R package h5r configure: error: Can't find HDF5
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I am trying to install the R-pbh-5 package for R, which requires h5r. When I try to install h5r with install_version("h5r", "1.4.7"), I receive the following error:
[...]
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘h5r’
I searched the Ubuntu package index for HDF5 and installed the libraries libhdf5-10, libhdf5-dev, hdf5-tools, and pbh5tools. It seems to be correctly installed as well:
$ whereis hdf5
hdf5: /usr/include/hdf5
I just spent the last hours googling, but I can't figure out what I'm missing here. Any advice?
> sessionInfo()
R Under development (unstable) (2018-02-12 r74246)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /opt/R/3.5.0/lib/R/lib/libRblas.so
LAPACK: /opt/R/3.5.0/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 yaml_2.1.17 Rhdf5lib_1.1.5
Update 1:
Following the suggestions in the comments, I managed to get one step further. When I run:
R CMD INSTALL h5r_1.4.7.tar.gz --configure-vars="LDFLAGS='-L/usr/lib/x86_64-linux-gnu/hdf5/serial/' CPPFLAGS='-I/usr/include/hdf5/serial'"
I now receive the following error:
-I/usr/include/hdf5/serial
-L/usr/lib/x86_64-linux-gnu/hdf5/serial/
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5_debug.c -o h5_debug.o
h5_debug.c:4:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'h5_debug.o' failed
make: *** [h5_debug.o] Error 1
ERROR: compilation failed for package ‘h5r’
16.04 package-management r
asked Feb 28 at 14:44
bgbrink
234
 |Â
show 4 more comments
up vote
4
down vote
favorite
I am trying to install the R-pbh-5 package for R, which requires h5r. When I try to install h5r with install_version("h5r", "1.4.7"), I receive the following error:
[...]
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘h5r’
I searched the Ubuntu package index for HDF5 and installed the libraries libhdf5-10, libhdf5-dev, hdf5-tools, and pbh5tools. It seems to be correctly installed as well:
$ whereis hdf5
hdf5: /usr/include/hdf5
I just spent the last hours googling, but I can't figure out what I'm missing here. Any advice?
> sessionInfo()
R Under development (unstable) (2018-02-12 r74246)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /opt/R/3.5.0/lib/R/lib/libRblas.so
LAPACK: /opt/R/3.5.0/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 yaml_2.1.17 Rhdf5lib_1.1.5
Update 1:
Following the suggestions in the comments, I managed to get one step further. When I run:
R CMD INSTALL h5r_1.4.7.tar.gz --configure-vars="LDFLAGS='-L/usr/lib/x86_64-linux-gnu/hdf5/serial/' CPPFLAGS='-I/usr/include/hdf5/serial'"
I now receive the following error:
-I/usr/include/hdf5/serial
-L/usr/lib/x86_64-linux-gnu/hdf5/serial/
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5_debug.c -o h5_debug.o
h5_debug.c:4:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'h5_debug.o' failed
make: *** [h5_debug.o] Error 1
ERROR: compilation failed for package ‘h5r’
16.04 package-management r
asked Feb 28 at 14:44
bgbrink
234
There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in aserialsubdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate--configure-varsto the build process?
– steeldriver
Feb 28 at 15:03
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to thehdf libs?
– bgbrink
Feb 28 at 15:08
1
Unfortunately I'm not either - there's some information here based on which I'd try something likeR CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'
– steeldriver
Feb 28 at 15:18
Did you trysudo apt-get install hdf5-helpers?
– N0rbert
Feb 28 at 19:25
Thank you for your suggestions. Installinghdf5-helpersdid not change anything, but @steeldriver was pointing me in the right direction. I updated the question.
– bgbrink
Mar 1 at 11:31
 |Â
show 4 more comments
up vote
4
down vote
favorite
up vote
4
down vote
favorite
I am trying to install the R-pbh-5 package for R, which requires h5r. When I try to install h5r with install_version("h5r", "1.4.7"), I receive the following error:
[...]
