===============================
R CMD BUILD
===============================
* checking for file MSTree/DESCRIPTION ... OK
* preparing MSTree:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 MSTree_0.99.5.tar.gz
===============================
BiocCheckGitClone('MSTree')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree
BiocVersion: 3.23
Package: MSTree
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree
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 remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.49.4 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/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree.Rcheck
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-11 13:30:37 UTC
* using option --no-vignettes
* checking for file MSTree/DESCRIPTION ... OK
* this is package MSTree version 0.99.5
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package MSTree can be installed ... OK
* checking installed package size ... OK
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] OK
* 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 files in vignettes ... OK
* checking examples ... [16s/16s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PlotMST 6.957 0.071 7.027
makeGraphFromChewBBACA 6.805 0.064 6.870
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTests.R [2s/2s]
[2s/2s] ERROR
Running the tests in tests/runTests.R failed.
Last 20 lines of output:
RUNIT TEST PROTOCOL -- Mon May 11 09:31:33 2026
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
MSTree RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /tmp/RtmpZvuRxA/RLIBS_30a7cc9677166/MSTree/unitTests/test_makeGraphFromChewBBACA_and_PlotMST.R: Error while sourcing /tmp/RtmpZvuRxA/RLIBS_30a7cc9677166/MSTree/unitTests/test_makeGraphFromChewBBACA_and_PlotMST.R : Error in library(testthat) : there is no package called 'testthat'
Test files with failing tests
test_makeGraphFromChewBBACA_and_PlotMST.R
/tmp/RtmpZvuRxA/RLIBS_30a7cc9677166/MSTree/unitTests/test_makeGraphFromChewBBACA_and_PlotMST.R
Error in BiocGenerics:::testPackage("MSTree") :
unit tests failed for package MSTree
Execution halted
* 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: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree.Rcheck/00check.log
for details.
===============================
BiocCheck('MSTree_0.99.5.tar.gz')
===============================
Installing MSTree
Package installed successfully
MSTree session metadata
sourceDir: /tmp/Rtmpj7R11O/file31157d21c79da6/MSTree
BiocVersion: 3.23
Package: MSTree
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4110/81e743492285fb1ef9728272e7f8772ed542926d/MSTree.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /tmp/Rtmpj7R11O/file31157d21c79da6/MSTree
installDir: /tmp/Rtmpj7R11O/file31157d7483432f
isTarBall: TRUE
platform: unix
Running BiocCheck on MSTree
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (17%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
MSTree_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MSTree...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
makeGraphFromChewBBACA.r (line 75, column 15)
makeGraphFromChewBBACA.r (line 110, column 15)
makeGraphFromChewBBACA.r (line 133, column 19)
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
makeGraphFromChewBBACA() (R/makeGraphFromChewBBACA.r): 133 lines
PlotMST() (R/PlotMST.r): 104 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; 1 lines (0%) are > 80 characters long.
First few lines:
R/makeGraphFromChewBBACA.r#L156 message("Additional edges (",max ...
i NOTE: Consider multiples of 4 spaces for line indents; 3 lines (1%) are not.
First few lines:
vignettes/MSTree_vignette.Rmd#L57 chewBBACA pipeline. ...
vignettes/MSTree_vignette.Rmd#L60 it generates a minimum ...
vignettes/MSTree_vignette.Rmd#L61 function from NetPathM ...
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 v1.49.4 results
0 ERRORS | 0 WARNINGS | i 7 NOTES
i See the MSTree.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.