===============================
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_0.99.6.tar.gz
===============================
BiocCheckGitClone('scLANE')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/dbb05de3d1db1da8588f869956021a8c399a46b5/scLANE
BiocVersion: 3.22
Package: scLANE
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/dbb05de3d1db1da8588f869956021a8c399a46b5/scLANE.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/dbb05de3d1db1da8588f869956021a8c399a46b5/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/dbb05de3d1db1da8588f869956021a8c399a46b5/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 0.99.6
* 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 ... [3s/3s] 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 ... [190s/200s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
testDynamic 68.415 0.814 69.238
bootstrapRandomEffects 57.685 1.262 58.951
fitGLMM 5.928 0.241 6.169
geneProgramSignificance 5.800 0.056 5.858
geneProgramDrivers 5.323 0.008 5.332
geneProgramScoring 5.036 0.078 5.115
enrichDynamicGenes 1.589 0.020 11.734
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [88s/247s]
[88s/247s] 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/dbb05de3d1db1da8588f869956021a8c399a46b5/scLANE.Rcheck/00check.log
for details.
===============================
BiocCheck('scLANE_0.99.6.tar.gz')
===============================
Installing scLANE
Package installed successfully
scLANE session metadata
sourceDir: /tmp/RtmpTJZXck/file22d1095de12969/scLANE
BiocVersion: 3.22
Package: scLANE
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/dbb05de3d1db1da8588f869956021a8c399a46b5/scLANE.BiocCheck
BiocCheckVersion: 1.45.12
sourceDir: /tmp/RtmpTJZXck/file22d1095de12969/scLANE
installDir: /tmp/RtmpTJZXck/file22d1094e3a4df
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...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 1 times:
F in R/geneProgramScoring.R (line 94, column 47)
* 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 | 2 WARNINGS | i 7 NOTES
i See the scLANE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.