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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scGraphVerse.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scGraphVerse_0.99.19.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.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 ‘scGraphVerse/DESCRIPTION’ ... OK
* this is package ‘scGraphVerse’ version ‘0.99.19’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 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 ... NOTE
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        55.795  1.131  83.071
community_path            30.610  0.499  34.936
community_similarity      30.435  0.203  33.405
plot_community_comparison 30.354  0.154  35.573
compute_topology_metrics  29.735  0.124  32.614
compute_community_metrics 29.541  0.131  32.719
edge_mining               27.422  0.087  39.350
plotg                     25.181  0.035  31.988
plot_network_comparison   24.809  0.091  27.574
pscores                   24.167  0.170  29.695
create_consensus          24.149  0.104  24.409
compare_consensus         24.105  0.091  24.427
cutoff_adjacency          23.800  0.072  24.039
classify_edges            21.955  0.295  22.302
symmetrize                10.447  0.068  11.271
plotROC                    9.764  0.059  10.033
generate_adjacency         8.561  0.813   9.099
build_network_se           8.174  0.152   8.448
infer_networks             7.071  0.012   7.144
toy_counts                 7.038  0.008   7.252
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scGraphVerse
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘scGraphVerse’ ...
** this is package ‘scGraphVerse’ version ‘0.99.19’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c regTree.c -o regTree.o
regTree.c: In function ‘findBestSplit’:
regTree.c:232:15: warning: variable ‘lc’ set but not used [-Wunused-but-set-variable]
  232 |     int last, lc, nl, nr, npopl, npopr;
      |               ^~
regTree.c: In function ‘predictRegTree’:
regTree.c:418:19: warning: unused variable ‘cbestsplit’ [-Wunused-variable]
  418 |     int i, k, m, *cbestsplit, s;
      |                   ^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c regrf.c -o regrf.o
regrf.c: In function ‘regRF’:
regrf.c:71:30: warning: unused variable ‘nodexts’ [-Wunused-variable]
   71 |     int *in, *nind, *nodex, *nodexts;
      |                              ^~~~~~~
regrf.c:71:22: warning: variable ‘nodex’ set but not used [-Wunused-but-set-variable]
   71 |     int *in, *nind, *nodex, *nodexts;
      |                      ^~~~~
regrf.c:69:10: warning: variable ‘oobpair’ set but not used [-Wunused-but-set-variable]
   69 |     int *oobpair, varImp, localImp, *varUsed, kk;
      |          ^~~~~~~
regrf.c:67:61: warning: variable ‘nPerm’ set but not used [-Wunused-but-set-variable]
   67 |     int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm,
      |                                                             ^~~~~
regrf.c:67:31: warning: unused variable ‘jout’ [-Wunused-variable]
   67 |     int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm,
      |                               ^~~~
regrf.c:67:22: warning: unused variable ‘nOOB’ [-Wunused-variable]
   67 |     int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm,
      |                      ^~~~
regrf.c:67:15: warning: unused variable ‘mr’ [-Wunused-variable]
   67 |     int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm,
      |               ^~
regrf.c:65:36: warning: unused variable ‘ytree’ [-Wunused-variable]
   65 |     double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww;
      |                                    ^~~~~
regrf.c:65:30: warning: variable ‘ytr’ set but not used [-Wunused-but-set-variable]
   65 |     double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww;
      |                              ^~~
regrf.c:65:18: warning: variable ‘xtmp’ set but not used [-Wunused-but-set-variable]
   65 |     double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww;
      |                  ^~~~
regrf.c:63:58: warning: variable ‘resOOB’ set but not used [-Wunused-but-set-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |                                                          ^~~~~~
regrf.c:63:50: warning: unused variable ‘delta’ [-Wunused-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |                                                  ^~~~~
regrf.c:63:38: warning: unused variable ‘ooberrperm’ [-Wunused-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |                                      ^~~~~~~~~~
regrf.c:63:30: warning: variable ‘ooberr’ set but not used [-Wunused-but-set-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |                              ^~~~~~
regrf.c:63:18: warning: unused variable ‘resid’ [-Wunused-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |                  ^~~~~
regrf.c:63:12: warning: variable ‘errb’ set but not used [-Wunused-but-set-variable]
   63 |           *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB;
      |            ^~~~
regrf.c:62:53: warning: unused variable ‘r’ [-Wunused-variable]
   62 |     double errts = 0.0, averrb,  *meanYts, *varYts, r, *xrand,
      |                                                     ^
regrf.c:62:25: warning: variable ‘averrb’ set but not used [-Wunused-but-set-variable]
   62 |     double errts = 0.0, averrb,  *meanYts, *varYts, r, *xrand,
      |                         ^~~~~~
regrf.c:62:12: warning: unused variable ‘errts’ [-Wunused-variable]
   62 |     double errts = 0.0, averrb,  *meanYts, *varYts, r, *xrand,
      |            ^~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o scGraphVerse.so init.o regTree.o regrf.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-scGraphVerse/00new/scGraphVerse/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scGraphVerse)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scGraphVerse)
> 
> test_check("scGraphVerse")
[ FAIL 0 | WARN 2227 | SKIP 10 | PASS 492 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• Complex internal function tested via cutoff_adjacency (1):
  'test-utilities.R:288:5'
• KEGG requires internet and annotation packages (1):
  'test-community-topology.R:228:5'
• Reactome requires internet and annotation packages (1):
  'test-community-topology.R:245:5'
• Seurat object creation requires full Seurat setup (1):
  'test-network-inference.R:749:5'
• Seurat objects require actual Seurat setup (1): 'test-utilities.R:198:5'
• robinCompare parameter compatibility varies by version (2):
  'test-community-topology.R:160:5', 'test-community-topology.R:263:5'
• spinglass can be slow and unstable in tests (1):
  'test-community-topology.R:383:5'
• {pcalg} is not installed (2): 'test-network-inference.R:845:5',
  'test-network-inference.R:883:5'

[ FAIL 0 | WARN 2227 | SKIP 10 | PASS 492 ]
> 
> proc.time()
   user  system elapsed 
271.436   8.551 291.366