===============================
R CMD BUILD
===============================
* 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_0.99.18.tar.gz
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BiocCheckGitClone('scGraphVerse')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/scGraphVerse
BiocVersion: 3.22
Package: scGraphVerse
PackageVersion: 0.99.18
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/scGraphVerse.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/scGraphVerse
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.45.20 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/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
* using option --no-vignettes
* checking for file scGraphVerse/DESCRIPTION ... OK
* this is package scGraphVerse version 0.99.18
* 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 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: doRNG
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 ... [32s/32s] 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 ... [413s/483s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
stringdb_adjacency 42.456 1.634 67.722
compute_topology_metrics 25.213 0.370 31.893
community_path 25.113 0.371 33.215
plot_community_comparison 25.198 0.192 33.057
community_similarity 25.204 0.107 31.637
compute_community_metrics 24.771 0.106 31.273
edge_mining 23.301 0.179 34.497
compare_consensus 20.787 0.138 20.925
create_consensus 20.498 0.405 20.906
plotg 20.866 0.030 20.896
plot_network_comparison 20.484 0.102 20.585
pscores 20.413 0.110 20.522
cutoff_adjacency 20.242 0.149 20.391
classify_edges 18.715 0.195 18.911
plotROC 8.590 0.001 8.591
symmetrize 8.163 0.053 8.216
build_network_se 7.407 0.125 7.531
generate_adjacency 7.186 0.037 7.223
infer_networks 6.383 0.002 6.385
toy_counts 6.300 0.006 6.306
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [184s/183s]
[184s/184s] 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/scGraphVerse.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scGraphVerse_0.99.18.tar.gz')
===============================
Installing scGraphVerse
Package installed successfully
scGraphVerse session metadata
sourceDir: /tmp/RtmpqNTVmO/file21f7805c1b9c94/scGraphVerse
BiocVersion: 3.22
Package: scGraphVerse
PackageVersion: 0.99.18
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3820/44e7369dabf306b87de451e8df3d157e280a0ebc/scGraphVerse.BiocCheck
BiocCheckVersion: 1.45.20
sourceDir: /tmp/RtmpqNTVmO/file21f7805c1b9c94/scGraphVerse
installDir: /tmp/RtmpqNTVmO/file21f78075acc9a7
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 (30%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* 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): 176 lines
* Checking man page documentation...
* 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 v1.45.20 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i See the scGraphVerse.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.