* using log directory ‘/srv/hornik/tmp/CRAN_pretest/maxaltall.Rcheck’
* using R Under development (unstable) (2024-09-17 r87161)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘maxaltall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maxaltall’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Philip D. Kiser <pkiser@uci.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  AltAll (3:57, 8:44)
  FASTA (3:17)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Alec", "S."),
                      family = "Chu",
                      role = "aut"),
               person(given = c("Philip", "D."),
                      family = "Kiser",
                      role = c("aut", "cre"),
                      email = "pkiser@uci.edu"))
as necessary.

The Title field should be in title case. Current version is:
  ‘Generate FASTA-formatted Maximum Likelihood and ‘AltAll’ Sequences from IQ-TREE .state files’
In title case that is:
  ‘Generate FASTA-Formatted Maximum Likelihood and ‘altall’ Sequences from IQ-TREE .state Files’

The Description field should not start with the package name,
  'This package' or similar.
* 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 serialization versions ... OK
* checking whether package ‘maxaltall’ can be installed ... [2s/2s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] NOTE
max_altall: no visible global function definition for ‘:=’
max_altall: no visible binding for global variable ‘.SD’
max_altall: no visible binding for global variable ‘max2’
max_altall: no visible binding for global variable ‘Node’
max_altall: no visible binding for global variable ‘alt’
Undefined global functions or variables:
  .SD := Node alt max2
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* 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 examples ... NONE
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs