===============================
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_0.99.7.tar.gz’
===============================
BiocCheckGitClone('scLANE')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/817817515c1e1f48a0c8344121af6b5d54d73925/scLANE
→ BiocVersion: 3.22
→ Package: scLANE
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/817817515c1e1f48a0c8344121af6b5d54d73925/scLANE.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/817817515c1e1f48a0c8344121af6b5d54d73925/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 for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.12 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/3705/817817515c1e1f48a0c8344121af6b5d54d73925/scLANE.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 ‘scLANE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scLANE’ version ‘0.99.7’
* 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 ... 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 ... [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 ... [16s/16s] NOTE
biasCorrectGEE: no visible binding for global variable ‘subject’
biasCorrectGEE: no visible binding for global variable ‘r_hat’
bootstrapRandomEffects : simFunction: no visible binding for global
variable ‘.’
bootstrapRandomEffects: no visible binding for global variable
‘subject’
bootstrapRandomEffects: no visible binding for global variable ‘b’
bootstrapRandomEffects: no visible binding for global variable ‘term’
bootstrapRandomEffects: no visible binding for global variable ‘effect’
chooseCandidateGenes: no visible binding for global variable ‘gene’
chooseCandidateGenes: no visible binding for global variable ‘mu’
chooseCandidateGenes: no visible binding for global variable ‘sigma’
chooseCandidateGenes: no visible binding for global variable ‘lambda’
chooseCandidateGenes: no visible binding for global variable
‘mean_rank’
clusterGenes: no visible binding for global variable ‘.’
embedGenes: no visible binding for global variable ‘leiden’
enrichDynamicGenes: no visible binding for global variable ‘Lineage’
enrichDynamicGenes: no visible binding for global variable
‘Gene_Dynamic_Lineage’
enrichDynamicGenes: no visible binding for global variable
‘Gene_Dynamic_Overall’
enrichDynamicGenes: no visible binding for global variable ‘Test_Stat’
enrichDynamicGenes: no visible binding for global variable ‘Gene’
fitGLMM: no visible binding for global variable ‘subject’
geneProgramDrivers: no visible binding for global variable ‘g’
geneProgramDrivers: no visible binding for global variable ‘pvalue’
geneProgramDrivers: no visible binding for global variable ‘corr’
geneProgramDrivers: no visible binding for global variable ‘pvalue_adj’
geneProgramSignificance: no visible binding for global variable
‘P_Value’
geneProgramSignificance: no visible binding for global variable
‘LRT_Stat’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘scLANE_pred_link’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘scLANE_se_link’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘rna’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘scLANE_pred’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘scLANE_ci_ll’
getFittedValues : <anonymous> : <anonymous>: no visible binding for
global variable ‘scLANE_ci_ul’
getFittedValues : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable ‘size_factor’
getFittedValues: no visible binding for global variable ‘cell’
getFittedValues: no visible binding for global variable ‘subj_id’
getFittedValues: no visible binding for global variable ‘lineage’
getFittedValues: no visible binding for global variable ‘gene’
getKnotDist: no visible binding for global variable ‘knot’
getResultsDE: no visible binding for global variable ‘Test_Stat’
getResultsDE: no visible binding for global variable ‘P_Val’
getResultsDE: no visible binding for global variable ‘P_Val_Adj’
getResultsDE: no visible binding for global variable ‘Gene’
getResultsDE: no visible binding for global variable
‘Gene_Dynamic_Lineage’
getResultsDE: no visible binding for global variable ‘Lineage’
plotClusteredGenes : <anonymous>: no visible binding for global
variable ‘FITTED’
plotClusteredGenes: no visible binding for global variable ‘Cluster’
plotClusteredGenes: no visible binding for global variable ‘CLUSTER’
plotModelCoefs: no visible binding for global variable ‘cell’
plotModelCoefs: no visible binding for global variable ‘rna_log1p’
plotModelCoefs: no visible binding for global variable
‘scLANE_pred_log1p’
plotModelCoefs: no visible binding for global variable
‘scLANE_ci_ll_log1p’
plotModelCoefs: no visible binding for global variable
‘scLANE_ci_ul_log1p’
plotModelCoefs: no visible binding for global variable ‘rna’
plotModelCoefs: no visible binding for global variable ‘scLANE_pred’
plotModelCoefs: no visible binding for global variable ‘scLANE_ci_ll’
plotModelCoefs: no visible binding for global variable ‘scLANE_ci_ul’
plotModelCoefs: no visible binding for global variable ‘knot’
plotModelCoefs: no visible binding for global variable ‘Breakpoint’
plotModelCoefs: no visible binding for global variable ‘Breakpoint_Lag’
plotModelCoefs: no visible binding for global variable
‘Breakpoint_Lead’
plotModelCoefs: no visible binding for global variable ‘Interval’
plotModelCoefs: no visible binding for global variable ‘Coef’
plotModelCoefs: no visible binding for global variable ‘.’
