===============================
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_0.99.0.tar.gz
===============================
BiocCheckGitClone('scLANE')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE
BiocVersion: 3.21
Package: scLANE
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* 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 v1.43.4 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/scLANE_20250203194337/scLANE.Rcheck
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 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 0.99.0
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* 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 C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 12.7Mb
sub-directories of 1Mb or more:
data 1.6Mb
libs 7.2Mb
testdata 2.7Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... [2s/2s] 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 ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
print:
function(x, ...)
print.summary.scLANE:
function(x)
summary:
function(object, ...)
summary.scLANE:
function(test.dyn.res, p.adj.method, fdr.cutoff)
See section Generic functions and methods in the Writing R
Extensions manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [14s/14s] 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 global function definition for
na.omit
bootstrapRandomEffects: no visible binding for global variable term
bootstrapRandomEffects: no visible binding for global variable effect
chooseCandidateGenes: no visible binding for global variable expr.mat
chooseCandidateGenes: no visible binding for global variable slot
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 expr.mat fit g gene i knot lambda leiden
lineage mRNA mean_rank mu na.omit 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 slot subj_id subject term
Consider adding
importFrom("methods", "slot")
importFrom("stats", "na.omit", "pt", "sigma")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... INFO
Packages unavailable to check Rd xrefs: glmtoolbox, multgee
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-O3 -march=native -mfma
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section Writing portable
packages in the Writing R Extensions manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-march=native -mfma
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [392s/417s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bootstrapRandomEffects 273.310 1.614 274.931
testDynamic 65.803 0.770 66.575
fitGLMM 6.202 0.431 6.634
enrichDynamicGenes 1.944 0.121 16.829
plotModelCoefs 0.792 0.067 5.962
getResultsDE 0.386 0.023 5.482
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [59s/149s]
[59s/149s] 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 ... [6s/6s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \Chi
l.1740 ...lated using an asymptotic \eqn{\Chi^2}{}
distribution, with the de...
! Undefined control sequence.
<recently read> \Chi
l.2671 ...lated using an asymptotic \eqn{\Chi^2}{}
distribution, with the de...
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 4 WARNINGs, 6 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scLANE_0.99.0.tar.gz')
===============================
Installing scLANE
Package installed successfully
scLANE session metadata
sourceDir: /tmp/RtmpOOMjBd/file24ba7a4494b9c0/scLANE
BiocVersion: 3.21
Package: scLANE
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /tmp/RtmpOOMjBd/file24ba7a4494b9c0/scLANE
installDir: /tmp/RtmpOOMjBd/file24ba7a74f8ad82
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 3.5.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/tmp/RtmpOOMjBd/file24ba7a4494b9c0/scLANE//inst/doc/scLANE.html
...
/tmp/RtmpOOMjBd/file24ba7a4494b9c0/scLANE/src/scLANE.so
* 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 .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 scLANE...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
backward_sel_WIC.R (line 49, column 48)
backward_sel_WIC.R (line 49, column 78)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/scoreTestGEE.R (line 114, column 10)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/biasCorrectGEE.R (line 42, column 17)
...
R/fitGLMM.R (line 102, column 23)
* 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 23
functions greater than 50 lines.
The longest 5 functions are:
marge2() (R/marge2.R): 834 lines
...
biasCorrectGEE() (R/biasCorrectGEE.R): 142 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/print.summary.scLANE.Rd
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
i NOTE: Use donttest instead of dontrun.
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; 786 lines (14%) are > 80 characters long.
First few lines:
R/backward_sel_WIC.R#L1 #' Backward selection function for MARGE ...
...
vignettes/scLANE.Rmd#L257 Lastly, we can perform pathway analysis ...
i NOTE: Consider multiples of 4 spaces for line indents; 2528 lines (45%) are
not.
First few lines:
R/backward_sel_WIC.R#L23 B_new = NUL ...
...
vignettes/scLANE.Rmd#L266 col.names = c("Term ID", ...
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...
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 v1.43.4 results
1 ERRORS | 3 WARNINGS | i 10 NOTES
i See the scLANE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.