===============================
R CMD BUILD
===============================
* 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_0.99.3.tar.gz’
===============================
BiocCheckGitClone('MetabolomicsPipeline')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/MetabolomicsPipeline
→ BiocVersion: 3.22
→ Package: MetabolomicsPipeline
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/MetabolomicsPipeline.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/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 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/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/MetabolomicsPipeline.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 ‘MetabolomicsPipeline/DESCRIPTION’ ... OK
* this is package ‘MetabolomicsPipeline’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘magick’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s/27s] NOTE
allSigSubpath: no visible binding for global variable ‘model’
allSigSubpath: no visible binding for global variable ‘sub_pathway’
allSigSubpath: no visible binding for global variable ‘pval’
logTransformation: no visible global function definition for ‘assay<-’
medianStandardization: no visible global function definition for
‘assay<-’
metEstHeatmap: no visible binding for global variable ‘metabolite’
metEstHeatmap: no visible binding for global variable ‘Overall_pval’
metEstHeatmap: no visible binding for global variable ‘Contrast’
metEstHeatmap: no visible binding for global variable ‘pval’
metEstHeatmap: no visible binding for global variable ‘Difference’
metPHeatmap: no visible binding for global variable ‘metabolite’
metPHeatmap: no visible binding for global variable ‘Overall_pval’
metPHeatmap: no visible binding for global variable ‘Contrast’
metPHeatmap: no visible binding for global variable ‘pval’
metPHeatmap: no visible binding for global variable ‘Difference’
metWithinSub: no visible binding for global variable ‘sub_pathway’
metWithinSub: no visible binding for global variable ‘chem_name’
metWithinSub : <anonymous>: no visible binding for global variable
‘sub_pathway’
metWithinSub : <anonymous>: no visible binding for global variable
‘chem_name’
metaboliteHeatmap: no visible binding for global variable ‘Row.names’
metaboliteHeatmap : <anonymous>: no visible binding for global variable
‘Row.names’
minValImpute: no visible global function definition for ‘assay<-’
subWithinSuperResults: no visible binding for global variable
‘super_pathway’
subWithinSuperResults: no visible binding for global variable
‘sub_pathway’
subWithinSuperResults: no visible binding for global variable ‘model’
subWithinSuperResults : <anonymous>: no visible binding for global
variable ‘super_pathway’
subWithinSuperResults : <anonymous>: no visible binding for global
variable ‘sub_pathway’
subWithinSuperResults : <anonymous>: no visible binding for global
variable ‘model’
subpathByModel: no visible binding for global variable ‘model’
subpathByModel: no visible binding for global variable ‘sub_pathway’
subpathWithinSuperpath: no visible binding for global variable ‘model’
subpathWithinSuperpath: no visible binding for global variable
‘sub_pathway’
subpathWithinSuperpath: no visible binding for global variable
‘super_pathway’
subpathWithinSuperpath: no visible binding for global variable
‘percent_sig’
subpathWithinSuperpath: no visible binding for global variable
‘sig_paths’
subpathWithinSuperpath: no visible binding for global variable
‘subpaths’
subpathwayAnalysis: no visible binding for global variable
‘sub_pathway’
subpathwayAnalysis : <anonymous>: no visible binding for global
variable ‘e’
subpathwayBoxplots: no visible binding for global variable ‘group’
subpathwayBoxplots: no visible binding for global variable ‘X’
subpathwayBoxplots: no visible binding for global variable ‘value’
subpathwayLineplots: no visible binding for global variable ‘treat’
subpathwayLineplots: no visible binding for global variable ‘X’
subpathwayLineplots: no visible binding for global variable ‘value’
Undefined global functions or variables:
Contrast Difference Overall_pval Row.names X assay<- chem_name e
group metabolite 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 ... [43s/43s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/MetabolomicsPipeline.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetabolomicsPipeline_0.99.3.tar.gz')
===============================
── Installing MetabolomicsPipeline ─────────────────────────────────────────────
✔ Package installed successfully
── MetabolomicsPipeline session metadata ───────────────────────────────────────
→ sourceDir: /tmp/RtmpS2NwCU/file1333997fbd1735/MetabolomicsPipeline
→ BiocVersion: 3.22
→ Package: MetabolomicsPipeline
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3790/6b91b2676991cadcacd79bab023fd115ecaa8642/MetabolomicsPipeline.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpS2NwCU/file1333997fbd1735/MetabolomicsPipeline
→ installDir: /tmp/RtmpS2NwCU/file1333994ff703e6
→ 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 (8%).
* 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 MetabolomicsPipeline...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/logTransformation.R (line 46, column 13)
• ...
• R/subpathwayLineplots.R (line 89, column 14)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/createMetSe.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 12
functions greater than 50 lines.
The longest 5 functions are:
• subpathwayAnalysis() (R/subpathwayAnalysis.R): 786 lines
• ...
• metEstHeatmap() (R/metEstHeatmap.R): 111 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• loadMetExcel.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; 42 lines (1%) are > 80 characters long.
First few lines:
• R/createMetSe.R#L10 #' @param chemical_annotation A `data.fr ...
• ...
• vignettes/MetabolomicsPipeline-vignette.Rmd#L539 * FC_cutoff: Numeric value
for the fold ...
i NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
First few lines:
• vignettes/MetabolomicsPipeline-vignette.Rmd#L602 * subpathway: Character
value of the sub ...
i NOTE: Consider multiples of 4 spaces for line indents; 290 lines (7%) are
not.
First few lines:
• R/createMetSe.R#L54 sample_metadat ...
• ...
• vignettes/MetabolomicsPipeline-vignette.Rmd#L648 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 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 11 NOTES
i See the MetabolomicsPipeline.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.