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 12:05 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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: /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_0.99.19.tar.gz |
StartedAt: 2025-10-18 01:16:55 -0400 (Sat, 18 Oct 2025) |
EndedAt: 2025-10-18 01:34:08 -0400 (Sat, 18 Oct 2025) |
EllapsedTime: 1033.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scGraphVerse.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_0.99.19.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 Monterey 12.7.6 * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 ... 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 57.867 1.984 82.862 plot_community_comparison 28.051 0.841 37.826 community_path 26.922 0.787 35.139 compute_topology_metrics 26.411 0.637 33.874 edge_mining 25.233 0.939 32.870 compute_community_metrics 25.573 0.539 32.996 community_similarity 25.301 0.522 32.713 plot_network_comparison 22.168 0.276 22.650 plotg 21.869 0.298 22.366 pscores 20.921 0.269 21.338 create_consensus 20.684 0.276 21.110 compare_consensus 20.597 0.258 20.986 cutoff_adjacency 20.323 0.303 20.794 classify_edges 18.076 0.165 18.388 symmetrize 8.848 0.786 9.731 plotROC 8.046 0.202 8.268 generate_adjacency 6.751 0.408 7.205 build_network_se 6.218 0.100 6.398 infer_networks 5.371 0.144 5.574 toy_counts 5.239 0.228 5.529 download_Atlas 0.041 0.008 7.823 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/scGraphVerse.Rcheck/00check.log’ for details.
scGraphVerse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scGraphVerse ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘scGraphVerse’ ... ** this is package ‘scGraphVerse’ version ‘0.99.19’ ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c regTree.c -o regTree.o regTree.c:232:15: warning: variable 'lc' set but not used [-Wunused-but-set-variable] int last, lc, nl, nr, npopl, npopr; ^ regTree.c:418:19: warning: unused variable 'cbestsplit' [-Wunused-variable] int i, k, m, *cbestsplit, s; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c regrf.c -o regrf.o regrf.c:62:53: warning: unused variable 'r' [-Wunused-variable] double errts = 0.0, averrb, *meanYts, *varYts, r, *xrand, ^ regrf.c:62:25: warning: variable 'averrb' set but not used [-Wunused-but-set-variable] double errts = 0.0, averrb, *meanYts, *varYts, r, *xrand, ^ regrf.c:63:23: warning: variable 'ooberr' set but not used [-Wunused-but-set-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:65:36: warning: unused variable 'ytree' [-Wunused-variable] double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww; ^ regrf.c:67:61: warning: variable 'nPerm' set but not used [-Wunused-but-set-variable] int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm, ^ regrf.c:63:11: warning: unused variable 'resid' [-Wunused-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:71:22: warning: variable 'nodex' set but not used [-Wunused-but-set-variable] int *in, *nind, *nodex, *nodexts; ^ regrf.c:71:30: warning: unused variable 'nodexts' [-Wunused-variable] int *in, *nind, *nodex, *nodexts; ^ regrf.c:63:5: warning: variable 'errb' set but not used [-Wunused-but-set-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:67:31: warning: unused variable 'jout' [-Wunused-variable] int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm, ^ regrf.c:63:51: warning: variable 'resOOB' set but not used [-Wunused-but-set-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:63:43: warning: unused variable 'delta' [-Wunused-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:63:31: warning: unused variable 'ooberrperm' [-Wunused-variable] *errb, resid=0.0, *ooberr, ooberrperm, delta, *resOOB; ^ regrf.c:62:12: warning: unused variable 'errts' [-Wunused-variable] double errts = 0.0, averrb, *meanYts, *varYts, r, *xrand, ^ regrf.c:65:30: warning: variable 'ytr' set but not used [-Wunused-but-set-variable] double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww; ^ regrf.c:67:15: warning: unused variable 'mr' [-Wunused-variable] int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm, ^ regrf.c:69:10: warning: variable 'oobpair' set but not used [-Wunused-but-set-variable] int *oobpair, varImp, localImp, *varUsed, kk; ^ regrf.c:65:18: warning: variable 'xtmp' set but not used [-Wunused-but-set-variable] double *yb, *xtmp, *xb, *ytr, *ytree, *tgini, *meanY, *varY, *ww; ^ regrf.c:67:22: warning: unused variable 'nOOB' [-Wunused-variable] int k, m, mr, n, nOOB, j, jout, idx, ntest, last, ktmp, nPerm, ^ 19 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scGraphVerse.so init.o regTree.o regrf.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 3251 | SKIP 8 | PASS 495 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • 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' [ FAIL 0 | WARN 3251 | SKIP 8 | PASS 495 ] > > proc.time() user system elapsed 287.636 8.210 297.808
scGraphVerse.Rcheck/scGraphVerse-Ex.timings
name | user | system | elapsed | |
PCzinb | 1.131 | 0.033 | 1.174 | |
build_network_se | 6.218 | 0.100 | 6.398 | |
classify_edges | 18.076 | 0.165 | 18.388 | |
community_path | 26.922 | 0.787 | 35.139 | |
community_similarity | 25.301 | 0.522 | 32.713 | |
compare_consensus | 20.597 | 0.258 | 20.986 | |
compute_community_metrics | 25.573 | 0.539 | 32.996 | |
compute_topology_metrics | 26.411 | 0.637 | 33.874 | |
create_consensus | 20.684 | 0.276 | 21.110 | |
create_mae | 0.302 | 0.007 | 0.310 | |
cutoff_adjacency | 20.323 | 0.303 | 20.794 | |
download_Atlas | 0.041 | 0.008 | 7.823 | |
earlyj | 0.245 | 0.005 | 0.250 | |
edge_mining | 25.233 | 0.939 | 32.870 | |
generate_adjacency | 6.751 | 0.408 | 7.205 | |
infer_networks | 5.371 | 0.144 | 5.574 | |
init_py | 0.765 | 0.367 | 1.194 | |
plotROC | 8.046 | 0.202 | 8.268 | |
plot_community_comparison | 28.051 | 0.841 | 37.826 | |
plot_network_comparison | 22.168 | 0.276 | 22.650 | |
plotg | 21.869 | 0.298 | 22.366 | |
pscores | 20.921 | 0.269 | 21.338 | |
selgene | 0.025 | 0.003 | 0.029 | |
stringdb_adjacency | 57.867 | 1.984 | 82.862 | |
symmetrize | 8.848 | 0.786 | 9.731 | |
toy_adj_matrix | 0.005 | 0.002 | 0.008 | |
toy_counts | 5.239 | 0.228 | 5.529 | |
zinb_simdata | 0.008 | 0.003 | 0.011 | |