##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scGraphVerse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scGraphVerse_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/scGraphVerse.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scGraphVerse/DESCRIPTION’ ... OK
* this is package ‘scGraphVerse’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘scGraphVerse’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  classify_edges.Rd: SummarizedExperiment-class
  community_path.Rd: SummarizedExperiment-class
  compare_consensus.Rd: SummarizedExperiment-class
  create_consensus.Rd: SummarizedExperiment-class
  cutoff_adjacency.Rd: MultiAssayExperiment-class,
    SummarizedExperiment-class
  earlyj.Rd: MultiAssayExperiment-class
  edge_mining.Rd: SummarizedExperiment-class
  generate_adjacency.Rd: SummarizedExperiment-class
  infer_networks.Rd: MultiAssayExperiment-class
  plotROC.Rd: SummarizedExperiment-class
  plotg.Rd: SummarizedExperiment-class
  pscores.Rd: SummarizedExperiment-class
  selgene.Rd: SingleCellExperiment-class
  symmetrize.Rd: SummarizedExperiment-class
  toy_counts.Rd: MultiAssayExperiment-class
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
stringdb_adjacency        56.759  1.934  85.121
plot_community_comparison 27.854  0.630  36.700
community_path            26.819  0.772  35.958
community_similarity      26.297  0.510  33.442
compute_community_metrics 26.033  0.516  33.073
edge_mining               24.738  0.648  32.284
compute_topology_metrics  24.515  0.448  36.230
plot_network_comparison   21.753  0.286  22.169
plotg                     21.626  0.309  22.041
pscores                   20.998  0.313  21.445
create_consensus          20.107  0.249  20.531
compare_consensus         20.097  0.233  20.511
cutoff_adjacency          20.057  0.246  20.408
classify_edges            17.367  0.147  17.603
symmetrize                 8.701  0.745   9.539
plotROC                    8.069  0.182   8.249
generate_adjacency         6.698  0.391   7.135
build_network_se           6.158  0.081   6.275
infer_networks             5.274  0.117   5.418
toy_counts                 5.097  0.217   5.354
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/scGraphVerse.Rcheck/00check.log’
for details.