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mannau / h5

Interface to the HDF5 Library
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ERROR: compilation failed for package ‘h5’ #37

Closed slejdops closed 7 years ago

slejdops commented 7 years ago

I am getting the following error while installing the h5 package on Ubuntu 12.04.5 LTS ( R version : 3.2.5) and Ubuntu 14.04.5 LTS ( R version : 3.3.1)

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install.packages('h5', repos='http://cran.rstudio.com/') Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'http://cran.rstudio.com/src/contrib/h5_0.9.8.tar.gz'

Content type 'application/x-gzip' length 393742 bytes (384 KB)

downloaded 384 KB

  • installing source package ‘h5’ ... * package ‘h5’ successfully unpacked and MD5 sums checked checking for h5c++... /usr/bin/h5c++ checking for ggrep... /bin/grep checking whether /bin/grep accepts -o... yes checking for ggrep... (cached) /bin/grep checking whether /bin/grep accepts -o... yes configure: creating ./config.status config.status: creating src/Makevars * libs g++ -std=c++0x -I/usr/share/R/include -DNDEBUG -I/usr/include -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Attribute.cpp -o Attribute.o Attribute.cpp: In function ‘Rcpp::XPtrH5::Attribute CreateAttribute_H5File(Rcpp::XPtrH5::H5File, std::string, char, Rcpp::NumericVector, int)’: Attribute.cpp:22:26: error: ‘class H5::H5File’ has no member named ‘createAttribute’ Attribute.cpp: In function ‘Rcpp::XPtrH5::Attribute OpenAttribute_H5File(Rcpp::XPtrH5::H5File, std::string)’: Attribute.cpp:116:25: error: ‘class H5::H5File’ has no member named ‘openAttribute’ make: *\ [Attribute.o] Error 1 ERROR: compilation failed for package ‘h5’
  • removing ‘/usr/local/lib/R/site-library/h5’

The downloaded source packages are in ‘/tmp/RtmpCMrULN/downloaded_packages’ Warning message: In install.packages("h5", repos = "http://cran.rstudio.com/") : installation of package ‘h5’ had non-zero exit status

`

mannau commented 7 years ago

As stated on CRAN the package requires libhdf5-dev (>= 1.8.12). This means that the standard package on Ubuntu 12.04 (1.8.4) and Ubuntu 14.04 (1.8.11) does not work any more. You can either

  1. Install the current Version of HDF5 from source.
  2. Upgrade your Ubuntu Version

Cheers, Mario

slejdops commented 7 years ago

Thank you very much for your help.