===============================
R CMD BUILD
===============================
* checking for file metabom8/DESCRIPTION ... OK
* preparing metabom8:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed 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 metabom8_0.99.6.tar.gz
===============================
BiocCheckGitClone('metabom8')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8
BiocVersion: 3.23
Package: metabom8
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8
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...
BiocCheck v1.47.25 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/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8.Rcheck
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-11 10:21:10 UTC
* using option --no-vignettes
* checking for file metabom8/DESCRIPTION ... OK
* checking extension type ... Package
* this is package metabom8 version 0.99.6
* 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 whether package metabom8 can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 13.5Mb
sub-directories of 1Mb or more:
data 5.5Mb
extdata 1.8Mb
libs 5.5Mb
* 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 ... [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 ... [1s/1s] 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 ... [12s/12s] NOTE
.check_preprocess: no visible binding for global variable X_mean
.check_preprocess: no visible binding for global variable X_sd
Undefined global functions or variables:
X_mean X_sd
* checking Rd files ... [1s/1s] 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 ... [1s/1s] 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* 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):
-Werror=format-security
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [43s/43s] ERROR
Running examples in metabom8-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .scaleMatRcpp
> ### Title: Column-wise matrix scaling (C++ backend)
> ### Aliases: .scaleMatRcpp
> ### Keywords: internal
>
> ### ** Examples
>
> X <- matrix(rnorm(20), ncol = 4)
> idc <- seq_len(nrow(X)) -1 # ! cpp indexing starts at zero !
> .scaleMatRcpp(X, idc, TRUE, 1L)
Error in .scaleMatRcpp(X, idc, TRUE, 1L) :
could not find function ".scaleMatRcpp"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
align_spectra 34.391 1.533 35.928
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [61s/61s]
[61s/61s] 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 ... [5s/5s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8.Rcheck/00check.log
for details.
===============================
BiocCheck('metabom8_0.99.6.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
Installing metabom8
Package installed successfully
metabom8 session metadata
sourceDir: /tmp/Rtmpj8t85u/file1f76b171adcd/metabom8
BiocVersion: 3.23
Package: metabom8
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/718e17a4df801a844041c454df632556fa6d6875/metabom8.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /tmp/Rtmpj8t85u/file1f76b171adcd/metabom8
installDir: /tmp/Rtmpj8t85u/file1f76b510a2c26
isTarBall: TRUE
platform: unix
Running BiocCheck on metabom8
* 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 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 (5%).
* 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 metabom8...
* Checking coding practice...
* 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 40
functions greater than 50 lines.
The longest 5 functions are:
.oplsEngine() (R/stats_fit_opls.R): 196 lines
...
.plsEngine() (R/stats_fit_pls.r): 155 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; 626 lines (7%) are > 80 characters long.
First few lines:
R/01-s4_generics.R#L5 #' @param cv Logical indicating whether ...
...
vignettes/getting-started.Rmd#L484 This vignette demonstrated the core
data ...
i NOTE: Consider multiples of 4 spaces for line indents; 2479 lines (26%) are
not.
First few lines:
R/00-s4_classes.R#L32 slots = c( ...
...
vignettes/getting-started.Rmd#L328 params) ...
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 v1.47.25 results
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the metabom8.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.