openCyto. The problem was an outdated R package: xml2. I updated it together with its dev and this solved the compilation issue. Apparently, flowWorkspace wouldn't compile with the old xml2. Anyway, I installed openCyto dependencies one by one. Namely, ncdfFlow and then flowWorkspace. Strange enough, for each of these dependencies R asked me to update the same libraries, e.g., plyr, nlme, and others. Tomorrow I'll be testing openCyto with my own data. Thanks to all people in the R and Bioconductor communities willing to help and to package developers. Best regards, Gerardo
ADD COMMENTlink modified 22 months ago • written 22 months ago by gmirkin0
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