===============================
BiocCheckGitClone('RFLOMICS')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS
→ BiocVersion: 3.20
→ Package: RFLOMICS
→ PackageVersion: 0.99.3
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RFLOMICS/DESCRIPTION’ ... OK
* this is package ‘RFLOMICS’ version ‘0.99.3’
* 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 ‘RFLOMICS’ 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘org.At.tair.db’
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 ... [50s/50s] NOTE
.applyNorm: no visible global function definition for ‘assay<-’
.applyTransformation: no visible global function definition for
‘assay<-’
.checkOmicInput: no visible binding for global variable ‘addDataNum’
.checkTransNorm: no visible global function definition for ‘assay<-’
.checkTransNorm: no visible global function definition for ‘setTrans’
.coseq.error.manage: no visible binding for global variable
‘error.message’
.coseq.error.manage: no visible binding for global variable ‘.’
.coseq.results.process: no visible binding for global variable ‘.’
.coseq.results.process: no visible binding for global variable
‘logLike’
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable ‘outsideGroup’
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable ‘groupComparison’
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable ‘contrast’
.edgeRAnaDiff: no visible global function definition for ‘Q’
.edgeRAnaDiff: no visible binding for global variable ‘.’
.edgeRAnaDiff: no visible binding for global variable ‘error.message’
.generateEcoseedExampleData: no visible binding for global variable
‘ecoseed.df’
.getExpressionContrastF: no visible binding for global variable
‘contrast’
.getExpressionContrastF: no visible binding for global variable
‘contrastName’
.getExpressionContrastF: no visible binding for global variable
‘groupComparison’
.getExpressionContrastF: no visible binding for global variable ‘type’
.integrationMethodsParam: no visible global function definition for
‘colData’
.integrationPrepareDataUI : <anonymous>: no visible global function
definition for ‘sd’
.limmaAnaDiff : fx: no visible binding for global variable ‘y’
.limmaAnaDiff : fx: no visible binding for global variable ‘z’
.limmaAnaDiff: no visible global function definition for ‘Q’
.limmaAnaDiff: no visible binding for global variable ‘.’
.limmaAnaDiff: no visible binding for global variable ‘error.message’
.modGLMmodel : <anonymous>: no visible binding for global variable
‘contrast’
.modIntegrationAnalysis : <anonymous> : <anonymous>: no visible global
function definition for ‘sd’
.outAnnotResults : <anonymous>: no visible binding for global variable
‘contrastName’
.outMOFAFactorsPlot: no visible binding for global variable ‘group’
.outMOFAHeatmap: no visible binding for global variable ‘group’
.plotExperimentalDesign: no visible binding for global variable ‘Count’
.plotExperimentalDesign: no visible binding for global variable
‘status’
.plotMA: no visible binding for global variable ‘.’
.plotPValue: no visible binding for global variable ‘pvalue’
.plot_MO_1: no visible binding for global variable ‘Dataset’
.plot_MO_1: no visible binding for global variable ‘% of explained
variance’
.plot_MO_1: no visible binding for global variable ‘Cumulative
Explained Variance’
.plot_MO_2: no visible binding for global variable ‘Dataset’
.plot_MO_2: no visible binding for global variable ‘Component’
.plot_MO_2: no visible binding for global variable ‘% of explained
variance’
.rbeFunction: no visible global function definition for ‘assay<-’
.relationsMOFA : <anonymous>: no visible global function definition for
‘p.adjust’
.rnaseqRBETransform: no visible global function definition for
‘assay<-’
.runCoseqClustermq: no visible global function definition for ‘Q_rows’
.runCoseqClustermq: no visible binding for global variable
‘error.message’
.runCoseqClustermq: no visible binding for global variable ‘iter’
.writeSessionInfo: no visible global function definition for
‘sessionInfo’
DiffExpAnalysis : <anonymous>: no visible binding for global variable
‘Adj.pvalue’
DiffExpAnalysis: no visible binding for global variable ‘contrastName’
RflomicsMAE: no visible global function definition for ‘ExperimentList’
createRflomicsMAE: no visible global function definition for ‘colData’
createRflomicsMAE: no visible binding for global variable ‘factorType’
createRflomicsMAE: no visible global function definition for ‘relevel’
createRflomicsSE: no visible binding for global variable ‘samples’
definition: no visible global function definition for ‘quantile’
definition: no visible binding for global variable ‘logLike’
integrationWrapper: no visible binding for global variable
‘omicsToIntegrate’
readExpDesign: no visible binding for global variable ‘.’
