<p>Try running this:</p>

<pre><code>source("https://bioconductor.org/biocLite.R")
biocLite("hdf5r")
</code></pre>

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

CC BY-SA 4.0
2019-02-28T21:38:25.237Z
Bioconductor packages now use 'install.packages("BiocManager")' / 'BiocManager::install("<packageName>")'
gringer
CC BY-SA 4.0
2019-02-28T19:21:18.407Z
2019-02-28T19:21:18.407Z
h3ab74
<p>I install hdf5r following <a href="https://github.com/hhoeflin/hdf5r%EF%BC%8Cit" rel="nofollow noreferrer">https://github.com/hhoeflin/hdf5r</a>， it shows two methods:
<img src="https://user-images.githubusercontent.com/30619010/52907396-e8e2ad00-329b-11e9-998b-96431b055ba0.png" alt="image">
When I use the second method to install from github,it showed many errors：
<img src="https://user-images.githubusercontent.com/30619010/52907457-e0d73d00-329c-11e9-9921-14408bd51967.png" alt="image">
<img src="https://user-images.githubusercontent.com/30619010/52907426-5989c980-329c-11e9-95a6-e122f7196071.png" alt="image"></p>

<pre><code>The downloaded source packages are in
‘C:\Users\dell\AppData\Local\Temp\RtmpI7TP9f\downloaded_packages’
√ 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.
  试开URL’https://github.com/mannau/h5-libwin/archive/master.zip'
  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'
  In R CMD INSTALL
  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
</code></pre>

<p>But when I use the first command:install.packages("hdf5r"), it worked:
  <img src="https://user-images.githubusercontent.com/30619010/52907413-23e4e080-329c-11e9-9e32-916eccdb0b2d.png" alt="image"></p>

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

CC BY-SA 4.0
2019-02-18T08:30:17.887Z
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?
llrs
<r><seurat><software-installation><rstudio>
R studio failed to install the latest development version of hdf5r from Github (win10)
# R studio failed to install the latest development version of hdf5r from Github (win10)

(Asked by: username_0 on 2019-02-17)

I install hdf5r following https://github.com/hhoeflin/hdf5r， it shows two methods:

When I use the second method to install from github,it showed many errors：


The downloaded source packages are in
‘C:\Users\dell\AppData\Local\Temp\RtmpI7TP9f\downloaded_packages’
√ 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.
  试开URL’https://github.com/mannau/h5-libwin/archive/master.zip'
  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'
  In R CMD INSTALL
  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:
  
Can anyone help me? I search many times, but I could't find the answer.

**Tags:** r, seurat, software-installation, rstudio
> **Comments:**
> **username_1**: 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?  

---

## 1 answers

### Answer by username_2 on 2019-02-28. Score: 2

Try running this:
source("https://bioconductor.org/biocLite.R")
biocLite("hdf5r")

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

> **Comments:**
> **username_3**: Bioconductor packages now use 'install.packages("BiocManager")' / 'BiocManager::install("<packageName>")'  

---

