Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/scLANE
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     ERROR     skipped     OK  

nebbiolo1 Summary

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Package: scLANE
Version: 0.99.0
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scLANE
BuildTime: 4 minutes 59.64 seconds
CheckCommand: BiocCheckGitClone('scLANE') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3705/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3705/scLANE_20250203194337/scLANE.install-out.txt scLANE_0.99.0.tar.gz && BiocCheck('scLANE_0.99.0.tar.gz', `new-package`=TRUE)
CheckTime: 10 minutes 59.86 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 15337.75 KiB
BuildID:: scLANE_20250203194337
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scLANE. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 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’


nebbiolo1 CHECK output

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===============================

 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.

nebbiolo1 BUILD BIN output

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