===============================
BiocCheckGitClone('HiCDOC')
===============================
This is BiocCheckGitClone version 1.29.14. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
2020_package_HiCDOC.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
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R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2212/HiCDOC_20210817122850/HiCDOC.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCDOC/DESCRIPTION’ ... OK
* this is package ‘HiCDOC’ version ‘0.99.0’
* 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 ... NOTE
Found the following hidden files and directories:
.lintr
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiCDOC’ can be installed ... [23s/23s] OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
doc 2.4Mb
libs 3.2Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [10s/10s] NOTE
.clusterize: no visible binding for global variable ‘chromosome’
.clusterize: no visible binding for global variable ‘condition’
.clusterize: no visible binding for global variable ‘bin’
.clusterize: no visible binding for global variable ‘compartment’
.clusterizeChromosomeCondition: no visible binding for global variable
‘chromosome’
.clusterizeChromosomeCondition: no visible binding for global variable
‘condition’
.clusterizeChromosomeCondition: no visible binding for global variable
‘bin’
.clusterizeChromosomeCondition: no visible binding for global variable
‘compartment’
.clusterizeChromosomeCondition: no visible binding for global variable
‘concordance’
.computePValues: no visible binding for global variable ‘chromosome’
.computePValues: no visible binding for global variable ‘bin’
.computePValues: no visible binding for global variable ‘condition’
.computePValues: no visible binding for global variable ‘chromosome.2’
.computePValues: no visible binding for global variable ‘bin.2’
.computePValues: no visible binding for global variable ‘concordance’
.computePValues: no visible binding for global variable ‘condition.1’
.computePValues: no visible binding for global variable ‘condition.2’
.computePValues: no visible binding for global variable ‘concordance.1’
.computePValues: no visible binding for global variable ‘concordance.2’
.computePValues: no visible binding for global variable ‘compartment’
.computePValues: no visible binding for global variable ‘compartment.1’
.computePValues: no visible binding for global variable ‘compartment.2’
.computePValues: no visible binding for global variable ‘difference’
.computePValues: no visible binding for global variable ‘H0_value’
.computePValues: no visible binding for global variable ‘pvalue’
.computePValues: no visible binding for global variable
‘pvalue.adjusted’
.computePValues: no visible binding for global variable ‘direction’
.computeSelfInteractionRatios: no visible binding for global variable
‘chromosome’
.computeSelfInteractionRatios: no visible binding for global variable
‘condition’
.computeSelfInteractionRatios: no visible binding for global variable
‘bin.1’
.computeSelfInteractionRatios: no visible binding for global variable
‘bin.2’
.computeSelfInteractionRatios: no visible binding for global variable
‘namepos’
.computeSelfInteractionRatios: no visible binding for global variable
‘bin’
.determinePositions: no visible binding for global variable
‘chromosome’
.determinePositions: no visible binding for global variable
‘position.1’
.determinePositions: no visible binding for global variable
‘position.2’
.determinePositions: no visible binding for global variable
‘maxPosition.1’
.determinePositions: no visible binding for global variable
‘maxPosition.2’
.determinePositions: no visible binding for global variable ‘bin’
.fillHiCDOCDataSet : <anonymous>: no visible binding for global
variable ‘chromosome’
.fillHiCDOCDataSet : <anonymous>: no visible binding for global
variable ‘condition’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘chromosome’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘bin.1’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘bin.2’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘total.interactions.y’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘total.interactions.x’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘condition’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘total.interactions’
.filterSparseReplicatesOfChromosome: no visible binding for global
variable ‘fillPct’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘chromosome’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘bin.1’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘bin.2’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘name’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘bin’
.filterWeakPositionsOfChromosome: no visible binding for global
variable ‘condition’
.matrixToSparseInteractions: no visible binding for global variable
‘bin.1’
.matrixToSparseInteractions: no visible binding for global variable
‘bin.2’
.normalizeDistanceEffectOfChromosome: no visible binding for global
variable ‘chromosome’
.normalizeDistanceEffectOfChromosome: no visible binding for global
variable ‘bin.2’
