Cannot install from source and no smurf() function

[ferygood]

Hello,

I am having two troubles using SmuRF. (1) Cannot install from source: After downloading SMuRFv2.0.10.tar.gz, I faced skipping pax global extended headers installation problem.

(2) could not find function "smurf" I also tried using devtools::install_github() function to install smurf. It can be install but when I try to call smurf function, I get a error Error in smurf() : could not find function "smurf"

I am using RStudio and R 4.2 environment on macOS (Monterey)

Hope you can give me some suggestion and help. Thank you for your time!

[tyler5huang]

Hi this is due to a roxygen issue with package documentation, failed to install/read package correctly.

Please use the latest release of SMuRF: https://github.com/skandlab/SMuRF/releases/tag/SMuRFv2.0.11

[tyler5huang]

devtools::install_github("skandlab/SMuRF", subdir="smurf") Downloading GitHub repo skandlab/SMuRF@HEAD √ checking for file 'skandlab-SMuRF-73b03fc\smurf/DESCRIPTION' ...

• preparing 'smurf': (2.8s) √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'smurf/data/cds-hg38.rds'
• building 'smurf_2.0.tar.gz'

Installing package into ‘Documents/R/win-library/4.1’ (as ‘lib’ is unspecified)

• installing source package 'smurf' ... using staged installation R data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading * help installing help indices converting help for package 'smurf' finding HTML links ... done CDSannotation_indel html
  CDSannotation_snv html
  indelRFpredict html
  newcutoffs html
  parsevcf_allfeaturesall html
  read.vcf html
  save.files html
  smurf html
  snvRFpredict html
  building package indices testing if installed package can be loaded from temporary location arch - i386 arch - x64 testing if installed package can be loaded from final location ** arch - i386 arch - x64 ** testing if installed package keeps a record of temporary installation path
• DONE (smurf)

  library(smurf) smurf() [1] "SMuRFv2.0.11 (4th Jul 2022)" smurf(directory=NULL, mode=NULL, nthreads = -1, annotation=F, output.dir=NULL, parse.dir=NULL, snv.cutoff = 'default', indel.cutoff = 'default', build=NULL, change.build=F, find.build=F, t.label=NULL, re.tabIndex=F, check.packages=T, file.exclude=NULL)

[ferygood]

Thank you for your response! R CMD INSTALL SMuRFv2.0.11.tar.gz cannot install facing ERROR: cannot extract package from '/Users/yaochung41/Downloads/SMuRF-SMuRFv2.0.11.tar.gz'

However, I have successfully install and use the function by first cloning github and than use install.packages("SMuRF/smurf", repos=NULL, type="source"