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R CMD BUILD
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* checking for file scGraphVerse/DESCRIPTION ... OK
* preparing scGraphVerse:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building scGraphVerse_0.99.9.tar.gz
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BiocCheckGitClone('scGraphVerse')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse
BiocVersion: 3.22
Package: scGraphVerse
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
check_results.log
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.45.12 results
1 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse.Rcheck
* using R version 4.5.1 (2025-06-13)
* 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
* using option --no-vignettes
* checking for file scGraphVerse/DESCRIPTION ... OK
* this is package scGraphVerse version 0.99.9
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 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 for future file timestamps ... 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/17s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking whether startup messages can be suppressed ... [16s/16s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
DOSE enrichplot
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [58s/57s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [48s/48s] ERROR
Running examples in scGraphVerse-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: community_similarity
> ### Title: Compare Community Assignments and Topological Properties
> ### Aliases: community_similarity
>
> ### ** Examples
>
> data(count_matrices)
> data(adj_truth)
> networks <- infer_networks(
+ count_matrices_list = count_matrices,
+ method = "GENIE3",
+ nCores = 1
+ )
> head(networks[[1]])
regulatoryGene targetGene weight
1 CD3E ARPC2 0.3480518
2 ARPC2 CD3E 0.2829467
3 ARPC3 CFL1 0.2814007
4 CFL1 ARPC3 0.2561004
5 CD74 ARPC3 0.2320403
6 CFL1 CD3D 0.2283077
>
> wadj_list <- generate_adjacency(networks)
> swadj_list <- symmetrize(wadj_list, weight_function = "mean")
>
> binary_listj <- cutoff_adjacency(
+ count_matrices = count_matrices,
+ weighted_adjm_list = swadj_list,
+ n = 2,
+ method = "GENIE3",
+ quantile_threshold = 0.95,
+ nCores = 1,
+ debug = TRUE
+ )
[Method: GENIE3] Matrix 1 Cutoff = 0.21716
[Method: GENIE3] Matrix 2 Cutoff = 0.26329
[Method: GENIE3] Matrix 3 Cutoff = 0.22931
> head(binary_listj[[1]])
ACTG1 ARPC2 ARPC3 CD3D CD3E CD74 CFL1 COX4I1 COX7C CXCR4
ACTG1 0 0 0 0 0 0 0 0 0 0
ARPC2 0 0 0 0 1 0 0 0 0 0
ARPC3 0 0 0 0 0 0 1 0 0 0
CD3D 0 0 0 0 0 0 0 0 0 0
CD3E 0 1 0 0 0 0 0 0 0 0
CD74 0 0 0 0 0 0 0 0 0 0
>
> consensus <- create_consensus(binary_listj, method = "vote")
> comm_cons <- community_path(consensus)
Detecting communities...
Warning in RColorBrewer::brewer.pal(ncommunities, "Set3") :
minimal value for n is 3, returning requested palette with 3 different levels
Running pathway enrichment...
> comm_truth <- community_path(adj_truth)
Detecting communities...
Running pathway enrichment...
>
> sim_score <- community_similarity(comm_truth, list(comm_cons))
Error in i_compare(comm1, comm2, method) :
At vendor/cigraph/src/community/community_misc.c:277 : Membership indices should be less than total number of vertices. Found member of cluster 10, but only 10 vertices. Invalid value
Calls: community_similarity ... .compare_communities -> <Anonymous> -> compare.membership -> i_compare
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
community_path 13.715 0.165 13.88
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [0s/0s]
[1s/0s] 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse.Rcheck/00check.log
for details.
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BiocCheck('scGraphVerse_0.99.9.tar.gz')
===============================
Installing scGraphVerse
Package installed successfully
scGraphVerse session metadata
sourceDir: /tmp/RtmpJHpUBa/file3467ce5c14e8a1/scGraphVerse
BiocVersion: 3.22
Package: scGraphVerse
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/68410d331aeaaa16e8a82fb66ea56169c351168c/scGraphVerse.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /tmp/RtmpJHpUBa/file3467ce5c14e8a1/scGraphVerse
installDir: /tmp/RtmpJHpUBa/file3467ce51e122dd
isTarBall: TRUE
platform: unix
Running BiocCheck on scGraphVerse
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scGraphVerse...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 44
functions greater than 50 lines.
The longest 5 functions are:
.jrf_onetarget() (R/JRF_internal.R): 272 lines
...
wlasso() (R/ZILGM_internal.R): 171 lines
* Checking man page documentation...
Registered S3 method overwritten by 'gplots':
method from
reorder.factor DescTools
Registered S3 method overwritten by 'fmsb':
method from
plot.roc spatstat.explore
Registered S3 methods overwritten by 'pROC':
method from
print.roc fmsb
plot.roc fmsb
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.12 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i See the scGraphVerse.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.