.normalizeDistanceEffectOfChromosome: no visible binding for global
variable ‘bin.1’
.normalizeDistanceEffectOfChromosome: no visible binding for global
variable ‘sampleDistance’
.parseOneCool: no visible binding for global variable ‘ide’
.parseOneCool: no visible binding for global variable ‘chromosome’
.parseOneCool: no visible binding for global variable ‘position’
.parseOneCool: no visible binding for global variable ‘id1’
.parseOneCool: no visible binding for global variable ‘id2’
.parseOneCool: no visible binding for global variable ‘chromosome.1’
.parseOneCool: no visible binding for global variable ‘chromosome.2’
.parseOneCool: no visible binding for global variable ‘position.1’
.parseOneCool: no visible binding for global variable ‘position.2’
.parseOneHiCPro: no visible binding for global variable ‘chromosome’
.parseOneHiCPro: no visible binding for global variable ‘index’
.parseOneHiCPro: no visible binding for global variable ‘startIndex’
.parseOneHiCPro: no visible binding for global variable ‘chromosome.1’
.parseOneHiCPro: no visible binding for global variable ‘chromosome.2’
.parseOneHiCPro: no visible binding for global variable ‘position.1’
.parseOneHiCPro: no visible binding for global variable ‘position.2’
.parseTabular: no visible binding for global variable
‘condition.replicate’
.parseTabular: no visible binding for global variable ‘CR’
.parseTabular: no visible binding for global variable ‘position 1’
.parseTabular: no visible binding for global variable ‘position 2’
.plotInteractionsGrid: no visible binding for global variable
‘position.1’
.plotInteractionsGrid: no visible binding for global variable
‘position.2’
.plotInteractionsWrap: no visible binding for global variable
‘position.1’
.plotInteractionsWrap: no visible binding for global variable
‘position.2’
.predictCompartmentsAB: no visible binding for global variable
‘chromosome’
.predictCompartmentsAB: no visible binding for global variable
‘compartment’
.predictCompartmentsAB: no visible binding for global variable ‘ratio’
.predictCompartmentsAB: no visible binding for global variable
‘ratio.1’
.predictCompartmentsAB: no visible binding for global variable
‘ratio.2’
.predictCompartmentsAB: no visible binding for global variable ‘A’
.predictCompartmentsAB: no visible binding for global variable ‘change’
.predictCompartmentsAB: no visible binding for global variable
‘concordance’
.reduceHiCDOCChromosomes: no visible binding for global variable
‘chromosome’
.reduceHiCDOCConditions: no visible binding for global variable
‘condition’
.reformatInteractions: no visible binding for global variable
‘chromosome’
.reformatInteractions: no visible binding for global variable
‘condition’
.reformatInteractions: no visible binding for global variable ‘bin.1’
.reformatInteractions: no visible binding for global variable ‘bin.2’
.replacePositionsByBins: no visible binding for global variable
‘chromosome’
.replacePositionsByBins: no visible binding for global variable ‘bin’
.replacePositionsByBins: no visible binding for global variable
‘condition’
.replacePositionsByBins: no visible binding for global variable ‘bin.1’
.replacePositionsByBins: no visible binding for global variable ‘bin.2’
.sortInteractions: no visible binding for global variable ‘chromosome’
.sortInteractions: no visible binding for global variable ‘condition’
.sortInteractions: no visible binding for global variable ‘bin.1’
.sortInteractions: no visible binding for global variable ‘bin.2’
.sortInteractions: no visible binding for global variable ‘position.1’
.sortInteractions: no visible binding for global variable ‘position.2’
.sparseInteractionsToMatrix: no visible binding for global variable
‘chromosome’
.sparseInteractionsToMatrix: no visible binding for global variable
‘condition’
.sparseInteractionsToMatrix: no visible binding for global variable
‘bin.1’
.sparseInteractionsToMatrix: no visible binding for global variable
‘bin.2’
.tieCentroids: no visible binding for global variable ‘compartment’
.tieCentroids: no visible binding for global variable ‘centroid’
.tieCentroids: no visible binding for global variable ‘condition’
.tieCentroids: no visible binding for global variable ‘chromosome’
.tieCentroids: no visible binding for global variable ‘centroid.1’
.tieCentroids: no visible binding for global variable ‘reference.1’
.tieCentroids: no visible binding for global variable ‘centroid.2’
.tieCentroids: no visible binding for global variable ‘reference.2’
.tieCentroids: no visible binding for global variable ‘cluster.1’
.tieCentroids: no visible binding for global variable ‘cluster.2’
.tieCentroids: no visible binding for global variable ‘change’
.tieCentroids: no visible binding for global variable ‘concordance’
.validateXlim: no visible binding for global variable ‘chromosome’
normalizeTechnicalBiases: no visible binding for global variable
‘chromosome’
normalizeTechnicalBiases: no visible binding for global variable
‘bin.1’
normalizeTechnicalBiases: no visible binding for global variable
‘bin.2’
normalizeTechnicalBiases: no visible binding for global variable
‘condition’
normalizeTechnicalBiases : <anonymous>: no visible binding for global
variable ‘condition’
