Cannot load vignettes

[lijing28101]

After I install and library synder in RStudio, I run the code vignette("intro",package = "synder").
The error message is "vignette ‘intro’ not found".
My R version is 3.3.3, RStudio is 0.99.903.

[arendsee]

Can you post the output of the command:

require(devtools)
require(synder)
session_info()

[lijing28101]

Session info -------------------------------------------------
setting value
version R version 3.3.3 (2017-03-06)
system x86_64, mingw32
ui RStudio (0.99.903)
language (EN)
collate English_United States.1252
tz America/Chicago
date 2017-03-15

Packages -----------------------------------------------------
package * version date
curl 2.3 2016-11-24
devtools * 1.12.0 2016-06-24
digest 0.6.12 2017-01-27
git2r 0.18.0 2017-01-01
httr 1.2.1 2016-07-03
magrittr 1.5 2014-11-22
memoise 1.0.0 2016-01-29
R6 2.2.0 2016-10-05
Rcpp 0.12.9 2017-01-14
synder * 0.19.13 2017-03-15
withr 1.0.2 2016-06-20
source
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
CRAN (R 3.3.3)
Github (369cdb4)
CRAN (R 3.3.3)

[arendsee]

Hmm, that all looks fine. Did you install synder with the command

install_github('arendsee/synder', build_vignettes=TRUE)

By the way, when you post formatted text or code, you should wrap it in backticks (see here).

[lijing28101]

Yes, I just copy the command in your README file to install it.

[arendsee]

Can you go to R home and tell me what files are in synder/doc?

There should be these files:

algorithm.Rmd
index.html
intro.Rmd
yeast.R
yeast.html
algorithm.html
intro.R
intro.html
yeast.Rmd

[lijing28101]

I didn't find a doc folder in synder, it includes data, help, html, libs, Meta, R, and tests folders.

[arendsee]

@priyanka8590 The vignettes build correctly on my machine when I install from github, so it is a little hard to diagnose what is going wrong.

Try installing again, using the command in the README. I've pushed a possible fix to master.

[arendsee]

@lijing28101 @priyanka8590 OK, so I don't think there is a solution to this on the Fagin side. Try doing this:

library(devtools)
install_github("arendsee/synder")
build_vignettes()

There is probably some button for this in RStudio. If this works for you, I will just update the README with these build instructions.

[arendsee]

The error "Could not find package root" means that you need to set your working directory to the synder package. If you can't compile it, you can also just view the vignette source files. They are written in markdown, which is as readable as plaintext.

…

On Fri, Jan 25, 2019 at 1:24 PM fkcoolman ***@***.***> wrote: I got the same problem, when using build_vignettes() I got this on my terminal: build_vignettes() Error: Could not find package root. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD0DT8EY3EVxZrnGyz9FPwFmHobXmatWks5vG1nagaJpZM4MeSLi> .

-- *Zebulun Arendsee | PhD Candidate* *Bioinformatics and Computational Biology program* Genetics Development and Cellular Biology department Github <https://github.com/zbwrnz> | LinkedIn <https://www.linkedin.com/in/zebulun-arendsee-1b073138> 532 Science II Iowa State University Ames, IA 50011