===============================
BiocCheckGitClone('RFLOMICS')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/RFLOMICS
BiocVersion: 3.21
Package: RFLOMICS
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/RFLOMICS.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/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 v1.43.4 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/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/RFLOMICS.Rcheck
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file RFLOMICS/DESCRIPTION ... OK
* this is package RFLOMICS version 0.99.7
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'shinyBS', 'dplyr',
'ggplot2', 'htmltools', 'knitr', 'coseq'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Imports includes 33 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 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] 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
Namespaces in Imports field not imported from:
org.At.tair.db reticulate
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
.applyFeatureFiltering: no visible global function definition for
assay
.applyFeatureFiltering: no visible global function definition for
assay<-
.applyLog: no visible global function definition for assay<-
.applyLog: no visible global function definition for assay
.applyNormalization: no visible global function definition for assay
.applyNormalization: no visible global function definition for
assay<-
.applyTransformation: no visible global function definition for assay
.applyTransformation: no visible global function definition for
assay<-
.coseq.results.process: no visible global function definition for
summarise
.coseq.results.process: no visible global function definition for
group_by
.coseq.results.process: no visible binding for global variable status
.coseq.results.process: no visible binding for global variable errors
.coseq.results.process: no visible global function definition for n
.coseq.results.process: no visible global function definition for
filter
.coseq.results.process: no visible binding for global variable n
.coseq.results.process: no visible global function definition for
mutate
.coseq.results.process: no visible global function definition for
summarize
.countSamplesPerCondition: no visible global function definition for
group_by_at
.countSamplesPerCondition: no visible global function definition for
count
.countSamplesPerCondition: no visible global function definition for
full_join
.countSamplesPerCondition: no visible global function definition for
mutate_at
.countSamplesPerCondition : <anonymous>: no visible global function
definition for if_else
.defineInteractionConstrastForPairsOfFactors: no visible global
function definition for mutate
.defineInteractionConstrastForPairsOfFactors: no visible global
function definition for group_by
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable outsideGroup
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable groupComparison
.defineInteractionConstrastForPairsOfFactors: no visible global
function definition for add_tally
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable contrast
.defineInteractionConstrastForPairsOfFactors: no visible binding for
global variable n
.define_averaged_contrasts: no visible global function definition for
group_by
.define_averaged_contrasts: no visible global function definition for
add_tally
.define_averaged_contrasts: no visible global function definition for
mutate
.define_partOfInteractionContrast_df: no visible global function
definition for mutate
.define_partOfSimpleContrast_df: no visible global function definition
for mutate
.edgeRAnaDiff: no visible global function definition for assay
.edgeRAnaDiff: no visible global function definition for rename
.generateEcoseedExampleData: no visible global function definition for
data
.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: no visible global function definition for
assay
.integrationPrepareDataUI : <anonymous>: no visible global function
definition for sd
.limmaAnaDiff: no visible global function definition for assay
.limmaAnaDiff: no visible global function definition for rename
.medianNormalization: no visible global function definition for assay
.modGLMmodel : <anonymous>: no visible global function definition for
filter
.modGLMmodel : <anonymous>: no visible binding for global variable
contrast
.modIntegrationAnalysis: no visible global function definition for
mutate
.modIntegrationAnalysis: no visible binding for global variable
full_join
.modIntegrationAnalysis: no visible global function definition for
across
.modIntegrationAnalysis : <anonymous>: no visible global function
definition for assay
.modIntegrationAnalysis : <anonymous> : <anonymous>: no visible global
function definition for sd
.modLoadData: no visible global function definition for filter
.modRunEnrichment: no visible global function definition for rename
.outAnnotResults : <anonymous>: no visible binding for global variable
contrastName
.outMOFAFactorsCor: no visible global function definition for cor
.outMOFAFactorsPlot: no visible binding for global variable group
.outMOFAHeatmap: no visible binding for global variable group
.plotExperimentalDesign: no visible global function definition for
mutate
.plotExperimentalDesign: no visible global function definition for
if_else
.plotExperimentalDesign: no visible binding for global variable Count
.plotExperimentalDesign: no visible binding for global variable
status
.plotMA: no visible global function definition for rename
.plotMA: no visible binding for global variable .
