===============================
R CMD BUILD
===============================
* checking for file ‘ClusterGVis/DESCRIPTION’ ... OK
* preparing ‘ClusterGVis’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* 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 ‘ClusterGVis_0.99.3.tar.gz’
===============================
BiocCheckGitClone('ClusterGVis')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis
→ BiocVersion: 3.22
→ Package: ClusterGVis
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis
→ 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 v1.45.18 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/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis.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 ‘ClusterGVis/DESCRIPTION’ ... OK
* this is package ‘ClusterGVis’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘ClusterGVis’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 1.2Mb
extdata 4.3Mb
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [23s/23s] 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 ... [5s/5s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [163s/163s] ERROR
Running examples in ‘ClusterGVis-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pre_pseudotime_matrix
> ### Title: Calculate and return a smoothed pseudotime matrix for the given
> ### gene list
> ### Aliases: pre_pseudotime_matrix
>
> ### ** Examples
>
>
> cds_subset <- readRDS(system.file('extdata','cds_subset.rds',
+ package = 'ClusterGVis'))
>
> genes <- sample(rownames(cds_subset), 20)
Loading required namespace: monocle3
Failed with error: ‘there is no package called ‘monocle3’’
Error in .requirePackage(package) :
unable to load required package ‘monocle3’
Calls: sample ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichCluster 142.000 2.310 144.342
getClusters 5.117 0.357 5.476
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/15s] 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis.Rcheck/00check.log’
for details.
===============================
BiocCheck('ClusterGVis_0.99.3.tar.gz')
===============================
── Installing ClusterGVis ──────────────────────────────────────────────────────
✔ Package installed successfully
── ClusterGVis session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmph0FX8E/file1763c61e30db58/ClusterGVis
→ BiocVersion: 3.22
→ Package: ClusterGVis
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/d64735d4cee1ddac739a7d801f8b894864c5f497/ClusterGVis.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmph0FX8E/file1763c61e30db58/ClusterGVis
→ installDir: /tmp/Rtmph0FX8E/file1763c6f686dec
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ClusterGVis ────────────────────────────────────────────
* 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 (12%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClusterGVis...
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
• visCluster() (R/4.visCluster.R): 1425 lines
• ...
• plot_pseudotime_heatmap2() (R/monocleHeatmap.R): 253 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...
i NOTE: Consider multiples of 4 spaces for line indents; 1710 lines (39%) are
not.
First few lines:
• R/1.getClusters.R#L39 # check datatype ...
• ...
• vignettes/vignette.Rmd#L122 cluster.order = c(1:9)) ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
! WARNING: The package already exists on CRAN. Packages submitted to
Bioconductor must be removed from CRAN before the next Bioconductor release.
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 4 NOTES
i See the ClusterGVis.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.