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘h5r’
I searched the Ubuntu package index for HDF5 and installed the libraries libhdf5-10, libhdf5-dev, hdf5-tools, and pbh5tools. It seems to be correctly installed as well:
$ whereis hdf5
hdf5: /usr/include/hdf5
I just spent the last hours googling, but I can't figure out what I'm missing here. Any advice?
> sessionInfo()
R Under development (unstable) (2018-02-12 r74246)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /opt/R/3.5.0/lib/R/lib/libRblas.so
LAPACK: /opt/R/3.5.0/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 yaml_2.1.17 Rhdf5lib_1.1.5
Update 1:
Following the suggestions in the comments, I managed to get one step further. When I run:
R CMD INSTALL h5r_1.4.7.tar.gz --configure-vars="LDFLAGS='-L/usr/lib/x86_64-linux-gnu/hdf5/serial/' CPPFLAGS='-I/usr/include/hdf5/serial'"
I now receive the following error:
-I/usr/include/hdf5/serial
-L/usr/lib/x86_64-linux-gnu/hdf5/serial/
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5_debug.c -o h5_debug.o
h5_debug.c:4:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'h5_debug.o' failed
make: *** [h5_debug.o] Error 1
ERROR: compilation failed for package ‘h5r’
16.04 package-management r
asked Feb 28 at 14:44
bgbrink
234
I am trying to install the R-pbh-5 package for R, which requires h5r. When I try to install h5r with install_version("h5r", "1.4.7"), I receive the following error:
[...]
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘h5r’
I searched the Ubuntu package index for HDF5 and installed the libraries libhdf5-10, libhdf5-dev, hdf5-tools, and pbh5tools. It seems to be correctly installed as well:
$ whereis hdf5
hdf5: /usr/include/hdf5
I just spent the last hours googling, but I can't figure out what I'm missing here. Any advice?
> sessionInfo()
R Under development (unstable) (2018-02-12 r74246)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /opt/R/3.5.0/lib/R/lib/libRblas.so
LAPACK: /opt/R/3.5.0/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 yaml_2.1.17 Rhdf5lib_1.1.5
Update 1:
Following the suggestions in the comments, I managed to get one step further. When I run:
R CMD INSTALL h5r_1.4.7.tar.gz --configure-vars="LDFLAGS='-L/usr/lib/x86_64-linux-gnu/hdf5/serial/' CPPFLAGS='-I/usr/include/hdf5/serial'"
I now receive the following error:
-I/usr/include/hdf5/serial
-L/usr/lib/x86_64-linux-gnu/hdf5/serial/
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c h5_debug.c -o h5_debug.o
h5_debug.c:4:18: fatal error: hdf5.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'h5_debug.o' failed
make: *** [h5_debug.o] Error 1
ERROR: compilation failed for package ‘h5r’
16.04 package-management r
16.04 package-management r
asked Feb 28 at 14:44
bgbrink
234
asked Feb 28 at 14:44
bgbrink
234
edited Mar 1 at 11:30
asked Feb 28 at 14:44
bgbrink
234
asked Feb 28 at 14:44
bgbrink
234
asked Feb 28 at 14:44
bgbrink
234
234
There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in aserialsubdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate--configure-varsto the build process?
– steeldriver
Feb 28 at 15:03
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to thehdf libs?
– bgbrink
Feb 28 at 15:08
1
Unfortunately I'm not either - there's some information here based on which I'd try something likeR CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'
– steeldriver
Feb 28 at 15:18
Did you trysudo apt-get install hdf5-helpers?
– N0rbert
Feb 28 at 19:25
Thank you for your suggestions. Installinghdf5-helpersdid not change anything, but @steeldriver was pointing me in the right direction. I updated the question.
– bgbrink
Mar 1 at 11:31
 |Â
show 4 more comments
There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in aserialsubdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate--configure-varsto the build process?
– steeldriver
Feb 28 at 15:03
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to thehdf libs?
– bgbrink
Feb 28 at 15:08
1
Unfortunately I'm not either - there's some information here based on which I'd try something likeR CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'
– steeldriver
Feb 28 at 15:18
Did you trysudo apt-get install hdf5-helpers?
