* using log directory ‘/srv/hornik/tmp/CRAN_pretest/pctax.Rcheck’
* using R Under development (unstable) (2024-11-29 r87393)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘pctax/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pctax’ version ‘0.1.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/10s] NOTE
Maintainer: ‘Chen Peng <pengchen2001@zju.edu.cn>’

Found the following (possibly) invalid URLs:
  URL: https://doi.org/waiting
    From: README.md
    Status: 400
    Message: Bad Request
  URL: https://zhuanlan.zhihu.com/p/25501130
    From: man/b_analyse.Rd
    Status: 403
    Message: Forbidden
* 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 ‘pctax’ can be installed ... [5s/5s] 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 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 ... [9s/9s] NOTE
convert_taxon_name: no visible binding for global variable
  ‘all_sp_la_zh_name’
save_all_sp_la_zh_name: no visible binding for global variable
  ‘all_sp_data’
Undefined global functions or variables:
  all_sp_data all_sp_la_zh_name
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.a_res.Rd: group_box, my_lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] ERROR
Running examples in ‘pctax-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geo_sim
> ### Title: Lm for sample similarity and geographical distance
> ### Aliases: geo_sim
> 
> ### ** Examples
> 
> if (requireNamespace("NST") && requireNamespace("geosphere")) {
+   library(ggplot2)
+   data(otutab, package = "pcutils")
+   metadata[, c("lat", "long")] -> geo
+   geo_sim(otutab, geo) -> geo_res
+   pcutils::my_lm(geo_res[4], "dis.geo", geo_res)
+ }
Loading required namespace: NST
Loading required namespace: geosphere
Error in lib_ps("ggpmisc", library = FALSE) : 
  exit, because some packages need to be installed:
1. ggpmisc
Calls: <Anonymous> -> lib_ps
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 NOTEs