.plotPValue: no visible binding for global variable pvalue
.plotVolcanoPlot: no visible global function definition for last
.plotVolcanoPlot: no visible global function definition for first
.plot_MO_1: no visible global function definition for group_by
.plot_MO_1: no visible binding for global variable Dataset
.plot_MO_1: no visible global function definition for summarise
.plot_MO_1: no visible binding for global variable % of explained
variance
.plot_MO_1: no visible global function definition for filter
.plot_MO_1: no visible binding for global variable Cumulative
Explained Variance
.plot_MO_2: no visible global function definition for filter
.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
.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
.rnaseqRBETransform: no visible global function definition for
assay<-
.runMixOmicsAnalysis: no visible global function definition for
select_if
.simpleContrastForOneFactor: no visible global function definition for
mutate
.tmmNormalization: no visible global function definition for assay
.totalSumNormalization: no visible global function definition for
assay
.updateColData: no visible global function definition for colData
.writeSessionInfo: no visible global function definition for
sessionInfo
CoSeqAnalysis: no visible global function definition for filter
CoSeqAnalysis: no visible binding for global variable status
DiffExpAnalysis: no visible global function definition for filter
DiffExpAnalysis: no visible binding for global variable contrastName
RflomicsMAE: no visible global function definition for ExperimentList
RflomicsMAE: no visible global function definition for packageVersion
createRflomicsMAE: no visible global function definition for assay
createRflomicsMAE: no visible global function definition for
sampleMap
createRflomicsMAE: no visible global function definition for colData
createRflomicsMAE: no visible global function definition for filter
createRflomicsMAE: no visible binding for global variable factorType
createRflomicsMAE: no visible global function definition for relevel
createRflomicsMAE: no visible global function definition for mutate
createRflomicsSE: no visible global function definition for filter
createRflomicsSE: no visible global function definition for mutate
createRflomicsSE: no visible binding for global variable samples
createRflomicsSE: no visible global function definition for DataFrame
definition: no visible global function definition for mutate
definition: no visible binding for global variable n
definition: no visible binding for global variable logLike
readExpDesign: no visible global function definition for mutate
readExpDesign: no visible global function definition for across
readExpDesign: no visible binding for global variable .
readOmicsData: no visible binding for global variable .
updateSelectedContrasts: no visible global function definition for
filter
updateSelectedContrasts: no visible binding for global variable
contrast
dataImputation,RflomicsSE: no visible global function definition for
assay
filterDiffAnalysis,RflomicsSE: no visible binding for global variable
SE.name
filterLowAbundance,RflomicsSE: no visible global function definition
for assay
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for filter
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for mutate
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable .
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for rename
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable variable
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for full_join
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for group_by
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable groups
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible global
function definition for summarise
getCoExpAnalysesSummary,RflomicsMAE : <anonymous>: no visible binding
for global variable y_profiles
getCoExpAnalysesSummary,RflomicsMAE: no visible global function
definition for mutate
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 global function definition for
mutate
getDEList,RflomicsSE: no visible binding for global variable .
getDEList,RflomicsSE: no visible binding for global variable DEF
getDEList,RflomicsSE: no visible global function definition for
filter
getDEList,RflomicsSE: no visible binding for global variable SUMCOL
getDEMatrix,RflomicsMAE: no visible binding for global variable
omicName
getDesignMat,RflomicsMAE: no visible global function definition for
colData
getDesignMat,RflomicsSE: no visible global function definition for
colData
getDiffAnalysesSummary,RflomicsMAE: no visible global function
definition for mutate
getDiffAnalysesSummary,RflomicsMAE: no visible binding for global
variable .
getDiffAnalysesSummary,RflomicsMAE: no visible global function
definition for filter
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
plotBoxplotDE,RflomicsSE: no visible global function definition for
assay
plotBoxplotDE,RflomicsSE: no visible global function definition for
full_join
plotBoxplotDE,RflomicsSE: no visible global function definition for
arrange
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
mutate
plotCoExpression,RflomicsSE: no visible binding for global variable n
plotCoExpression,RflomicsSE: no visible binding for global variable
logLike
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for mutate
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable .
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for rename
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable variable
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for full_join
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for arrange
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable groups
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable y_profiles
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for filter
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable observations
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for group_by
plotCoExpressionProfile,RflomicsSE: no visible global function
definition for summarise
plotCoExpressionProfile,RflomicsSE: no visible binding for global
variable mean.y_profiles
plotConditionsOverview,RflomicsMAE: no visible global function
definition for mutate
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable .
plotConditionsOverview,RflomicsMAE: no visible global function
definition for sampleMap
plotConditionsOverview,RflomicsMAE: no visible global function
definition for left_join
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable assay
plotConditionsOverview,RflomicsMAE: no visible global function
definition for group_by_at
plotConditionsOverview,RflomicsMAE: no visible global function
definition for count
plotConditionsOverview,RflomicsMAE: no visible global function
definition for right_join
plotConditionsOverview,RflomicsMAE: no visible global function
definition for mutate_at
plotConditionsOverview,RflomicsMAE : <anonymous>: no visible global
function definition for if_else
plotConditionsOverview,RflomicsMAE: no visible global function
definition for if_else
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable Count
plotConditionsOverview,RflomicsMAE: no visible binding for global
variable status
plotCoseqContrasts,RflomicsSE: no visible global function definition
for filter
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
does.belong
plotCoseqContrasts,RflomicsSE: no visible global function definition
for mutate
plotCoseqContrasts,RflomicsSE: no visible global function definition
for group_by
plotCoseqContrasts,RflomicsSE: no visible global function definition
for left_join
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
DEF
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
C
plotCoseqContrasts,RflomicsSE: no visible global function definition
for across
plotCoseqContrasts,RflomicsSE: no visible global function definition
for count
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
value
plotCoseqContrasts,RflomicsSE: no visible global function definition
for distinct
plotCoseqContrasts,RflomicsSE: no visible global function definition
for ungroup
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
n
plotCoseqContrasts,RflomicsSE: no visible binding for global variable
prop
plotDataDistribution,RflomicsSE: no visible global function definition
for assay
plotDataDistribution,RflomicsSE: no visible global function definition
for full_join
plotDataDistribution,RflomicsSE: no visible global function definition
for arrange
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 global function definition for
full_join
plotDataOverview,RflomicsMAE: no visible global function definition for
sampleMap
plotDataOverview,RflomicsMAE: no visible global function definition for
mutate
plotDataOverview,RflomicsMAE: no visible binding for global variable
assay
plotDataOverview,RflomicsMAE: no visible global function definition for
arrange
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 global function definition for
arrange
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
Adj.pvalue
plotHeatmapDesign,RflomicsSE: no visible global function definition for
assay
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
samples
plotHeatmapDesign,RflomicsSE: no visible binding for global variable
groups
plotLibrarySize,RflomicsSE: no visible global function definition for
assay
plotLibrarySize,RflomicsSE: no visible global function definition for
arrange
plotLibrarySize,RflomicsSE: no visible global function definition for
full_join
plotLibrarySize,RflomicsSE: no visible binding for global variable
groups
plotLibrarySize,RflomicsSE: no visible binding for global variable
samples
plotLibrarySize,RflomicsSE: no visible binding for global variable
value
plotOmicsPCA,RflomicsSE: no visible global function definition for
right_join
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
prepareForIntegration,RflomicsMAE : <anonymous>: no visible global
function definition for assay
rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for
experiments
rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for
colData
rflomicsMAE2MAE,RflomicsMAE: no visible global function definition for
sampleMap
runAnnotationEnrichment,RflomicsSE : <anonymous>: no visible global
function definition for filter
runAnnotationEnrichment,RflomicsSE: no visible global function
definition for mutate
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable .
runAnnotationEnrichment,RflomicsSE: no visible global function
definition for relocate
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable Contrast
runAnnotationEnrichment,RflomicsSE: no visible binding for global
variable Cluster
runCoExpression,RflomicsSE: no visible global function definition for
assay
runNormalization,RflomicsSE: no visible global function definition for
assay
runOmicsPCA,RflomicsSE: no visible global function definition for
assay
Undefined global functions or variables:
% of explained variance . Adj.pvalue All C Cluster Component Contrast
Count Cumulative Explained Variance DEF DataFrame Dataset
ExperimentList SE.name SUMCOL Up_Down across add_tally arrange assay
assay<- cluster colData colData<- contrast contrastName cor count
data dataset desc distinct does.belong ecoseed.df errors experiments
factorType filter first full_join group groupComparison group_by
group_by_at groups if_else intersectColumns last left_join logLike
mean.y_profiles mutate mutate_at n observations omicName outsideGroup
p.adjust packageVersion percent primary prop pvalue relevel relocate
rename right_join sampleMap samples sd select_if sessionInfo status
summarise summarize tabel type ungroup value variable y.axis
y_profiles
Consider adding
importFrom("stats", "C", "cor", "filter", "p.adjust", "relevel", "sd")
importFrom("utils", "data", "packageVersion", "sessionInfo")
to your NAMESPACE file.
* 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 ... [66s/65s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCoExpression 7.562 1.149 7.690
runOmicsIntegration 5.971 0.176 6.147
prepareForIntegration 5.223 0.113 5.336
runDataProcessing 5.028 0.175 5.203
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [198s/207s]
[198s/207s] 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/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/RFLOMICS.Rcheck/00check.log
for details.
===============================
BiocCheck('RFLOMICS_0.99.7.tar.gz')
===============================
Installing RFLOMICS
Package installed successfully
RFLOMICS session metadata
sourceDir: /tmp/RtmpSiW7Zs/file2b6f637bdac285/RFLOMICS
BiocVersion: 3.21
Package: RFLOMICS
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3477/33b6e82660218f5328ea4f5f561ebbb8503ae79e/RFLOMICS.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /tmp/RtmpSiW7Zs/file2b6f637bdac285/RFLOMICS
installDir: /tmp/RtmpSiW7Zs/file2b6f631903b79b
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...
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...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, ExperimentalDesign, GeneExpression, RNASeq, ImmunoOncology
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 590, column 22)
...
R/utils_02_set_stat_model.R (line 599, column 25)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
server.R (line 159, column 38)
...
utils_03_data_explor.R (line 421, column 28)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/module_06_annot_enrichment.R (line 1664, column 18)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/RFLOMICS-Methods_03_data_explor.R (line 1028, column 22)
...
R/utils_04_diff_analysis.R (line 140, column 19)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/RFLOMICS-Methods_03_data_explor.R (line 668, column 29)
R/RFLOMICS-Methods_03_data_explor.R (line 803, column 29)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils_00_common.R (line 226, column 13)
R/utils_00_common.R (line 229, column 13)
i NOTE: Avoid system() ; use system2()
Found in files:
system() in R/RFLOMICS-Methods_00_Common.R (line 211, 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 88, column 23)
<<- in R/utils_00_common.R (line 91, column 23)
<<- in R/utils_07_integration.R (line 303, column 52)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressWarnings() in R/RFLOMICS-Methods_06_annot_enrichment.R (line 805,
column 9)
suppressWarnings() in R/RFLOMICS-Methods_06_annot_enrichment.R (line 1200,
column 46)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 87
functions greater than 50 lines.
The longest 5 functions are:
QCNormalizationTab() (R/module_03_data_explor.R): 611 lines
...
.modLoadData() (R/module_01_load_data.R): 399 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
getAnalysis.Rd
rflomicsMAE2MAE.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; 670 lines (3%) are > 80 characters long.
First few lines:
R/coverPage.R#L12 h1(tags$span("An int ...
...
vignettes/RFLOMICS.Rmd#L495 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#L302 #' A DataFrame or data.frame of assay n ...
R/utils_01_load_data.R#L303 #' and colname samples ...
i NOTE: Consider multiples of 4 spaces for line indents; 6090 lines (29%) are
not.
First few lines:
R/coverPage.R#L8 fluidPage( ...
...
vignettes/RFLOMICS.Rmd#L483 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 v1.43.4 results
0 ERRORS | 0 WARNINGS | i 17 NOTES
i See the RFLOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.