normalizeTechnicalBiases: no visible binding for global variable ‘bin’
normalizeTechnicalBiases: no visible binding for global variable
‘index’
plotCentroids: no visible binding for global variable ‘name’
plotCentroids: no visible binding for global variable ‘condition’
plotCentroids: no visible binding for global variable ‘compartment’
plotCentroids: no visible binding for global variable ‘centroid’
plotCentroids: no visible binding for global variable ‘group’
plotCentroids: no visible binding for global variable ‘PC1’
plotCentroids: no visible binding for global variable ‘PC2’
plotCompartments: no visible binding for global variable ‘compartment’
plotCompartments: no visible binding for global variable ‘position’
plotCompartments: no visible binding for global variable ‘condition’
plotConcordanceDifferences: no visible binding for global variable
‘compartment.1’
plotConcordanceDifferences: no visible binding for global variable
‘compartment.2’
plotConcordanceDifferences: no visible binding for global variable
‘difference’
plotConcordanceDifferences: no visible binding for global variable
‘changed’
plotConcordances: no visible binding for global variable ‘condition’
plotConcordances: no visible binding for global variable
‘pvalue.adjusted’
plotConcordances: no visible binding for global variable ‘position’
plotConcordances: no visible binding for global variable ‘concordance’
plotDistanceEffect: no visible binding for global variable ‘bin.2’
plotDistanceEffect: no visible binding for global variable ‘bin.1’
plotInteractions: no visible binding for global variable ‘bin’
plotInteractions: no visible binding for global variable ‘condition’
plotInteractions: no visible binding for global variable ‘facetVar’
plotSelfInteractionRatios: no visible binding for global variable
‘compartment’
plotSelfInteractionRatios: no visible binding for global variable
‘ratio’
compartments,HiCDOCDataSet: no visible binding for global variable
‘chromosome’
compartments,HiCDOCDataSet: no visible binding for global variable
‘condition’
compartments,HiCDOCDataSet: no visible binding for global variable
‘compartment’
compartments,HiCDOCDataSet: no visible binding for global variable
‘consecutive’
compartments,HiCDOCDataSet: no visible binding for global variable
‘switching’
compartments,HiCDOCDataSet: no visible binding for global variable
‘group’
concordances,HiCDOCDataSet: no visible binding for global variable
‘chromosome’
concordances,HiCDOCDataSet: no visible binding for global variable
‘condition’
concordances,HiCDOCDataSet: no visible binding for global variable
‘compartment’
concordances,HiCDOCDataSet: no visible binding for global variable
‘concordance’
differences,HiCDOCDataSet: no visible binding for global variable
‘chromosome’
differences,HiCDOCDataSet: no visible binding for global variable
‘condition.1’
differences,HiCDOCDataSet: no visible binding for global variable
‘condition.2’
differences,HiCDOCDataSet: no visible binding for global variable
‘pvalue’
differences,HiCDOCDataSet: no visible binding for global variable
‘pvalue.adjusted’
differences,HiCDOCDataSet: no visible binding for global variable
‘direction’
differences,HiCDOCDataSet: no visible binding for global variable
‘significance’
interactions,HiCDOCDataSet: no visible binding for global variable
‘chromosome’
interactions,HiCDOCDataSet: no visible binding for global variable
‘bin’
interactions,HiCDOCDataSet: no visible binding for global variable
‘position.1’
interactions,HiCDOCDataSet: no visible binding for global variable
‘position.2’
interactions,HiCDOCDataSet: no visible binding for global variable
‘condition’
Undefined global functions or variables:
A CR H0_value PC1 PC2 bin bin.1 bin.2 centroid centroid.1 centroid.2
change changed chromosome chromosome.1 chromosome.2 cluster.1
cluster.2 compartment compartment.1 compartment.2 concordance
concordance.1 concordance.2 condition condition.1 condition.2
condition.replicate consecutive difference direction facetVar fillPct
group id1 id2 ide index maxPosition.1 maxPosition.2 name namepos
position position 1 position 2 position.1 position.2 pvalue
pvalue.adjusted ratio ratio.1 ratio.2 reference.1 reference.2
sampleDistance significance startIndex switching total.interactions
total.interactions.x total.interactions.y
* 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [519s/389s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCentroids 64.485 1.830 40.964
plotCompartmentChanges 56.134 2.616 37.902
HiCDOC 55.043 3.454 48.412
normalizeTechnicalBiases 52.207 1.500 35.494
plotCompartments 48.938 2.115 39.736
detectCompartments 48.489 2.042 40.861
plotConcordances 47.765 2.517 39.150
plotSelfInteractionRatios 45.285 2.232 33.513
plotConcordanceDifferences 44.693 2.070 37.407
plotDistanceEffect 14.717 0.572 15.290
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [160s/130s]
[161s/130s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2212/HiCDOC_20210817122850/HiCDOC.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('HiCDOC_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.29.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 159 object(s) are initialized.
