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R CMD BUILD
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* checking for file MetabolomicsPipeline/DESCRIPTION ... OK
* preparing MetabolomicsPipeline:
* 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 MetabolomicsPipeline_0.99.1.tar.gz
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BiocCheckGitClone('MetabolomicsPipeline')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline
BiocVersion: 3.22
Package: MetabolomicsPipeline
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline
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 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 v1.45.7 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline.Rcheck
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MetabolomicsPipeline/DESCRIPTION ... OK
* this is package MetabolomicsPipeline version 0.99.1
* 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 MetabolomicsPipeline 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [25s/25s] NOTE
all_sig_subpath: no visible binding for global variable model
all_sig_subpath: no visible binding for global variable sub_pathway
all_sig_subpath: no visible global function definition for ends_with
all_sig_subpath: no visible binding for global variable pval
log_transformation: no visible global function definition for assay<-
median_standardization: no visible global function definition for
assay<-
met_est_heatmap: no visible binding for global variable Overall_pval
met_est_heatmap: no visible binding for global variable Contrast
met_est_heatmap: no visible binding for global variable Difference
met_p_heatmap: no visible binding for global variable Overall_pval
met_p_heatmap: no visible binding for global variable Contrast
met_p_heatmap: no visible binding for global variable P_value
met_within_sub: no visible binding for global variable sub_pathway
met_within_sub: no visible binding for global variable chem_name
met_within_sub : <anonymous>: no visible binding for global variable
sub_pathway
met_within_sub : <anonymous>: no visible binding for global variable
chem_name
metabolite_heatmap: no visible binding for global variable Row.names
metabolite_heatmap : <anonymous>: no visible binding for global
variable Row.names
min_val_impute: no visible global function definition for assay<-
subpath_by_model: no visible binding for global variable model
subpath_by_model: no visible binding for global variable sub_pathway
subpath_by_model: no visible global function definition for ends_with
subpath_within_superpath: no visible binding for global variable
model
subpath_within_superpath: no visible binding for global variable
sub_pathway
subpath_within_superpath: no visible binding for global variable
super_pathway
subpath_within_superpath: no visible global function definition for
ends_with
subpath_within_superpath: no visible binding for global variable
percent_sig
subpath_within_superpath: no visible binding for global variable
sig_paths
subpath_within_superpath: no visible binding for global variable
subpaths
subpathway_analysis: no visible binding for global variable
sub_pathway
subpathway_boxplots: no visible binding for global variable group
subpathway_boxplots: no visible binding for global variable X
subpathway_boxplots: no visible binding for global variable value
subpathway_lineplots: no visible binding for global variable treat
subpathway_lineplots: no visible binding for global variable X
subpathway_lineplots: no visible binding for global variable value
Undefined global functions or variables:
Contrast Difference Overall_pval P_value Row.names X assay<-
chem_name ends_with group model percent_sig pval sig_paths
sub_pathway subpaths super_pathway treat value
* 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [40s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
met_est_heatmap 5.396 0.084 5.480
met_p_heatmap 5.349 0.068 5.417
metabolite_pairwise 5.383 0.011 5.394
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [12s/12s]
[12s/12s] 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline.Rcheck/00check.log
for details.
===============================
BiocCheck('MetabolomicsPipeline_0.99.1.tar.gz')
===============================
Installing MetabolomicsPipeline
Package installed successfully
MetabolomicsPipeline session metadata
sourceDir: /tmp/Rtmpss0kD1/file3e1de2678773d4/MetabolomicsPipeline
BiocVersion: 3.22
Package: MetabolomicsPipeline
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/MetabolomicsPipeline_20250530073618/MetabolomicsPipeline.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /tmp/Rtmpss0kD1/file3e1de2678773d4/MetabolomicsPipeline
installDir: /tmp/Rtmpss0kD1/file3e1de2476e92c6
isTarBall: TRUE
platform: unix
Running BiocCheck on MetabolomicsPipeline
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4.0 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 (9%).
* 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 .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 MetabolomicsPipeline...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/log_transformation.R (line 46, column 13)
...
R/subpathway_lineplots.R (line 89, column 14)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/create_met_se.R (line 91, column 7)
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
subpathway_analysis() (R/subpathway_analysis.R): 674 lines
...
met_p_heatmap() (R/met_p_heatmap.R): 89 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
load_met_excel.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 18 lines (1%) are > 80 characters long.
First few lines:
R/create_met_se.R#L10 #' @param chemical_annotation A `data.fr ...
...
vignettes/MetabolomicsPipeline-vignette.Rmd#L471 experimental groups at the
metabolite le ...
i NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
First few lines:
vignettes/MetabolomicsPipeline-vignette.Rmd#L576 * subpathway: Character
value of the sub ...
i NOTE: Consider multiples of 4 spaces for line indents; 101 lines (3%) are
not.
First few lines:
R/create_met_se.R#L54 sample_metadat ...
...
vignettes/MetabolomicsPipeline-vignette.Rmd#L622 SUB_PATHWAY = "SUB_PATHWAY",
Gender = ...
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 Unable to connect to the Bioc-devel mailing list: HTTP 502 Bad Gateway.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.7 results
0 ERRORS | 0 WARNINGS | i 11 NOTES
i See the MetabolomicsPipeline.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.