##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scGraphVerse.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scGraphVerse_0.99.21.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scGraphVerse/DESCRIPTION’ ... OK
* this is package ‘scGraphVerse’ version ‘0.99.21’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... ERROR
Running examples in ‘scGraphVerse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stringdb_adjacency
> ### Title: Build Adjacency Matrices for Physical Interactions from STRING
> ###   (POST API)
> ### Aliases: stringdb_adjacency
> 
> ### ** Examples
> 
> data(toy_counts)
> genes <- selgene(
+     object = toy_counts[[1]],
+     top_n = 5,
+     cell_type = "T_cells",
+     cell_type_col = "CELL_TYPE",
+     remove_rib = TRUE,
+     remove_mt = TRUE,
+     assay = "counts"
+ )
Using SCE assay 'counts' (log-normalized).
Subsetted to 40 cells where CELL_TYPE = 'T_cells'.
Removed mitochondrial genes matching '^MT-'.
Removed ribosomal genes matching '^RP[SL]'.
Top 5 genes selected based on mean expression.
> 
> str_res <- stringdb_adjacency(
+     genes = genes,
+     species = 9606,
+     required_score = 900,
+     keep_all_genes = FALSE
+ )
Initializing STRINGdb...
Warning in open.connection(file, "rt") :
  cannot open URL 'https://string-db.org/api/tsv-no-header/version': HTTP status was '400 Bad Request'
Error in open.connection(file, "rt") : 
  cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
Calls: stringdb_adjacency ... <Anonymous> -> read.table -> open -> open.connection
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
plot_community_comparison 27.368  0.760  35.641
compute_topology_metrics  27.504  0.231  34.903
community_path            26.991  0.465  35.532
compute_community_metrics 27.214  0.114  33.671
community_similarity      27.048  0.252  34.617
edge_mining               27.047  0.138  33.267
plotg                     23.323  0.252  23.575
compare_consensus         23.113  0.192  23.305
pscores                   23.093  0.141  23.234
plot_network_comparison   22.731  0.431  23.162
create_consensus          22.335  0.042  22.381
cutoff_adjacency          22.116  0.120  22.238
classify_edges            19.962  0.249  20.210
plotROC                    8.908  0.333   9.200
generate_adjacency         7.960  0.799   8.288
build_network_se           7.334  0.097   7.432
infer_networks             6.469  0.050   6.521
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘case_study.Rmd’ using rmarkdown

Quitting from case_study.Rmd:234-265 [stringdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
---
Backtrace:
    ▆
 1. └─scGraphVerse::stringdb_adjacency(...)
 2.   └─STRINGdb::STRINGdb$new(...)
 3.     └─methods::new(def, ...)
 4.       ├─methods::initialize(value, ...)
 5.       └─methods::initialize(value, ...)
 6.         └─.Object$initialize(...)
 7.           └─utils::read.table(...)
 8.             ├─base::open(file, "rt")
 9.             └─base::open.connection(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'case_study.Rmd' failed with diagnostics:
cannot open the connection to 'https://string-db.org/api/tsv-no-header/version'
--- failed re-building ‘case_study.Rmd’

--- re-building ‘simulation_study.Rmd’ using rmarkdown
--- finished re-building ‘simulation_study.Rmd’

SUMMARY: processing the following file failed:
  ‘case_study.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scGraphVerse
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scGraphVerse’ ...
** this is package ‘scGraphVerse’ version ‘0.99.21’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/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;
      |                   ^~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/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,
      |            ^~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scGraphVerse.so init.o regTree.o regrf.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
216.257   9.195 224.494