Maybe they are part of a data set loaded with data(), or perhaps
part of an object referenced in with() or within().
function (object)
.clusterize (chromosome)
.clusterize (condition)
.clusterize (bin)
.clusterize (compartment)
.clusterizeChromosomeCondition (chromosome)
.clusterizeChromosomeCondition (condition)
.clusterizeChromosomeCondition (bin)
.clusterizeChromosomeCondition (compartment)
.clusterizeChromosomeCondition (concordance)
.computePValues (chromosome)
.computePValues (bin)
.computePValues (condition)
.computePValues (chromosome.2)
.computePValues (bin.2)
.computePValues (concordance)
.computePValues (condition.1)
.computePValues (condition.2)
.computePValues (concordance.1)
.computePValues (concordance.2)
.computePValues (compartment)
.computePValues (compartment.1)
.computePValues (compartment.2)
.computePValues (difference)
.computePValues (H0_value)
.computePValues (pvalue)
.computePValues (pvalue.adjusted)
.computePValues (direction)
.computeSelfInteractionRatios (chromosome)
.computeSelfInteractionRatios (condition)
.computeSelfInteractionRatios (bin.1)
.computeSelfInteractionRatios (bin.2)
.computeSelfInteractionRatios (namepos)
.computeSelfInteractionRatios (bin)
.determinePositions (chromosome)
.determinePositions (position.1)
.determinePositions (position.2)
.determinePositions (maxPosition.1)
.determinePositions (maxPosition.2)
.determinePositions (bin)
.fillHiCDOCDataSet (chromosome)
.fillHiCDOCDataSet (condition)
.filterSparseReplicatesOfChromosome (chromosome)
.filterSparseReplicatesOfChromosome (bin.1)
.filterSparseReplicatesOfChromosome (bin.2)
.filterSparseReplicatesOfChromosome (total.interactions.y)
.filterSparseReplicatesOfChromosome (total.interactions.x)
.filterSparseReplicatesOfChromosome (condition)
.filterSparseReplicatesOfChromosome (total.interactions)
.filterSparseReplicatesOfChromosome (fillPct)
.filterWeakPositionsOfChromosome (chromosome)
.filterWeakPositionsOfChromosome (bin.1)
.filterWeakPositionsOfChromosome (bin.2)
.filterWeakPositionsOfChromosome (name)
.filterWeakPositionsOfChromosome (bin)
.filterWeakPositionsOfChromosome (condition)
.matrixToSparseInteractions (bin.1)
.matrixToSparseInteractions (bin.2)
.normalizeDistanceEffectOfChromosome (chromosome)
.normalizeDistanceEffectOfChromosome (bin.2)
.normalizeDistanceEffectOfChromosome (bin.1)
.normalizeDistanceEffectOfChromosome (sampleDistance)
.parseOneCool (ide)
.parseOneCool (chromosome)
.parseOneCool (position)
.parseOneCool (id1)
.parseOneCool (id2)
.parseOneCool (chromosome.1)
.parseOneCool (chromosome.2)
.parseOneCool (position.1)
.parseOneCool (position.2)
.parseOneHiCPro (chromosome)
.parseOneHiCPro (index)
.parseOneHiCPro (startIndex)
.parseOneHiCPro (chromosome.1)
.parseOneHiCPro (chromosome.2)
.parseOneHiCPro (position.1)
.parseOneHiCPro (position.2)
.parseTabular (condition.replicate)
.parseTabular (CR)
.parseTabular (position 1)
.parseTabular (position 2)
.plotInteractionsGrid (position.1)
.plotInteractionsGrid (position.2)
.plotInteractionsWrap (position.1)
.plotInteractionsWrap (position.2)
.predictCompartmentsAB (chromosome)
.predictCompartmentsAB (compartment)
.predictCompartmentsAB (ratio)
.predictCompartmentsAB (ratio.1)
.predictCompartmentsAB (ratio.2)
.predictCompartmentsAB (A)
.predictCompartmentsAB (change)
.predictCompartmentsAB (concordance)
.reduceHiCDOCChromosomes (chromosome)
.reduceHiCDOCConditions (condition)
.reformatInteractions (chromosome)
.reformatInteractions (condition)
.reformatInteractions (bin.1)
.reformatInteractions (bin.2)
.replacePositionsByBins (chromosome)
.replacePositionsByBins (bin)
.replacePositionsByBins (condition)
.replacePositionsByBins (bin.1)
.replacePositionsByBins (bin.2)
.sortInteractions (chromosome)
.sortInteractions (condition)
.sortInteractions (bin.1)
.sortInteractions (bin.2)
.sortInteractions (position.1)
.sortInteractions (position.2)
.sparseInteractionsToMatrix (chromosome)
.sparseInteractionsToMatrix (condition)
.sparseInteractionsToMatrix (bin.1)
.sparseInteractionsToMatrix (bin.2)
.tieCentroids (compartment)
.tieCentroids (centroid)
