Installing "Sleuth" in R

Question

[dr.fatemeh.askari]

Hey all,

I have RNA-seq outputs from Kallisto, trying to analyze it by Sleuth in R. But, I am facing problem in installing it. below is the codes;

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install()
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Old packages: 'data.table'

> library("devtools").          # "devtools" is already installed.
> BiocManager::install("pachterlab/sleuth")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing github package(s) 'pachterlab/sleuth'
Error: Failed to install 'sleuth' from GitHub:
  Timeout was reached: [api.github.com] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received

My output;

> library('sleuth')
Error in library("sleuth") : there is no package called 'sleuth'

I don't know why I can have sleuth library. Am I missing a step?

[dr.fatemeh.askari]

Hey Kevin,

Unfortunately, it did not work.

>if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
>
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ +     install.packages("BiocManager")
> BiocManager::install()
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
> library("devtools")
> devtools::install_github('pachterlab/sleuth')
Downloading GitHub repo pachterlab/sleuth@HEAD
tar: Failed to set default locale
tar: Failed to set default locale
Skipping 1 packages not available: rhdf5
Skipping 1 packages ahead of CRAN: vctrs
v  checking DESCRIPTION meta-information ...
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'sleuth_0.30.0.tar.gz'

Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted
Error: Failed to install 'sleuth' from GitHub:
  (converted from warning) installation of package '/var/folders/yl/10tygz_910l9wmkjtjncxpw40000gn/T//RtmpE6vLD1/filef23636392e9/sleuth_0.30.0.tar.gz' had non-zero exit status

here, it gives error!!

> library("sleuth")
Error in library("sleuth") : there is no package called 'sleuth'
> library(rhdf5)
> library(vctrs)

Attaching package: 'vctrs'

The following object is masked from 'package:dplyr':

    data_frame

> library(dplyr)
>

[GenoMax]

Always use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[Kevin Blighe]

It looks like your R installation is not setup correctly - from where do you run R? Can you output the result of sessionInfo()?

library(Sleuth) will return an error because the package did not install correctly. Looking at the error messages, you may need to first install rhdf5 and vctrs.

If you still have issues, I would recommend setting up a MiniConda environment and installing these R packages via that.

[dr.fatemeh.askari]

Thanks Kevin,

I first installed rhdf5 and vctrs. and then dealt with locale

I wrote " system("defaults write org.R-project.R force.LANG en_US.UTF-8") and quiet and restart R.

Now, it is working.

[Kevin Blighe]

Sounds good - excellent.

Answer 1

[Kevin Blighe]

Hey,

You should be using:

devtools::install_github('pachterlab/sleuth')

This will also work:

remotes::install_github('pachterlab/sleuth')

Note: remotes has much less dependencies than devtools

Kevin

Answer 2

[swbarnes2]

Always Google to see how to install things. Not everything installs through bioconductor.