readOmicsData: no visible binding for global variable ‘.’
updateSelectedContrasts: no visible binding for global variable
‘contrast’
filterFeatures,RflomicsMAE: no visible global function definition for
‘colData’
filterFeatures,RflomicsMAE: no visible global function definition for
‘sampleMap’
generateContrastMatrix,RflomicsMAE: no visible binding for global
variable ‘modelFormula’
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘.’
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘variable’
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘groups’
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘y_profiles’
getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘groups’
getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘cluster’
getCoExpAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘dataset’
getDEList,RflomicsSE: no visible binding for global variable ‘.’
getDEList,RflomicsSE: no visible binding for global variable ‘DEF’
getDEList,RflomicsSE: no visible binding for global variable ‘SUMCOL’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘.’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘All’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘Up_Down’
getDiffAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘contrastName’
getDiffAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable ‘.’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘tabel’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘percent’
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable ‘variable’
initialize,RflomicsMAE: no visible global function definition for
‘packageVersion’
integrationWrapper,RflomicsMAE: no visible global function definition
for ‘experiments’
plotBoxplotDE,RflomicsSE: no visible binding for global variable ‘DE’
plotBoxplotDE,RflomicsSE: no visible binding for global variable
‘groups’
plotBoxplotDE,RflomicsSE: no visible binding for global variable
‘value’
plotCoExpression,RflomicsSE: no visible global function definition for
‘quantile’
plotCoExpression,RflomicsSE: no visible binding for global variable
‘logLike’
plotCoExpressionProfile,RflomicsMAE: no visible binding for global
variable ‘observation’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘.’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘variable’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘groups’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘y_profiles’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘observations’
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable ‘mean.y_profiles’
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable ‘.’
plotConditionsOverview,RflomicsMAE: no visible global function
definition for ‘sampleMap’
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable ‘Count’
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable ‘status’
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
‘does.belong’
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
‘DEF’
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
‘C’
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
‘value’
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
‘prop’
plotDataDistribution,RflomicsSE: no visible binding for global variable
‘groups’
plotDataDistribution,RflomicsSE: no visible binding for global variable
‘value’
plotDataDistribution,RflomicsSE: no visible binding for global variable
‘samples’
plotDataOverview,RflomicsMAE: no visible binding for global variable
‘primary’
plotDataOverview,RflomicsMAE: no visible binding for global variable
‘y.axis’
plotDataOverview,RflomicsMAE: no visible global function definition for
‘desc’
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
‘Adj.pvalue’
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
‘samples’
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
‘groups’
plotLibrarySize,RflomicsSE: no visible binding for global variable ‘.’
plotLibrarySize,RflomicsSE: no visible binding for global variable
‘groups’
plotLibrarySize,RflomicsSE: no visible binding for global variable
‘value’
plotOmicsPCA,RflomicsSE: no visible binding for global variable ‘.’
plotOmicsPCA,RflomicsSE: no visible binding for global variable
‘samples’
prepareForIntegration,RflomicsMAE: no visible global function
definition for ‘experiments’
prepareForIntegration,RflomicsMAE: no visible global function
definition for ‘colData’
prepareForIntegration,RflomicsMAE: no visible global function
definition for ‘sampleMap’
prepareForIntegration,RflomicsMAE: no visible global function
definition for ‘colData<-’
prepareForIntegration,RflomicsMAE: no visible global function
definition for ‘intersectColumns’
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable ‘.’
