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BiocCheckGitClone('lcmsPlot')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/lcmsPlot
BiocVersion: 3.22
Package: lcmsPlot
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/lcmsPlot.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/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/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/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 0.99.4
* 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 21.445 2.970 20.979
get_XCMSnExp_object_example 16.731 2.008 13.717
rt_diff_plot 13.582 3.132 11.967
total_ion_current 10.651 1.944 9.222
create_rt_diff 9.274 2.754 8.466
create_full_rt_chromatograms 8.357 2.089 6.879
create_total_ion_current 6.995 2.024 5.557
create_chromatograms_from_features 7.148 1.779 5.526
create_intensity_map 7.046 1.731 5.376
get_grouped_peaks 6.450 0.962 4.702
layout 3.949 1.061 4.916
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [29s/29s]
[29s/29s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 71 ]
Failed tests
Error ('test-creators-chromatograms.R:3:3'): create_chromatograms_from_feature_ids creates correct chromatograms from the grouped peak IDs
Error in `CentWaveParam(peakwidth = c(20, 80), noise = 10000, prefilter = c(6,
10000))`: could not find function "CentWaveParam"
Backtrace:
1. lcmsPlot:::get_XCMSnExp_object(should_detect_peaks = TRUE, should_group_peaks = TRUE) at test-creators-chromatograms.R:3:3
Error ('test-data-adapters.R:94:3'): get_detected_peaks returns the detected peaks for an XCMSnExp object
Error in `CentWaveParam(peakwidth = c(20, 80), noise = 10000, prefilter = c(6,
10000))`: could not find function "CentWaveParam"
Backtrace:
1. lcmsPlot:::get_XCMSnExp_object(should_detect_peaks = TRUE) at test-data-adapters.R:94:3
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 71 ]
Error: Test failures
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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/lcmsPlot.Rcheck/00check.log
for details.
===============================
BiocCheck('lcmsPlot_0.99.4.tar.gz')
===============================
Installing lcmsPlot
Package installed successfully
lcmsPlot session metadata
sourceDir: /tmp/RtmpPmjf2H/file12e9bc26d32fc6/lcmsPlot
BiocVersion: 3.22
Package: lcmsPlot
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3971/75777f6e4061a665dbcd236235fd5e7c9cd851b4/lcmsPlot.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmpPmjf2H/file12e9bc26d32fc6/lcmsPlot
installDir: /tmp/RtmpPmjf2H/file12e9bc6abfd3b2
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$set()` in /tmp/RtmpPmjf2H/file12e9bc26d32fc6/lcmsPlot/vignettes/creating_publication_ready_plots.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpPmjf2H/file12e9bc26d32fc6/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...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/create_chromatogram.Rd
...
man/total_ion_current.Rd
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#L99 { 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 | 1 WARNINGS | i 10 NOTES
i See the lcmsPlot.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.