* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mappeR.Rcheck’
* using R Under development (unstable) (2024-09-28 r87201)
* 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 ‘mappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mappeR’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘George Clare Kennedy <george-clarekennedy@uiowa.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Carlsson (6:34)
  Cytoscape (10:11)
  Mémoli (6:23)
  TDA (3:32)
  igraph (9:30)

Found the following (possibly) invalid URLs:
  URL: http://cran.r-project.org/bin/windows/Rtools/
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://arxiv.org/pdf/1901.07410.pdf (moved to http://arxiv.org/pdf/1901.07410)
    From: README.md
    Status: 301
    Message: Moved Permanently
Canonical CRAN.R-project.org URLs use https.
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

The Description field contains
  free \href{https://cytoscape.org/}{here}) for further analysis.
Please enclose URLs in angle brackets (<...>).
The Description field contains
  \doi{doi:10.2312/SPBG/SPBG07/091-100}, along with other tools for
Please write DOIs as <doi:prefix/suffix>.
* 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 ‘mappeR’ can be installed ... [4s/4s] 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK
* 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 ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [3s/3s] OK
  Running ‘testthat.R’ [3s/3s]
* checking PDF version of manual ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> x_j = \displaystyle \argmin 
                                       _j\sum _{i}\text {dist}(x_i, x_j)
l.88 ...e\argmin_j\sum_{i}\text{dist}(x_i, x_j)}{}
                                                   A smaller value indicates...
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘mappeR-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs