* using log directory ‘/srv/hornik/tmp/CRAN_pretest/UCSCXenaTools.Rcheck’
* using R Under development (unstable) (2024-08-28 r87070)
* 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 ‘UCSCXenaTools/DESCRIPTION’ ... OK
* this is package ‘UCSCXenaTools’ version ‘1.5.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/8s] NOTE
Maintainer: ‘Shixiang Wang <w_shixiang@163.com>’

Found the following (possibly) invalid URLs:
  URL: https://singlecellnew.xenahubs.net/
    From: inst/doc/USCSXenaTools.html
          README.md
    Status: Error
    Message: Could not resolve host: singlecellnew.xenahubs.net
* 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 ‘UCSCXenaTools’ can be installed ... [3s/3s] 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 ... [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 whether startup messages can be suppressed ... [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 ... [4s/4s] 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 ... WARNING
Undocumented code objects:
  ‘.p_all_cohorts’ ‘.p_all_datasets’ ‘.p_all_datasets_n’
  ‘.p_all_field_metadata’ ‘.p_cohort_samples’ ‘.p_cohort_summary’
  ‘.p_dataset_fetch’ ‘.p_dataset_field’ ‘.p_dataset_field_examples’
  ‘.p_dataset_field_n’ ‘.p_dataset_gene_probe_avg’
  ‘.p_dataset_gene_probes_values’ ‘.p_dataset_list’
  ‘.p_dataset_metadata’ ‘.p_dataset_probe_signature’
  ‘.p_dataset_probe_values’ ‘.p_dataset_samples’
  ‘.p_dataset_samples_ndense_matrix’ ‘.p_dataset_sources’
  ‘.p_dataset_status’ ‘.p_datasets_null_rows’ ‘.p_feature_list’
  ‘.p_field_codes’ ‘.p_field_metadata’ ‘.p_gene_transcripts’
  ‘.p_match_fields’ ‘.p_probe_count’ ‘.p_probemap_list’
  ‘.p_ref_gene_exons’ ‘.p_ref_gene_position’ ‘.p_ref_gene_range’
  ‘.p_segment_data_examples’ ‘.p_segmented_data_range’ ‘.p_sparse_data’
  ‘.p_sparse_data_examples’ ‘.p_sparse_data_match_field’
  ‘.p_sparse_data_match_field_slow’
  ‘.p_sparse_data_match_partial_field’ ‘.p_sparse_data_range’
  ‘.p_transcript_expression’ ‘.xq_all_cohorts’ ‘.xq_all_datasets’
  ‘.xq_all_datasets_n’ ‘.xq_all_field_metadata’ ‘.xq_cohort_samples’
  ‘.xq_cohort_summary’ ‘.xq_dataset_fetch’ ‘.xq_dataset_field’
  ‘.xq_dataset_field_examples’ ‘.xq_dataset_field_n’
  ‘.xq_dataset_gene_probe_avg’ ‘.xq_dataset_gene_probes_values’
  ‘.xq_dataset_list’ ‘.xq_dataset_metadata’
  ‘.xq_dataset_probe_signature’ ‘.xq_dataset_probe_values’
  ‘.xq_dataset_samples’ ‘.xq_dataset_samples_ndense_matrix’
  ‘.xq_dataset_sources’ ‘.xq_dataset_status’ ‘.xq_datasets_null_rows’
  ‘.xq_feature_list’ ‘.xq_field_codes’ ‘.xq_field_metadata’
  ‘.xq_gene_transcripts’ ‘.xq_match_fields’ ‘.xq_probe_count’
  ‘.xq_probemap_list’ ‘.xq_ref_gene_exons’ ‘.xq_ref_gene_position’
  ‘.xq_ref_gene_range’ ‘.xq_segment_data_examples’
  ‘.xq_segmented_data_range’ ‘.xq_sparse_data’
  ‘.xq_sparse_data_examples’ ‘.xq_sparse_data_match_field’
  ‘.xq_sparse_data_match_field_slow’
  ‘.xq_sparse_data_match_partial_field’ ‘.xq_sparse_data_range’
  ‘.xq_transcript_expression’
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 ... 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 ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/13s] 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: 1 WARNING, 1 NOTE