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BiocCheckGitClone('lcmsPlot')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot
BiocVersion: 3.22
Package: lcmsPlot
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot
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...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.45.18 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot.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 lcmsPlot/DESCRIPTION ... OK
* checking extension type ... Package
* this is package lcmsPlot 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 lcmsPlot can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [6s/6s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'create_chromatograms_from_feature_ids.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_chromatograms_from_features.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_full_rt_chromatograms.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_intensity_map.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_rt_diff.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_spectra.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'create_total_ion_current.Rd':
\examples lines wider than 100 characters:
data_container <- create_data_container_from_obj(data_obj, sample_id_column = "sample_name", metadata = NULL)
Rd file 'get_plot.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'grid.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'iterate_plot_batches.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'labels.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'legend.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'mass_trace.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'next_plot.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'rt_line.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
Rd file 'spectra.Rd':
\examples lines wider than 100 characters:
lcmsPlot::chromatogram(features = rbind(c(mzmin = 334.9, mzmax = 335.1, rtmin = 2700, rtmax = 2900))) +
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 ... [188s/148s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
create_chromatograms_from_feature_ids 22.331 3.174 21.905
get_XCMSnExp_object_example 16.723 2.110 13.860
rt_diff_plot 13.611 3.169 11.971
total_ion_current 10.753 1.948 9.301
create_rt_diff 9.196 2.599 8.311
create_full_rt_chromatograms 9.003 2.003 7.561
create_chromatograms_from_features 7.223 1.787 5.617
create_intensity_map 7.093 1.776 5.339
get_grouped_peaks 6.354 1.067 4.651
create_total_ion_current 4.325 1.085 5.398
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [47s/40s]
[47s/40s] 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 ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot.Rcheck/00check.log
for details.
===============================
BiocCheck('lcmsPlot_0.99.6.tar.gz')
===============================
Installing lcmsPlot
Package installed successfully
lcmsPlot session metadata
sourceDir: /tmp/RtmpVV49yL/file12faab6fc6b5bb/lcmsPlot
BiocVersion: 3.22
Package: lcmsPlot
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/f36313180320452b54f6eb08de793be592030e2a/lcmsPlot.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmpVV49yL/file12faab6fc6b5bb/lcmsPlot
installDir: /tmp/RtmpVV49yL/file12faab31bb2ff7
isTarBall: TRUE
platform: unix
Running BiocCheck on lcmsPlot
* 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 4.3.0 to 4.5.0
* 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 (53%).
* 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:
creating_publication_ready_plots.Rmd
lcms_data_plotting.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpVV49yL/file12faab6fc6b5bb/lcmsPlot/vignettes/creating_publication_ready_plots.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpVV49yL/file12faab6fc6b5bb/lcmsPlot/vignettes/lcms_data_plotting.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of lcmsPlot...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/helpers-data.R (line 104, column 15)
...
R/processing-xcms.R (line 39, column 24)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
creators-spectra.R (line 129, column 32)
helpers-data.R (line 41, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/lcms_data_plotting.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
definition() (R/creators-spectra.R): 136 lines
...
chromatogram() (R/lcmsPlot-class.R): 61 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
lcmsPlot.Rd
pipe.Rd
set_plot.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; 158 lines (4%) are > 80 characters long.
First few lines:
R/constructors-spectra.R#L101 { if (!is.null(rt_range)) filter(. ...
...
vignettes/lcms_data_plotting.Rmd#L438 Often, it is preferable to plot spectra
...
i NOTE: Consider multiples of 4 spaces for line indents; 1127 lines (30%) are
not.
First few lines:
R/constructors-chromatograms.R#L8 hdr <- mzR::header(raw_data) ...
...
vignettes/lcms_data_plotting.Rmd#L447 legend(position = "bottom") ...
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 v1.45.18 results
0 ERRORS | 0 WARNINGS | i 10 NOTES
i See the lcmsPlot.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.