.tieCentroids (condition)
.tieCentroids (chromosome)
.tieCentroids (centroid.1)
.tieCentroids (reference.1)
.tieCentroids (centroid.2)
.tieCentroids (reference.2)
.tieCentroids (cluster.1)
.tieCentroids (cluster.2)
.tieCentroids (change)
.tieCentroids (concordance)
.validateXlim (chromosome)
normalizeTechnicalBiases (chromosome)
normalizeTechnicalBiases (bin.1)
normalizeTechnicalBiases (bin.2)
normalizeTechnicalBiases (condition)
normalizeTechnicalBiases (condition)
normalizeTechnicalBiases (bin)
normalizeTechnicalBiases (index)
plotCentroids (name)
plotCentroids (condition)
plotCentroids (compartment)
plotCentroids (centroid)
plotCentroids (group)
plotCentroids (PC1)
plotCentroids (PC2)
plotCompartments (compartment)
plotCompartments (position)
plotCompartments (condition)
plotConcordanceDifferences (compartment.1)
plotConcordanceDifferences (compartment.2)
plotConcordanceDifferences (difference)
plotConcordanceDifferences (changed)
plotConcordances (condition)
plotConcordances (pvalue.adjusted)
plotConcordances (position)
plotConcordances (concordance)
plotDistanceEffect (bin.2)
plotDistanceEffect (bin.1)
plotInteractions (bin)
plotInteractions (condition)
plotInteractions (facetVar)
plotSelfInteractionRatios (compartment)
plotSelfInteractionRatios (ratio)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* 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...
* NOTE: Update R version dependency from 4.0.0 to 4.1.0.
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* NOTE: License 'LGPL (>= 3) + file LICENSE' unknown; licenses
cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/HiCDOC.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCDOC...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.....................................................
* NOTE: Recommended function length <= 50 lines.
There are 28 functions > 50 lines.
The longest 5 functions are:
.computePValues() (R/detectCompartments.R, line 621): 134 lines
.clusterizeChromosomeCondition() (R/detectCompartments.R, line
209): 125 lines
.predictCompartmentsAB() (R/detectCompartments.R, line 495):
113 lines
normalizeTechnicalBiases() (R/normalizeTechnicalBiases.R, line
55): 113 lines
plotConcordances() (R/plotConcordances.R, line 32): 110 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
HiCDOCDataSetFromCool.Rd, HiCDOCDataSetFromHiC.Rd,
HiCDOCDataSetFromHiCPro.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
12% of man pages use one of these cases.
Found in the following files:
HiCDOCDataSetFromCool.Rd
HiCDOCDataSetFromHiC.Rd
HiCDOCDataSetFromHiCPro.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
HiCDOCDataSetFromCool.Rd
HiCDOCDataSetFromHiC.Rd
HiCDOCDataSetFromHiCPro.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...
* NOTE: Consider shorter lines; 46 lines (1%) are > 80 characters
long.
First 6 lines:
R/RcppExports.R:4 constrainedClustering <- function(rMatrix, rLinks, ma...
R/RcppExports.R:5 .Call('_HiCDOC_constrainedClustering', PACKAGE = ...
man/detectCompartments.Rd:21 \item{kMeansDelta}{The convergence stop cr...
man/detectCompartments.Rd:26 \item{kMeansIterations}{The maximum number...
man/detectCompartments.Rd:30 \item{kMeansRestarts}{The amount of times ...
man/filterSmallChromosomes.Rd:12 \item{threshold}{The minimum length (n...
* NOTE: Consider multiples of 4 spaces for line indents, 151
lines(2%) are not.
First 6 lines:
R/detectCompartments.R:717 quantile = ifelse(
R/detectCompartments.R:721 )
R/internalmApply.R:5 warning("The use of RNGseed may not b...
R/internalmApply.R:6 "See ?detectCompartments for more det...
R/internalmApply.R:11 BPPARAM = BiocPara...
R/internalParsers.R:70 replicate = purrr::map_chr...
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
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Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
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Tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 11
For detailed information about these checks, see the BiocCheck
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