* using log directory ‘/srv/hornik/tmp/CRAN/scaper.Rcheck’
* using R Under development (unstable) (2023-10-15 r85333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (15)
    GNU Fortran (Debian 13.2.0-4) 13.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘scaper/DESCRIPTION’ ... OK
* this is package ‘scaper’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Azka Javaid <azka.javaid.gr@dartmouth.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  CytoSig (9:227, 9:378)
  Cytokine (2:42, 9:60)
  Jiang (9:412)
  Reactome (9:243, 9:467)
  SCAPER (9:18)
  VAM (9:314, 9:559)
  al (9:421, 9:515)
  cytokine (9:136)
  et (9:512)
  scRNA (9:361)
  transcriptomics (2:20, 9:38)

The Title field should be in title case. Current version is:
‘Single cell transcriptomics-level Cytokine Activity Prediction and Estimation’
In title case that is:
‘Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scaper’ can be installed ... [9s/9s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] NOTE
genesetCytoSig: no visible global function definition for ‘read.csv’
genesetCytoSig: no visible global function definition for ‘desc’
genesetCytoSig: no visible binding for global variable ‘Value’
genesetCytoSig: no visible binding for global variable ‘Gene’
genesetCytoSig: no visible binding for global variable ‘cytokine’
genesetReactome: no visible binding for global variable
  ‘Ligand.ApprovedSymbol’
genesetReactome: no visible binding for global variable
  ‘Receptor.ApprovedSymbol’
genesetReactome: no visible binding for global variable ‘cytokine’
scape: no visible binding for global variable ‘weight’
scape: no visible global function definition for ‘desc’
scapeForSeurat: no visible binding for global variable ‘weight’
scapeForSeurat: no visible global function definition for ‘desc’
scapeForSeurat: no visible global function definition for
  ‘CreateAssayObject’
Undefined global functions or variables:
  CreateAssayObject Gene Ligand.ApprovedSymbol Receptor.ApprovedSymbol
  Value cytokine desc read.csv weight
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'genesetCytoSig.Rd':
  \examples lines wider than 100 characters:
     genesetCytoSig(cytokine.eval = "IL6", file.name = system.file("extdata", "IL6_output.csv", package = "scaper")) %>% head(10)
     genesetCytoSig(cytokine.eval = c("IL4", "IL6"), file.name = c(system.file("extdata", "IL4_output.csv", package = "scaper"), 

Rd file 'genesetReactome.Rd':
  \examples lines wider than 100 characters:
     genesetReactome(cytokine.eval = "IL6", file.name = system.file("extdata", "IL6_Interleukin6_signaling.xml", 
     genesetReactome(cytokine.eval = c("IL4", "IL6"), file.name = c(system.file("extdata", "IL4_Interleukin_18_signaling.xml", package = "sc ... [TRUNCATED]
     system.file("extdata", "IL6_Interleukin6_signaling.xml", package = "scaper"))) %>% dplyr::arrange(gene) %>% head(10)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    576Kb    344Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [12s/12s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs