* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ucsfindustrydocs.Rcheck’
* using R Under development (unstable) (2025-04-19 r88162)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ucsfindustrydocs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ucsfindustrydocs’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [2s/2s] NOTE
Maintainer: ‘Rolando Rodriguez <rolando@ad.unc.edu>’

New submission

Non-FOSS package license (What license is it under?)

Possibly misspelled words in DESCRIPTION:
  UCSF (3:8)

DESCRIPTION fields with placeholder content:
  Description: more about what it does (maybe more than one line).
    continuation lines should be indented.
* 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 ... NOTE
Found the following hidden files and directories:
  .Rtestignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .Rtestignore
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ucsfindustrydocs’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
  Warning: ucsf_api.Rd:1: All text must be in a section
  Warning: ucsf_api.Rd:62: All text must be in a section
See ‘/srv/hornik/tmp/CRAN_pretest/ucsfindustrydocs.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  What license is it under?
Standardizable: FALSE
* 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: ucsf_api.Rd:1: All text must be in a section
prepare_Rd: ucsf_api.Rd:62: All text must be in a section
checkRd: (7) ucsf_api.Rd:14: Tag \strong is invalid in a \usage block
* checking Rd metadata ... WARNING
Rd files with duplicated name 'IndustryDocsSearch':
  ‘IndustryDocsSearch.Rd’ ‘ucsf_api.Rd’
Rd files with duplicated alias 'IndustryDocsSearch':
  ‘IndustryDocsSearch.Rd’ ‘ucsf_api.Rd’
* checking Rd line widths ... NOTE
Error: 14: Tag \strong not expected in code block
Execution halted
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘format_date’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'clean_query_text.Rd':
  ‘query’

Bad \usage lines found in Rd file 'ucsf_api.Rd':
  <unescaped bksl>strong{IndustryDocsSearch}

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [0s/0s] OK
* checking PDF version of manual ... [3s/3s] 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: 6 WARNINGs, 3 NOTEs