Question: Rhdf5lib install problems
0
gravatar for cem45
11 months ago by
cem450
cem450 wrote:

I have recently upgraded to R-3.5 and am having problems installing packages that should be compatible with R-3.5.

 

Using the following commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Rhdf5lib", version = "3.8")

 

On this setup:

             _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          5.1                         
year           2018                        
month          07                          
day            02                          
svn rev        74947                       
language       R                           
version.string R version 3.5.1 (2018-07-02)
nickname       Feather Spray 

 

The install fails with the following output (including confusion references to the non-existant C: drive on this unix system):

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'Rhdf5lib'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/Rhdf5lib_1.4.0.tar.gz'
Content type 'application/x-gzip' length 9211917 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

* installing *source* package ‘Rhdf5lib’ ...
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
untarring hdf5small_cxx_1.10.3.tar.gz ...
building the szip library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... no
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... mkdir: cannot create directory 'C:/Rtmp/cg27307-5984': No such file or directory
mkdir: cannot create directory 'C:/Rtmp/cg-27307': No such file or directory
config.guess: cannot create a temporary directory in C:/Rtmp
configure: error: cannot guess build type; you must specify one
make: *** No targets specified and no makefile found.  Stop.
building the hdf5 library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... no
checking whether make supports nested variables... (cached) no
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... mkdir: cannot create directory 'C:/Rtmp/cg27529-6174': No such file or directory
mkdir: cannot create directory 'C:/Rtmp/cg-27529': No such file or directory
config.guess: cannot create a temporary directory in C:/Rtmp
configure: error: cannot guess build type; you must specify one
sh configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... no
checking whether make supports nested variables... (cached) no
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... mkdir: cannot create directory 'C:/Rtmp/cg27716-1717': No such file or directory
mkdir: cannot create directory 'C:/Rtmp/cg-27716': No such file or directory
config.guess: cannot create a temporary directory in C:/Rtmp
configure: error: cannot guess build type; you must specify one
Makefile:32: recipe for target '_config' failed
make: *** [_config] Error 1
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib/include"
cp hdf5/src/*.h /home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib/include
cp hdf5/c++/src/*.h /home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib/include
mkdir -p "/home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib/lib/
cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
Makevars:25: recipe for target 'copying' failed
make: *** [copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/home/gp444/R/x86_64-pc-linux-gnu-library/3.5/Rhdf5lib’

The downloaded source packages are in
    ‘/tmp/Rtmpt6a5ei/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘Rhdf5lib’ had non-zero exit status

 

How do we go about troubleshooting this issue?

ADD COMMENTlink written 11 months ago by cem450

Thanks for the report, I'm not immediately sure what the issue is here, but I'll look into it.  Can you just confirm that the following command produces the same error for you - this work for me on Linux Mint 18 with R-3.5.1

install.packages('https://bioconductor.org/packages/3.8/bioc/src/contrib/Rhdf5lib_1.4.0.tar.gz', repos = NULL)

 

ADD REPLYlink written 11 months ago by Mike Smith4.0k

I am having the same problem. Is there any chance for some help in order to debug this error? Tried compiling on CentOS 6.2 and Gentoo.

Log:

  CC       H5PL.lo
  CC       H5PLint.lo
  CC       H5PLpath.lo
In file included from H5PLpath.c:42:
H5PLpath.c: In function 'H5PL__create_path_table':
H5PLpkg.h:37:33: error: 'H5_DEFAULT_PLUGINDIR' undeclared (first use in this function); did you mean 'H5_DEFAULT_VFD'?
 #define H5PL_DEFAULT_PATH       H5_DEFAULT_PLUGINDIR
                                 ^~~~~~~~~~~~~~~~~~~~
H5PLpath.c:260:29: note: in expansion of macro 'H5PL_DEFAULT_PATH'
         paths = H5MM_strdup(H5PL_DEFAULT_PATH);
                             ^~~~~~~~~~~~~~~~~
H5PLpkg.h:37:33: note: each undeclared identifier is reported only once for each function it appears in
 #define H5PL_DEFAULT_PATH       H5_DEFAULT_PLUGINDIR
                                 ^~~~~~~~~~~~~~~~~~~~
H5PLpath.c:260:29: note: in expansion of macro 'H5PL_DEFAULT_PATH'
         paths = H5MM_strdup(H5PL_DEFAULT_PATH);
                             ^~~~~~~~~~~~~~~~~
H5PLpath.c: In function 'H5PL__find_plugin_in_path':
H5PLpath.c:639:5: error: unknown type name 'DIR'
     DIR            *dirp = NULL;            /* Directory stream */
     ^~~
In file included from /usr/include/string.h:637,
                 from H5private.h:58,
                 from H5PLpath.c:39:
H5PLpath.c:665:26: error: dereferencing pointer to incomplete type 'struct dirent'
         if (!HDstrncmp(dp->d_name, "lib", (size_t)3) &&
                          ^~
/usr/include/bits/string2.h:922:32: note: in definition of macro 'strncmp'
     && ((__builtin_constant_p (s1)         \
                                ^~
H5PLpath.c:665:14: note: in expansion of macro 'HDstrncmp'
         if (!HDstrncmp(dp->d_name, "lib", (size_t)3) &&
              ^~~~~~~~~
make[2]: *** [Makefile:1437: H5PLpath.lo] Error 1
make[2]: Leaving directory '/tmp/RtmpXl7r9N/R.INSTALL6a0644d5aec3/Rhdf5lib/src/hdf5/src'
make[1]: *** [Makefile:1937: lib] Error 1
make[1]: Leaving directory '/tmp/RtmpXl7r9N/R.INSTALL6a0644d5aec3/Rhdf5lib/src/hdf5/src'
make: *** [Makefile:1083: lib] Error 1
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/INS/home/user/R/library/Rhdf5lib/include"
cp hdf5/src/*.h /INS/home/user/R/library/Rhdf5lib/include
cp hdf5/c++/src/*.h /INS/home/user/R/library/Rhdf5lib/include
mkdir -p "/INS/home/user/R/library/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /INS/home/user/R/library/Rhdf5lib/lib/
cp: cannot stat 'hdf5/src/.libs/libhdf5.a': No such file or directory
make: *** [Makevars:29: copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/INS/home/user/R/library/Rhdf5lib’
ERROR: dependency ‘Rhdf5lib’ is not available for package ‘rhdf5’
* removing ‘/INS/home/user/R/library/rhdf5’
ERROR: dependency ‘rhdf5’ is not available for package ‘HDF5Array’
* removing ‘/INS/home/user/R/library/HDF5Array’
ERROR: dependency ‘HDF5Array’ is not available for package ‘DelayedMatrixStats’
* removing ‘/INS/home/user/R/library/DelayedMatrixStats’
ADD REPLYlink modified 6 months ago • written 6 months ago by Firas0

This doesn't look like the same error other than the final outcome is a failure to install Rhdf5lib. Please can you start a separate thread for this and include the entire output of the installation process. If this scrolls too much, I find the easiest way to capture everything is to run this in a command terminal:

R -e 'BiocManager::install("Rhdf5lib")' > /tmp/Rhdf5lib_install.log
ADD REPLYlink written 6 months ago by Mike Smith4.0k
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