I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: image When I use the second method to install from github,it showed many errors: image image

The downloaded source packages are in
√ checking for file 'C:\Users\dell\AppData\Local\Temp\RtmpI7TP9f\remotes8c87faaf3d\hhoeflin-hdf5r-cc278c1/DESCRIPTION'

* preparing 'hdf5r': (4.9s)
  √  checking DESCRIPTION meta-information ...
* cleaning src
* checking for LF line-endings in source and make files and shell scripts (676ms)
* checking for empty or unneeded directories (1.5s)
* building 'hdf5r_1.0.1.tar.gz'
  Warning: file 'hdf5r/cleanup' did not have execute permissions: corrected
  Warning: file 'hdf5r/configure' did not have execute permissions: corrected

* installing _source_ package 'hdf5r' ...
  checking hdf5 headers and libraries
  Environment variable LIB_HDF5 is not set. Attempting to download HDF5 files from repository.
  Content type 'application/zip' length unknown
  ** libs
  错误: (由警告转换成)this package has a non-empty 'configure.win' file,
  so building only the main architecture
* removing 'D:/soft ware/R-3.5.2/library/hdf5r'
  Error in i.p(...) :
  (converted from warning) installation of package ‘C:/Users/dell/AppData/Local/Temp/RtmpI7TP9f/file8c863b6795/hdf5r_1.0.1.tar.gz’ had non-zero exit status
  In addition: Warning messages:
  1: In untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers
  2: In untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers

But when I use the first command:install.packages("hdf5r"), it worked: image

Can anyone help me? I search many times, but I could't find the answer.

  • 2
    $\begingroup$ Usually installing a package from github means installing the developing version, so it might have errors, you probably should install the stable release stored in CRAN by using the install.packages("hdf5r"). Also it is incompatible to have two versions of the same package at the same localization. Decide either if you need both version and where do you want to install them if you want both versions. Are you sure you need the development version of this package? $\endgroup$
    – llrs
    Commented Feb 18, 2019 at 8:30

1 Answer 1


Try running this:


Just a different method of installing packages besides github. It is more centred around bioinformatics packages as well so it is pretty useful.

  • 1
    $\begingroup$ Bioconductor packages now use 'install.packages("BiocManager")' / 'BiocManager::install("<packageName>")' $\endgroup$
    – gringer
    Commented Feb 28, 2019 at 21:38

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