Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1918/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scGraphVerse 0.99.19 (landing page) Francesco Cecere
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scGraphVerse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scGraphVerse.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: scGraphVerse |
Version: 0.99.19 |
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_0.99.19.tar.gz |
StartedAt: 2025-10-18 04:23:10 -0400 (Sat, 18 Oct 2025) |
EndedAt: 2025-10-18 04:38:16 -0400 (Sat, 18 Oct 2025) |
EllapsedTime: 905.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scGraphVerse.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_0.99.19.tar.gz ### ############################################################################## ############################################################################## * 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 ‘0.99.19’ * 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: ‘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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed stringdb_adjacency 49.598 3.754 75.986 plot_community_comparison 27.169 1.063 36.246 community_path 27.037 0.468 34.953 community_similarity 27.090 0.253 34.342 compute_topology_metrics 26.581 0.206 34.382 edge_mining 25.934 0.149 34.018 compute_community_metrics 25.656 0.118 32.509 plotg 23.778 0.587 24.365 plot_network_comparison 23.034 0.956 23.991 pscores 22.651 0.391 23.042 compare_consensus 21.706 0.173 21.878 cutoff_adjacency 21.683 0.107 21.791 create_consensus 21.434 0.007 21.441 classify_edges 20.296 0.215 20.512 symmetrize 9.564 1.002 10.566 generate_adjacency 8.108 1.673 8.857 plotROC 8.998 0.306 9.258 build_network_se 7.384 0.115 7.501 toy_counts 6.632 0.071 6.702 infer_networks 6.472 0.051 6.523 * 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 Error: processing vignette 'case_study.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘case_study.Rmd’ --- re-building ‘simulation_study.Rmd’ using rmarkdown Error: processing vignette 'simulation_study.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘simulation_study.Rmd’ SUMMARY: processing the following files failed: ‘case_study.Rmd’ ‘simulation_study.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck/00check.log’ for details.
scGraphVerse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scGraphVerse ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scGraphVerse’ ... ** this is package ‘scGraphVerse’ version ‘0.99.19’ ** 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)
scGraphVerse.Rcheck/tests/testthat.Rout
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 201.533 10.545 211.154
scGraphVerse.Rcheck/scGraphVerse-Ex.timings
name | user | system | elapsed | |
PCzinb | 1.294 | 0.006 | 1.302 | |
build_network_se | 7.384 | 0.115 | 7.501 | |
classify_edges | 20.296 | 0.215 | 20.512 | |
community_path | 27.037 | 0.468 | 34.953 | |
community_similarity | 27.090 | 0.253 | 34.342 | |
compare_consensus | 21.706 | 0.173 | 21.878 | |
compute_community_metrics | 25.656 | 0.118 | 32.509 | |
compute_topology_metrics | 26.581 | 0.206 | 34.382 | |
create_consensus | 21.434 | 0.007 | 21.441 | |
create_mae | 0.235 | 0.000 | 0.235 | |
cutoff_adjacency | 21.683 | 0.107 | 21.791 | |
download_Atlas | 0.071 | 0.006 | 1.418 | |
earlyj | 0.207 | 0.000 | 0.207 | |
edge_mining | 25.934 | 0.149 | 34.018 | |
generate_adjacency | 8.108 | 1.673 | 8.857 | |
infer_networks | 6.472 | 0.051 | 6.523 | |
init_py | 0.384 | 0.110 | 0.433 | |
plotROC | 8.998 | 0.306 | 9.258 | |
plot_community_comparison | 27.169 | 1.063 | 36.246 | |
plot_network_comparison | 23.034 | 0.956 | 23.991 | |
plotg | 23.778 | 0.587 | 24.365 | |
pscores | 22.651 | 0.391 | 23.042 | |
selgene | 0.018 | 0.000 | 0.018 | |
stringdb_adjacency | 49.598 | 3.754 | 75.986 | |
symmetrize | 9.564 | 1.002 | 10.566 | |
toy_adj_matrix | 0.006 | 0.000 | 0.005 | |
toy_counts | 6.632 | 0.071 | 6.702 | |
zinb_simdata | 0.007 | 0.003 | 0.011 | |