Install problem

[Juneil-Jang]

Install problem

[LifanLiang]

Hi, I'm sorry to hear what happened to your computer system. But I don't think installing GSFA will cause that much damage though... My random guess is that installing GSFA in Ubuntu may require additional C++ compiler toolkits. Please post the detailed error message when devtool install failed so we may be able to spot related issues.

[hanhuajun40]

Hi, Lifan,

I also had an issue when installing GFSA package. The error is below:

Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
checking for file ‘/tmp/RtmpJqXqOr/remotesc32347216eed/xinhe-lab-GSFA-8e7cf03✔ checking for file ‘/tmp/RtmpJqXqOr/remotesc32347216eed/xinhe-lab-GSFA-8e7cf03/DESCRIPTION’ (1.2s)
─ preparing ‘GSFA’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to build vignettes
E creating vignettes (47m 55.8s)
--- re-building ‘gsfa_intro.Rmd’ using rmarkdown
Using Factor as id variables
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

   filter, lag

The following objects are masked from 'package:base':

   intersect, setdiff, setequal, union

Loading required package: ggplot2
Using gene as id variables
Using gene as id variables
Warning: Using size for a discrete variable is not advised.
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "gsfa_intro", and the latter is "Applying GSFA in a simulated dataset". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
Warning in file(con, "r") :
cannot open file 'gsfa_intro.Rmd': No such file or directory
Error: tangling vignette 'gsfa_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘gsfa_intro.Rmd’

SUMMARY: processing the following file failed:
‘gsfa_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'GSFA' from GitHub:
! System command 'R' failed

Do you have some suggestions. Thanks!

Best,

[LifanLiang]

Thanks for your feedback. We are still figuring out what happened.

Meanwhile, you may first try installing GSFA with build_vignettes set to false. If installation finish without errors, you can download and run the Rmd file stored here: https://github.com/xinhe-lab/GSFA/blob/master/vignettes/gsfa_intro.Rmd and see what the problem is.