===============================
R CMD BUILD
===============================
* checking for file scLANE/DESCRIPTION ... OK
* preparing scLANE:
* 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 scLANE_0.99.99.tar.gz
===============================
BiocCheckGitClone('scLANE')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE
BiocVersion: 3.22
Package: scLANE
PackageVersion: 0.99.99
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE
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/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE.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 scLANE/DESCRIPTION ... OK
* checking extension type ... Package
* this is package scLANE version 0.99.99
* 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 scLANE can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* checking installed package size ... INFO
installed size is 19.3Mb
sub-directories of 1Mb or more:
data 1.6Mb
libs 17.3Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking build directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [15s/15s] 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 ... [6s/6s] 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 ... [95s/105s] ERROR
Running examples in scLANE-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sortObservations
> ### Title: Sort observations by sample ID and pseudotime.
> ### Aliases: sortObservations
>
> ### ** Examples
>
> data(sim_counts)
> data(sim_pseudotime)
> sorted_counts <- sortObservations(sim_counts,
+ pt.vec = sim_pseudotime$PT,
+ id.vec = sim_counts$subject
+ )
Loading required namespace: GenomeInfoDb
Failed with error: there is no package called GenomeInfoDb
Error in .requirePackage(package) :
unable to load required package GenomeInfoDb
Calls: sortObservations ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bootstrapRandomEffects 46.644 1.116 47.770
fitGLMM 5.504 0.349 5.854
enrichDynamicGenes 1.437 0.016 11.400
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [11s/11s]
[12s/12s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
2. Seurat:::as.Seurat.SingleCellExperiment(sim_counts)
3. SingleCellExperiment::altExpNames(x = x)
4. SingleCellExperiment::altExpNames(x = x)
5. SingleCellExperiment (local) .local(x, ...)
6. SingleCellExperiment:::.get_internal_names(...)
7. BiocGenerics::updateObject(x)
8. SingleCellExperiment::updateObject(x)
9. methods::callNextMethod()
10. SummarizedExperiment (local) .nextMethod(object = object)
11. BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
12. GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
13. BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
14. GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
15. BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
16. methods:::.extendsForS3(`<chr>`)
17. methods::extends(Class, maybe = FALSE)
18. methods::getClassDef(class1)
19. methods:::.requirePackage(package)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
* 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 ... [5s/5s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE.Rcheck/00check.log
for details.
===============================
BiocCheck('scLANE_0.99.99.tar.gz')
===============================
Installing scLANE
Package installed successfully
scLANE session metadata
sourceDir: /tmp/Rtmpf2FKni/file10f52477d2a95e/scLANE
BiocVersion: 3.22
Package: scLANE
PackageVersion: 0.99.99
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/616e9d0c6ae674c3dc4a949521c251a945fdc846/scLANE.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/Rtmpf2FKni/file10f52477d2a95e/scLANE
installDir: /tmp/Rtmpf2FKni/file10f5243363aa9c
isTarBall: TRUE
platform: unix
Running BiocCheck on scLANE
* 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
scLANE.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scLANE...
* 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 31
functions greater than 50 lines.
The longest 5 functions are:
marge2() (R/marge2.R): 1062 lines
...
biasCorrectGEE() (R/biasCorrectGEE.R): 189 lines
* Checking man page documentation...
Registered S3 method overwritten by 'gamlss':
method from
print.ri bit
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
plotClusteredGenes.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
plotClusteredGenes.Rd
* 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 shorter lines; 107 lines (1%) are > 80 characters long.
First few lines:
R/backward_sel_WIC.R#L82 wald_stat <- unname(stats::c ...
...
vignettes/scLANE.Rmd#L301 Lastly, we can perform pathway analysis ...
i NOTE: Consider multiples of 4 spaces for line indents; 19 lines (0%) are not.
First few lines:
R/embedGenes.R#L67 warning("'genes' is too small.Rec ...
...
vignettes/scLANE.Rmd#L40 install.packages("BiocManager") ...
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...
* 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 v1.45.18 results
0 ERRORS | 1 WARNINGS | i 6 NOTES
i See the scLANE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.