##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqArchRplus_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqArchRplus.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqArchRplus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqArchRplus’ version ‘1.10.0’
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqArchRplus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'generate_all_plots.Rd':
  ‘[CAGEr]{clusterCTSS}’

Non-topic package-anchored link(s) in Rd file 'handle_tc_from_cage.Rd':
  ‘[CAGEr]{tagClusters}’

Non-topic package-anchored link(s) in Rd file 'per_cluster_annotations.Rd':
  ‘[CAGEr]{tagClusters}’

Non-topic package-anchored link(s) in Rd file 'per_cluster_go_term_enrichments.Rd':
  ‘[CAGEr]{tagClusters}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  seqArchRplus.Rd: prepare_data_from_FASTA, get_one_hot_encoded_seqs,
    plot_arch_for_clusters, plot_ggseqlogo_of_seqs, viz_bas_vec,
    viz_seqs_acgt_mat, viz_pwm
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
generate_all_plots              54.832  1.317  67.103
per_cluster_go_term_enrichments 53.644  0.675  60.563
curate_clusters                 14.175  0.331  15.870
per_cluster_annotations         11.544  0.020  12.411
plot_motif_heatmaps2             7.507  0.211   9.009
per_cluster_seqlogos             3.672  0.031   5.073
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/seqArchRplus.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL seqArchRplus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘seqArchRplus’ ...
** this is package ‘seqArchRplus’ version ‘1.10.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'seqArchRplus' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'seqArchRplus' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (seqArchRplus)