– N0rbert
Feb 28 at 19:25
Thank you for your suggestions. Installinghdf5-helpersdid not change anything, but @steeldriver was pointing me in the right direction. I updated the question.
– bgbrink
Mar 1 at 11:31
There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in a
serial subdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate --configure-vars to the build process?– steeldriver
Feb 28 at 15:03
There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in a
serial subdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate --configure-vars to the build process?– steeldriver
Feb 28 at 15:03
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to the
hdf libs?– bgbrink
Feb 28 at 15:08
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to the
hdf libs?– bgbrink
Feb 28 at 15:08
1
1
Unfortunately I'm not either - there's some information here based on which I'd try something like
R CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'– steeldriver
Feb 28 at 15:18
Unfortunately I'm not either - there's some information here based on which I'd try something like
R CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'– steeldriver
Feb 28 at 15:18
Did you try
sudo apt-get install hdf5-helpers?– N0rbert
Feb 28 at 19:25
Did you try
sudo apt-get install hdf5-helpers?– N0rbert
Feb 28 at 19:25
Thank you for your suggestions. Installing
hdf5-helpers did not change anything, but @steeldriver was pointing me in the right direction. I updated the question.– bgbrink
Mar 1 at 11:31
Thank you for your suggestions. Installing
hdf5-helpers did not change anything, but @steeldriver was pointing me in the right direction. I updated the question.– bgbrink
Mar 1 at 11:31
 |Â
show 4 more comments
1 Answer
1
active
oldest
votes
up vote
0
down vote
accepted
I managed to do it, although in slightly messy way. I used sudo cp -rs /usr/include/hdf5/serial/* /usr/share/R/include to create links to all the hdf5 files within the R/include folder, which is included in the build by default.
answered Mar 5 at 9:48
bgbrink
234
add a comment |Â
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
0
down vote
accepted
I managed to do it, although in slightly messy way. I used sudo cp -rs /usr/include/hdf5/serial/* /usr/share/R/include to create links to all the hdf5 files within the R/include folder, which is included in the build by default.
answered Mar 5 at 9:48
bgbrink
234
add a comment |Â
up vote
0
down vote
accepted
I managed to do it, although in slightly messy way. I used sudo cp -rs /usr/include/hdf5/serial/* /usr/share/R/include to create links to all the hdf5 files within the R/include folder, which is included in the build by default.
answered Mar 5 at 9:48
bgbrink
234
add a comment |Â
up vote
0
down vote
accepted
up vote
0
down vote
accepted
I managed to do it, although in slightly messy way. I used sudo cp -rs /usr/include/hdf5/serial/* /usr/share/R/include to create links to all the hdf5 files within the R/include folder, which is included in the build by default.
answered Mar 5 at 9:48
bgbrink
234
I managed to do it, although in slightly messy way. I used sudo cp -rs /usr/include/hdf5/serial/* /usr/share/R/include to create links to all the hdf5 files within the R/include folder, which is included in the build by default.
answered Mar 5 at 9:48
bgbrink
234
answered Mar 5 at 9:48
bgbrink
234
answered Mar 5 at 9:48
bgbrink
234
answered Mar 5 at 9:48
bgbrink
234
234
add a comment |Â
add a comment |Â
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There are some historic issues with Debian (and derivatives) packaging the HDF5 headers / libraries in a
serialsubdirectory - I wonder if that's the issue here? Perhaps there's a way around it by passing appropriate--configure-varsto the build process?– steeldriver
Feb 28 at 15:03
I am not so familiar with custom build commands. Could you help me out and formulate the appropriate option which would point to the
hdf libs?– bgbrink
Feb 28 at 15:08
1
Unfortunately I'm not either - there's some information here based on which I'd try something like
R CMD INSTALL <whatever> --configure-vars='LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial/'– steeldriver
Feb 28 at 15:18
Did you try
sudo apt-get install hdf5-helpers?– N0rbert
Feb 28 at 19:25
Thank you for your suggestions. Installing
hdf5-helpersdid not change anything, but @steeldriver was pointing me in the right direction. I updated the question.– bgbrink
Mar 1 at 11:31