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable ‘Contrast’
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable ‘Cluster’
sumDiffExp,RflomicsSE : <anonymous>: no visible binding for global
variable ‘Adj.pvalue’
sumDiffExp,RflomicsSE : <anonymous>: no visible binding for global
variable ‘logFC’
Undefined global functions or variables:
% of explained variance . Adj.pvalue All C Cluster Component Contrast
Count Cumulative Explained Variance DE DEF Dataset ExperimentList Q
Q_rows SUMCOL Up_Down addDataNum assay<- cluster colData colData<-
contrast contrastName dataset desc does.belong ecoseed.df
error.message experiments factorType group groupComparison groups
intersectColumns iter logFC logLike mean.y_profiles modelFormula
observation observations omicsToIntegrate outsideGroup p.adjust
packageVersion percent primary prop pvalue quantile relevel sampleMap
samples sd sessionInfo setTrans status tabel type value variable y
y.axis y_profiles z
Consider adding
importFrom("stats", "C", "p.adjust", "quantile", "relevel", "sd")
importFrom("utils", "packageVersion", "sessionInfo")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘RFLOMICS/R/utils_06_annot_enrichment.R’:
data("bods", package = "pathview")
See section ‘Good practice’ in ‘?data’.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/70s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
filterFeatures 10.605 2.074 10.739
runCoExpression 4.298 1.607 4.735
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [222s/200s]
[222s/201s] 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
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS.Rcheck/00check.log’
for details.
===============================
BiocCheck('RFLOMICS_0.99.3.tar.gz')
===============================
── Installing RFLOMICS ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RFLOMICS session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNO75sB/file38eb555d54f95d/RFLOMICS
→ BiocVersion: 3.20
→ Package: RFLOMICS
→ PackageVersion: 0.99.3
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3477/16eb3808e86c24ab32594dddbbb3859e203a28b3/RFLOMICS.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpNO75sB/file38eb555d54f95d/RFLOMICS
→ installDir: /tmp/RtmpNO75sB/file38eb55625ddf84
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RFLOMICS ───────────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, ExperimentalDesign, RNASeq
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/RFLOMICS-input-data.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of RFLOMICS...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/module_04_diff_analysis.R (line 710, column 20)
• ...
• R/utils_06_annot_enrichment.R (line 30, column 17)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• server.R (line 147, column 38)
• ...
• utils_01_load_data.R (line 715, column 28)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/RFLOMICS-Methods_04_diff_analysis.R (line 136, column 34)
• ...
• R/utils_05_coexp_analysis.R (line 415, column 22)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/RFLOMICS-Methods_00_Common.R (line 196, column 7)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 3 times)
• <<- in R/utils_00_common.R (line 174, column 23)
• <<- in R/utils_00_common.R (line 177, column 23)
• <<- in R/utils_07_integration.R (line 316, column 52)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressWarnings() in R/RFLOMICS-Methods_06_annot_enrichment.R (line 870,
column 5)
• ...
• suppressWarnings() in R/utils_06_annot_enrichment.R (line 160, column 3)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 93
functions greater than 50 lines.
The longest 5 functions are:
• DiffExpAnalysis() (R/module_04_diff_analysis.R): 700 lines
• ...
• .modLoadData() (R/module_01_load_data.R): 387 lines
* Checking man page documentation...
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• getAnalysis.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; 831 lines (4%) are > 80 characters long.
First few lines:
• R/coverPage.R#L7 h1(tags$span("An int ...
• ...
• vignettes/RFLOMICS.Rmd#L485 All methods from the MultiAssayExperimen ...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
• R/utils_01_load_data.R#L254 #' A DataFrame or data.frame of assay n ...
• R/utils_01_load_data.R#L255 #' and colname samples ...
i NOTE: Consider multiples of 4 spaces for line indents; 6709 lines (32%) are
not.
First few lines:
• R/coverPage.R#L2 ...
• ...
• vignettes/RFLOMICS.Rmd#L473 factorInfo = factorInfo ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 13 NOTES
i See the RFLOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.