===============================
BiocCheckGitClone('ATACCoGAPS')
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─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.2
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/9788c414021fb941d3bed2751870548c1abdf3c4/ATACCoGAPS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2557/9788c414021fb941d3bed2751870548c1abdf3c4/ATACCoGAPS.Rcheck’
* using R version 4.2.0 beta (2022-04-12 r82161)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* this is package ‘ATACCoGAPS’ version ‘0.99.2’
* 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 ‘ATACCoGAPS’ can be installed ... [24s/24s] 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 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 ... WARNING
'::' or ':::' import not declared from: ‘stringr’
Namespaces in Imports field not imported from:
‘Homo.sapiens’ ‘JASPAR2016’ ‘Mus.musculus’ ‘msigdbr’ ‘tidyverse’
All declared Imports should be used.
Package in Depends field not imported from: ‘CoGAPS’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
RNAseqTFValidation: no visible global function definition for ‘head’
cgapsPlot: no visible global function definition for ‘rainbow’
cgapsPlot: no visible global function definition for ‘par’
cgapsPlot: no visible global function definition for ‘legend’
findOverlap: no visible global function definition for ‘queryHits’
geneAccessibility: no visible global function definition for
‘subjectHits’
heatmapGeneAccessibility: no visible global function definition for
‘rainbow’
heatmapPatternMarkers: no visible global function definition for
‘rainbow’
heatmapPatternMatrix: no visible global function definition for
‘rainbow’
paths: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
head legend p.adjust par queryHits rainbow subjectHits
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "legend", "par")
importFrom("stats", "p.adjust")
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'ATACTransferLearning.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroFinalSubsetData.Rdata?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroGRanges.Rdata?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroCellTypes.Rdata?raw=true")
projectRResults <- ATACTransferLearning(newData = BuenrostroFinalSubsetData, CoGAPSResult = schepCogapsResult, originalPeaks = schepFil ... [TRUNCATED]
Rd file 'RNAseqTFValidation.Rd':
\examples lines wider than 100 characters:
gseaList = RNAseqTFValidation(TFMatchResult$RegulatoryNetworks, RNACoGAPS, c(1,3), c(2,7), matrix = FALSE)
Rd file 'applyGREAT.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
GOenrichment <- applyGREAT(cogapsResult = schepCogapsResult, granges = schepGranges, genome = "hg19")
Rd file 'cgapsPlot.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
Rd file 'dataSubsetBySparsity.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/schepATACPreFilter.Rdata?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/schepUnfilteredCells.Rdata?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/schepUnfilteredPeaks.Rdata?raw=true")
dataSubset = dataSubsetBySparsity(data = schepATACPreFilter, cell_list = schepUnfilteredCells, peak_list = schepUnfilteredPeaks, cell_c ... [TRUNCATED]
Rd file 'foldAccessibility.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepFilteredData.rda?raw=true")
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = schepFilteredData, genome = Homo.sapie ... [TRUNCATED]
foldAccessibility(peaksAccessibility = accessiblePeaks$TAL1, cellTypeList = schepCelltypes, cellType = "K562 Erythroleukemia", binaryMa ... [TRUNCATED]
Rd file 'geneAccessibility.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepFilteredData.rda?raw=true")
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = schepFilteredData, genome = Homo.sapie ... [TRUNCATED]
Rd file 'genePatternMatch.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
Rd file 'heatmapGeneAccessibility.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepFilteredData.rda?raw=true")
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = schepFilteredData, genome = Homo.sapie ... [TRUNCATED]
Rd file 'heatmapPatternMarkers.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepFilteredData.rda?raw=true")
Rd file 'heatmapPatternMatrix.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
Rd file 'motifSummarization.Rd':
\examples lines wider than 100 characters:
motifSummTest = motifSummarization(motifList = motifs, scATACData = scatac, granges = peakGranges, genome = "hg19", cellNames = cells, ... [TRUNCATED]
Rd file 'pathwayMatch.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
Rd file 'patternMarkerCellClassifier.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
Rd file 'simpleMotifTFMatch.Rd':
\examples lines wider than 100 characters:
repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘schepCellTypes’ ‘schepCogapsResult’ ‘schepGranges’ ‘schepPeaks’
‘subsetSchepData’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' imports not declared from:
‘dplyr’ ‘repmis’
'library' or 'require' call not declared from: ‘dplyr’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
schepCogapsResult.rda 1.5Mb 743Kb xz
schepGranges.rda 20Kb 14Kb xz
schepPeaks.rda 45Kb 26Kb xz
subsetSchepData.rda 902Kb 450Kb bzip2
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/25s] ERROR
Running examples in ‘ATACCoGAPS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ATACTransferLearning
> ### Title: Transfer Learning between ATACseq data sets using projectR
> ### Aliases: ATACTransferLearning
>
> ### ** Examples
>
> repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true")
Downloading data from: https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/data/schepCogapsResult.rda?raw=true
SHA-1 hash of the downloaded data file is:
b240af6b27f7f4619aa4d166bf8b95bf4d52e9a2
[1] "schepCogapsResult"
> data(schepFilteredPeaks)
Warning in data(schepFilteredPeaks) :
data set ‘schepFilteredPeaks’ not found
> data(schepGranges)
>
>
> #getting count matrix - peaks x cells
> repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroFinalSubsetData.Rdata?raw=true")
Downloading data from: https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroFinalSubsetData.Rdata?raw=true
SHA-1 hash of the downloaded data file is:
e0edce13d2d860806c0f14494e6c09edff5aee35
[1] "BuenrostroFinalSubsetData"
>
> #getting GRanges for peaks
> repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroGRanges.Rdata?raw=true")
Downloading data from: https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroGRanges.Rdata?raw=true
SHA-1 hash of the downloaded data file is:
c88541375c4fd38464225b1932b7b25656a0dd0b
[1] "BuenrostroGRanges"
>
> #getting celltypes
> repmis::source_data("https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroCellTypes.Rdata?raw=true")
Downloading data from: https://github.com/FertigLab/ATACCoGAPS/blob/PaperVersion/BuenrostroCellTypes.Rdata?raw=true
SHA-1 hash of the downloaded data file is:
60ba17a8ee4784858b7d76d3194e397dd05f2b25
[1] "BuenrostroCellTypes"
>
> projectRResults <- ATACTransferLearning(newData = BuenrostroFinalSubsetData, CoGAPSResult = schepCogapsResult, originalPeaks = schepFilteredPeaks, originalGranges = schepGranges,newGranges = BuenrostroGRanges)
Error in ATACTransferLearning(newData = BuenrostroFinalSubsetData, CoGAPSResult = schepCogapsResult, :
object 'schepFilteredPeaks' not found
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
‘dplyr’ ‘viridis’
'library' or 'require' call not declared from: ‘dplyr’
* 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: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2557/9788c414021fb941d3bed2751870548c1abdf3c4/ATACCoGAPS.Rcheck/00check.log’
for details.
===============================
BiocCheck('ATACCoGAPS_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.31.37
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.2
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpsrwPlM/file158a57cc7e63c/ATACCoGAPS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpsrwPlM/file158a58eb2aee
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/9788c414021fb941d3bed2751870548c1abdf3c4/ATACCoGAPS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* 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 10 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().
* 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...
* NOTE: Update R version dependency from 3.5.0 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Transcription, Sequencing, Microarray, Pathways, Bayesian,
Clustering, GeneExpression, RNASeq, ImmunoOncology,
DifferentialExpression, GeneSetEnrichment, MultipleComparison,
GO, DimensionReduction, TimeCourse
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import msigdbr, tidyverse, JASPAR2016, Homo.sapiens,
Mus.musculus in NAMESPACE as well as DESCRIPTION.
* 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 ATACCoGAPS...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* WARNING: Remove set.seed usage (found 4 times)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6
times)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 5
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
motifPatternMatch.Rd, motifSummarization.Rd,
RNAseqTFValidation.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.12% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 126 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 664 lines
(28%) are not.
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.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
2 ERRORS | 3 WARNINGS | 15 NOTES
See the ATACCoGAPS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.