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KChen-lab / SCMarker

Marker gene selection from scRNA-seq data

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Error in installation

kendomaniac opened this issue · comments

commented

Dear Sir,
Can you please fix the issue I encountered in installing your package?
Cheers
Calogero
###########
I tried installing your package:
library(devtools)
Loading required package: usethis

install_github("KChen-lab/SCMarker")
Downloading GitHub repo KChen-lab/SCMarker@master
✔ checking for file ‘/private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/Rtmpgv8C6V/remotes15f6348ff42e/KChen-lab-SCMarker-c07d842/DESCRIPTION’ ...
─ preparing ‘SCMarker’:
✔ checking DESCRIPTION meta-information ...
Warning: /private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/RtmpeP6Kqc/Rbuild17d32bd5251d/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}
'
─ installing the package to process help pages
─ saving partial Rd database (1.3s)
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘SCMarker_2.0.tar.gz’

  • installing source package ‘SCMarker’ ...
    ** using staged installation
    ** R
    ** data
    ** byte-compile and prepare package for lazy loading
    ** help
    Error : (converted from warning) /private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/RtmpSdymSM/R.INSTALL17fe3db0335f/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}
    '
    ERROR: installing Rd objects failed for package ‘SCMarker’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/SCMarker’
    Error: Failed to install 'SCMarker' from GitHub:
    (converted from warning) installation of package ‘/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T//Rtmpgv8C6V/file15f656e812f7/SCMarker_2.0.tar.gz’ had non-zero exit status

I cloned the repository and I did a build test and I got the following issues:

warning 1

✔ checking DESCRIPTION meta-information ...
Warning: /private/var/folders/_b/4rmqysy94j91kb8xjyc551z40000gn/T/RtmpOtbfSW/Rbuild16401f1c0c3c/SCMarker/man/HeatmapCluster.Rd:86: unexpected END_OF_INPUT '}

error 1:
checking for unstated dependencies in examples ... WARNING
Warning: parse error in file 'SCMarker-Ex.R':
156:5: unexpected symbol
155: topmarker=as.data.frame(feature
156: topmarker
^

commented

Dear authors,
I encountered the same problem that the package cannot be installed.
Thanks for your attention!

commented

Hi Calogero,
I noticed you installed SCMarker under R/3.6. Did you try R/3.5 or other version less 3.6? SCMarker was packaged in R/3.5. We'll update SCMarker to R/3.6 ASAP.

commented

Dear authors,

I am trying to install the package but encountered the same problem as they did. I wonder if you could add a '}' on line 87 in HeatmapCluster.Rd file? It seems that a '}' is missing there.

Thank you for your attention!

commented

If you are running R on linux you can install the package by downloading it from source.

cd /tmp
git clone https://github.com/KChen-lab/SCMarker.git

Then in R type in this command:

library(devtools)
build("SCMarker")

This will produce the tarball you can then install in R with:

install.packages("SCMarker_2.0.tar.gz", repose=NULL, type="source")
library(SCMarker)
commented

Hi @Fang0828!

I am getting the same error as everyone. I have followed @dfermin's suggestion but get the following error when running the last two lines of code.

Warning in install.packages :
  package ‘SCMarker_2.0.tar.gz’ is not available for this version of R

My R version is 4.0.5. Any suggestions on how to install your package?

Thanks!

Best regards,

Hani

commented

FYI, I have tried to install on an older version of R (3.5.2), but still get the same error.

> install.packages("SCMarker_2.0.tar.gz",  type="source")
Warning in install.packages :
  package ‘SCMarker_2.0.tar.gz’ is not available (for R version 3.5.2)