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_0.99.3.tar.gz’

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 BiocCheckGitClone('ATACCoGAPS')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/ATACCoGAPS_20220509094246/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/ATACCoGAPS_20220509094246/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 ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ATACCoGAPS’ can be installed ... [53s/60s] 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 ... [37s/46s] 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 ... [1s/1s] 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:
  ‘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 ':::' 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
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [235s/380s] ERROR
Running examples in ‘ATACCoGAPS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genePatternMatch
> ### Title: Match genes to pattern differentiating peaks
> ### Aliases: genePatternMatch
> 
> ### ** Examples
> 
> data("schepCogapsResult")
> data(schepGranges)
> 
> genes = genePatternMatch(cogapsResult = schepCogapsResult, generanges = schepGranges, genome = Homo.sapiens)
[1] Number of peaks used for each pattern:
Pattern 1 Pattern 2 Pattern 3 Pattern 4 Pattern 5 Pattern 6 Pattern 7 Pattern 8 
       80       640       906      2055        35       501        28       776 
Pattern 9 
       15 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'genes': object 'Homo.sapiens' not found
Calls: genePatternMatch -> suppressMessages -> withCallingHandlers
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/ATACCoGAPS_20220509094246/ATACCoGAPS.Rcheck/00check.log’
for details.





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 BiocCheck('ATACCoGAPS_0.99.3.tar.gz')

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─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: ATACCoGAPS
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp410I2k/file31f539926dfe/ATACCoGAPS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp410I2k/file31f539abc130
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2557/ATACCoGAPS_20220509094246/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...
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * 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; 104 lines (4%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 664 lines
      (29%) 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 ──
3 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_0.99.3.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)