Seurat: Installation error/package load failed for 'Seurat'

[fly4all]

I've been trying to install Seurat following the directions on the website.
Version of R: 3.5

Code shown below:

install.packages("Seurat")
library(Seurat)
library(dplyr)

# Load the PBMC dataset
data_dir <- '/Downloads/'
list.files(data_dir)
pbmc.data <- Read10X(data.dir = data_dir)

The output I got is displayed below:

> install.packages("Seurat")
Installing package into ‘/Users/ahmedmar/Library/R/3.5/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/Seurat_2.3.4.tgz'
Content type 'application/x-gzip' length 2653423 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

The downloaded binary packages are in
    /var/folders/77/pdjzg7792t54dw36kjhw147m2yxqts/T//RtmpLofqVO/downloaded_packages
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
> library(dplyr)
> 
>  Load the PBMC dataset
> data_dir <- '/Downloads/'
> list.files(data_dir)
[1] "pbmc3k_filtered_gene_bc_matrices.tar" "practice_seurat.R"                   
> pbmc.data <- Read10X(data.dir = data_dir)
Error in Read10X(data.dir = data_dir) : could not find function "Read10X"

[mojaveazure]

What happens if you try to install stringi separately? That's the part of the installation that's failing.

[fly4all]

I was able to get around this by installing stringi separately. but now I'm getting an error about ‘hdf5r’

This is the part where it starts giving an error:

checking for h5cc... no
checking for h5pcc... no
checking for HDF5 libraries... no
configure: WARNING:
Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).

configure: error: hdf5 does not seem to be installed on your platform.
  Please install the hdf5 library.
  The required HDF5 library files can be installed as follows:
      - Debian-based (e.g. Debian >= 8.0, Ubuntu >= 15.04): 'sudo apt-get install libhdf5-dev'
        - Old Debian-based (e.g Debian < 8.0, Ubuntu < 15.04): Install from source (see INSTALL)
        - OS X using Homebrew: 'brew install homebrew/science/hdf5'
        - RPM-based (e.g Fedora): 'sudo yum install hdf5-devel'
ERROR: configuration failed for package ‘hdf5r’
* removing ‘/home/ahmedmar/Rlibrary/3.4.1/hdf5r’
ERROR: dependency ‘hdf5r’ is not available for package ‘Seurat’
* removing ‘/home/ahmedmar/Rlibrary/3.4.1/Seurat’

The downloaded source packages are in
    ‘/tmp/RtmpsTTujs/downloaded_packages’
Warning messages:
1: In install.packages("Seurat", repos = "http://cran.r-project.org") :
  installation of package ‘hdf5r’ had non-zero exit status
2: In install.packages("Seurat", repos = "http://cran.r-project.org") :
  installation of package ‘Seurat’ had non-zero exit status

[evolvedmicrobe]

The hdf5r library is one of a few set of R packages that requires code not installed by R. You don't have this code available, and so cannot install that package.

By analogy, some TVs come with a built in cable-box or antenna and work just fine on their own. Other TVs need a separate and pre-existing cable box or antenna to produce anything but jibberish on the screen. The hdf5r package is such a TV, and you will need to separately install the hdf5 library (the equivalent of the cable-box/antenna) before it will work. See the key instructions in the error message (below) and try again.

The required HDF5 library files can be installed as follows:
- Debian-based (e.g. Debian >= 8.0, Ubuntu >= 15.04): 'sudo apt-get install libhdf5-dev'
- Old Debian-based (e.g Debian < 8.0, Ubuntu < 15.04): Install from source (see INSTALL)
- OS X using Homebrew: 'brew install homebrew/science/hdf5'
- RPM-based (e.g Fedora): 'sudo yum install hdf5-devel'

[satijalab]

See #655

[117999]

got similar problem when I tried to
library(Seurat)
it appeared that
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘multtest’
I have tried to
install.packages('multtest') separately, still it comes as
package ‘multtest’ is not available (for R version 3.6.3) don't know what's the problem, anyone can help?

[timoast]

multtest is on bioconductor: https://www.bioconductor.org/packages/release/bioc/html/multtest.html

To install:

BiocManager::install(multtest)

[117999]

I have got a new problem when I am trying to reinstall Seurat or update it
it appears to be successfully installed
but when I tried to use it
library (Seurat)
The output I got is displayed below:
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 0.4.5 is already loaded, but >= 0.4.6 is required
what should I do then?

[mailcolm9]

multtest is on bioconductor: https://www.bioconductor.org/packages/release/bioc/html/multtest.html

To install:

BiocManager::install(multtest)

Hi,

I encounter the same issue, and don't know what happened.