plotModels : <anonymous>: no visible binding for global variable ‘ID’
plotModels : <anonymous>: no visible binding for global variable ‘CELL’
plotModels : <anonymous>: no visible binding for global variable
‘LINEAGE’
plotModels : <anonymous>: no visible binding for global variable
‘COUNT’
plotModels : <anonymous>: no visible binding for global variable ‘PT’
plotModels : <anonymous>: no visible binding for global variable
‘CELL_OFFSET’
plotModels : <anonymous>: no visible binding for global variable
‘MODEL’
plotModels: no visible binding for global variable ‘MODEL’
plotModels: no visible binding for global variable ‘RESPONSE’
plotModels: no visible binding for global variable ‘SE’
plotModels: no visible binding for global variable ‘COUNT’
plotModels: no visible binding for global variable ‘CELL_OFFSET’
plotModels: no visible binding for global variable ‘PRED’
plotModels: no visible binding for global variable ‘CI_LL’
plotModels: no visible binding for global variable ‘CI_UL’
plotModels: no visible binding for global variable ‘LINEAGE’
plotModels: no visible binding for global variable ‘PT’
plotModels: no visible binding for global variable ‘ID’
pullMARGESummary: no visible binding for global variable ‘fit’
pullMARGESummary: no visible binding for global variable ‘se.fit’
pullNullSummary: no visible binding for global variable ‘fit’
pullNullSummary: no visible binding for global variable ‘se.fit’
sortGenesHeatmap : <anonymous>: no visible binding for global variable
‘mRNA’
sortGenesHeatmap : <anonymous>: no visible binding for global variable
‘gene’
sortGenesHeatmap : <anonymous>: no visible binding for global variable
‘pseudotime’
sortGenesHeatmap: no visible binding for global variable ‘gene’
sortGenesHeatmap: no visible binding for global variable ‘pseudotime’
sortGenesHeatmap: no visible binding for global variable ‘mu’
sortObservations: no visible binding for global variable ‘pt’
sortObservations: no visible binding for global variable ‘ID’
sortObservations: no visible binding for global variable ‘PT’
summarizeModel: no visible binding for global variable ‘.’
summarizeModel : <anonymous>: no visible binding for global variable
‘subject’
testDynamic: no visible binding for global variable ‘i’
testDynamic : <anonymous>: no visible binding for global variable ‘i’
testSlope: no visible binding for global variable ‘Test_Stat’
testSlope: no visible binding for global variable ‘P_Val’
testSlope: no visible binding for global variable ‘Gene’
testSlope: no visible binding for global variable ‘Breakpoint’
testSlope: no visible binding for global variable ‘P_Val_Adj’
testSlope: no visible binding for global variable ‘Lineage’
testSlope: no visible binding for global variable
‘Gene_Dynamic_Lineage_Slope’
testSlope: no visible binding for global variable
‘Gene_Dynamic_Lineage’
Undefined global functions or variables:
. Breakpoint Breakpoint_Lag Breakpoint_Lead CELL CELL_OFFSET CI_LL
CI_UL CLUSTER COUNT Cluster Coef FITTED Gene Gene_Dynamic_Lineage
Gene_Dynamic_Lineage_Slope Gene_Dynamic_Overall ID Interval LINEAGE
LRT_Stat Lineage MODEL PRED PT P_Val P_Val_Adj P_Value RESPONSE SE
Test_Stat b cell corr effect fit g gene i knot lambda leiden lineage
mRNA mean_rank mu pseudotime pt pvalue pvalue_adj r_hat rna rna_log1p
scLANE_ci_ll scLANE_ci_ll_log1p scLANE_ci_ul scLANE_ci_ul_log1p
scLANE_pred scLANE_pred_link scLANE_pred_log1p scLANE_se_link se.fit
sigma size_factor subj_id subject term
Consider adding
importFrom("stats", "pt", "sigma")
to your NAMESPACE file.
* 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 ... [179s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
testDynamic 65.249 0.540 65.792
bootstrapRandomEffects 56.247 1.245 57.494
fitGLMM 5.699 0.233 5.932
geneProgramDrivers 4.997 0.008 5.007
enrichDynamicGenes 1.558 0.028 12.190
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [84s/240s]
[84s/240s] 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/3705/817817515c1e1f48a0c8344121af6b5d54d73925/scLANE.Rcheck/00check.log’
for details.
===============================
BiocCheck('scLANE_0.99.7.tar.gz')
===============================
── Installing scLANE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── scLANE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp11WDjB/file25ffde6f164374/scLANE
→ BiocVersion: 3.22
→ Package: scLANE
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/817817515c1e1f48a0c8344121af6b5d54d73925/scLANE.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/Rtmp11WDjB/file25ffde6f164374/scLANE
→ installDir: /tmp/Rtmp11WDjB/file25ffde593a719b
→ 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...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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 .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; 17 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 7 NOTES
i See the scLANE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.