Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* preparing ‘ATACCoGAPS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ATACCoGAPS_0.99.5.tar.gz’

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 BiocCheckGitClone('ATACCoGAPS')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/30f7d7dc0019cecadb0d6fc05344127f8d62aef0/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')




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 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2557/30f7d7dc0019cecadb0d6fc05344127f8d62aef0/ATACCoGAPS.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* 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 ‘0.99.5’
* 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/17s] 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 '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:
     GOenrichment <- applyGREAT(cogapsResult = schepCogapsResult, granges = schepGranges, genome = "hg19")

Rd file 'foldAccessibility.Rd':
  \examples lines wider than 100 characters:
     accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]
     foldAccessibility(peaksAccessibility = accessiblePeaks$TAL1, cellTypeList = schepCellTypes, cellType = "K562 Erythroleukemia", binaryMa ... [TRUNCATED]

Rd file 'geneAccessibility.Rd':
  \examples lines wider than 100 characters:
     accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]

Rd file 'genePatternMatch.Rd':
  \examples lines wider than 100 characters:
     genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)

Rd file 'heatmapGeneAccessibility.Rd':
  \examples lines wider than 100 characters:
     accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens ... [TRUNCATED]

Rd file 'motifSummarization.Rd':
  \examples lines wider than 100 characters:
     motifSummTest = motifSummarization(motifList = motifs, scATACData = scatac, granges = peakGranges, genome = "hg19", cellNames = cells,  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘exampleMotifList’ ‘schepCellTypes’ ‘schepCogapsResult’
  ‘schepGranges’ ‘schepPeaks’ ‘subsetSchepData’ ‘tfData’
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 ':::' import not declared from: ‘dplyr’
'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
  tfData.rda               466Kb    197Kb       xz
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [126s/225s] ERROR
Running examples in ‘ATACCoGAPS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmapGeneAccessibility
> ### Title: Heatmap Gene Accessibility
> ### Aliases: heatmapGeneAccessibility
> 
> ### ** Examples
> 
> library(Homo.sapiens)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
> geneList <- c("TAL1", "EGR1")
> data(schepGranges)
> data("subsetSchepData")
> data(schepCellTypes)
> accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens)
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:1 mapping between keys and columns
[1] "No overlapping peaks with TAL1"
> heatmapGeneAccessibility(genePeaks = accessiblePeaks$TAL1, celltypes = schepCellTypes)
Error in genePeaks[-c(ind), ] : incorrect number of dimensions
Calls: heatmapGeneAccessibility
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/2557/30f7d7dc0019cecadb0d6fc05344127f8d62aef0/ATACCoGAPS.Rcheck/00check.log’
for details.





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 BiocCheck('ATACCoGAPS_0.99.5.tar.gz')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpYXYaRt/file8abc79ef16a6/ATACCoGAPS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpYXYaRt/file8abc5403e4fa
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/30f7d7dc0019cecadb0d6fc05344127f8d62aef0/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 man pages that
      documentexported objects.
    * NOTE: Usage of dontrun{} / donttest{} found in man page
      examples.12% of man pages use one of these cases.
* 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; 112 lines (5%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 665 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...
    Maintainer is registered at support site.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

─ BiocCheck results ──
2 ERRORS | 3 WARNINGS | 14 NOTES

See the ATACCoGAPS.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir ATACCoGAPS_0.99.5.tar.gz'
>>>>>>> 

* installing *source* package ‘ATACCoGAPS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ATACCoGAPS)