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sshen82 / BandNorm

Simple Normalization Method for single-cell Hi-C
GNU General Public License v3.0
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Issue installing package with `devtools` - installed from source instead #3

Closed terencewtli closed 2 years ago

terencewtli commented 2 years ago

Hi,

Thank you for this package! I tried installing this package with the following command:

devtools::install_github('sshen82/BandNorm', build_vignettes = TRUE)

I got the error below:

 checking DESCRIPTION meta-information ... 
 installing the package to build vignettes
 creating vignettes (38.8s)
 --- re-building ‘BandNorm-tutorial.Rmd’ using rmarkdown
 Warning in engine$weave(file, quiet = quiet, encoding = enc) :
   Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. 
 Error: processing vignette 'BandNorm-tutorial.Rmd' failed with diagnostics:
 The 'markdown' package should be installed and declared as a dependency of the 'BandNorm' package (e.g.
, in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'mar
own' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.
 --- failed re-building ‘BandNorm-tutorial.Rmd’

 --- re-building ‘scGAD-tutorial.Rmd’ using rmarkdown
 Warning in engine$weave(file, quiet = quiet, encoding = enc) :
   Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. 
 Error: processing vignette 'scGAD-tutorial.Rmd' failed with diagnostics:
 The 'markdown' package should be installed and declared as a dependency of the 'BandNorm' package (e.g.
, in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'mar
own' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.
 --- failed re-building ‘scGAD-tutorial.Rmd’

 SUMMARY: processing the following files failed:
   ‘BandNorm-tutorial.Rmd’ ‘scGAD-tutorial.Rmd’

 Error: Vignette re-building failed.
 Execution halted
Error: Failed to install 'BandNorm' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
   Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. 
 Error: processing vignette 'scGAD-tutorial.Rmd' failed with diagnostics:
 The 'markdown' package should be installed and declared as a dependency of the 'BandNorm' package (e.g.
, in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'mar
own' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.
 --- failed re-building ‘scGAD-tutorial.Rmd’

 SUMMARY: processing the following files failed:
   ‘BandNorm-tutorial.Rmd’ ‘scGAD-tutorial.Rmd’

 Error: Vignette re-building failed.

I have the rmarkdown and markdown packages installed, but the installation still didn't work. I checked out the Github issue and as suggested, edited the DESCRIPTION file to include markdown in the Suggests tab, then installed from source successfully:

install.packages('/path/to/BandNorm', repos = NULL, source = TRUE)

To summarize, I was wondering if I overlooked a dependency when trying to install using devtools, and whether or not markdown should ultimately be added to the DESCRIPTION file. Thank you!

sshen82 commented 2 years ago

Hi, Thank you for using the package!

As you might notice, we are actually still testing the package. When I tried installing the package, it succeeded without any warning, but I think it is indeed necessary to add markdown in DESCRIPTION file judging from the Github issue you shared. We will further look at this to see if there are any other things important to include. Thank you for sharing this with me!

If there are any other questions, feel free to let me know!

Yours sincerely, Siqi Shen