===============================
R CMD BUILD
===============================
* checking for file ‘LACHESIS/DESCRIPTION’ ... OK
* preparing ‘LACHESIS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘LACHESIS_0.99.2.tar.gz’
===============================
BiocCheckGitClone('LACHESIS')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS
→ BiocVersion: 3.22
→ Package: LACHESIS
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS
→ 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...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS.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 ‘LACHESIS/DESCRIPTION’ ... OK
* this is package ‘LACHESIS’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘LACHESIS’ can be installed ... OK
* checking installed package size ... INFO
installed size is 8.9Mb
sub-directories of 1Mb or more:
extdata 8.5Mb
* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [21s/21s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'readVCF.Rd':
\examples lines wider than 100 characters:
dkfz_vcf <- system.file("extdata", "NBE15", "snvs_NBE15_somatic_snvs_conf_8_to_10.vcf", package = "LACHESIS")
These lines will be truncated in the PDF manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [232s/231s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LACHESIS 44.100 1.085 44.876
plotNB 23.867 0.230 23.881
plotSurvival 18.966 0.046 18.876
plotLachesis 18.851 0.111 18.801
estimateClonality 17.684 0.373 17.963
plotClonality 17.414 0.077 17.422
plotClinicalCorrelations 16.811 0.200 16.899
classifyLACHESIS 16.441 0.223 16.548
nbImport 8.718 0.202 8.790
plotMutationDensities 5.578 0.053 5.592
MRCA 5.341 0.018 5.334
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’ [290s/287s]
[290s/287s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('LACHESIS_0.99.2.tar.gz')
===============================
── Installing LACHESIS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── LACHESIS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplFqv53/file14eec35b0931e5/LACHESIS
→ BiocVersion: 3.22
→ Package: LACHESIS
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3965/c8054ae7eba1a03963da5a8d5952f8f4de14d15a/LACHESIS.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmplFqv53/file14eec35b0931e5/LACHESIS
→ installDir: /tmp/RtmplFqv53/file14eec3e39c6b7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on LACHESIS ───────────────────────────────────────────────
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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...
i Bioconductor dependencies found in Imports & Depends (8%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* 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 LACHESIS...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/estimateClonality.R (line 356, column 13)
• print() in R/LACHESIS.R (line 873, column 9)
* 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 22
functions greater than 50 lines.
The longest 5 functions are:
• LACHESIS() (R/LACHESIS.R): 720 lines
• ...
• plotNB() (R/nbImport.R): 261 lines
* Checking man page documentation...
* 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; 253 lines (4%) are > 80 characters long.
First few lines:
• R/estimateClonality.R#L220 "Missing input. Please provi ...
• ...
• vignettes/vignette_LACHESIS.Rmd#L990 In case of any questions, feel free to o
...
i NOTE: Consider multiples of 4 spaces for line indents; 67 lines (1%) are not.
First few lines:
• R/clonalMutationCounter.R#L34 chromo ...
• ...
• vignettes/vignette_LACHESIS.Rmd#L582 ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.22/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.22/data/annotation
* 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 v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the LACHESIS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.