Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘betAS/DESCRIPTION’ ... OK
* preparing ‘betAS’:
* 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 ‘betAS_0.99.0.tar.gz’

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 BiocCheckGitClone('betAS')

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─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: betAS
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2810/betAS_20230103191407/betAS
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      betAS.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
1 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/2810/betAS_20230103191407/betAS.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘betAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘betAS’ 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:
  .github
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 ‘betAS’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [19s/19s] NOTE
bigPicturePlot: no visible binding for global variable ‘value’
bigPicturePlot: no visible binding for global variable ‘variable’
plotDensitiesFromEventObjList: no visible binding for global variable
  ‘labA’
plotDensitiesFromEventObjList: no visible binding for global variable
  ‘labB’
plotDensitiesFromEventObjList: no visible binding for global variable
  ‘samples’
plotDensitiesFromEventObjList: no visible binding for global variable
  ‘group’
plotDensitiesFromEventObjList: no visible binding for global variable
  ‘psis’
plotIndividualDensities: no visible binding for global variable
  ‘samples’
plotIndividualDensities: no visible binding for global variable ‘group’
plotIndividualDensities: no visible binding for global variable ‘psis’
plotIndividualDensitiesList: no visible binding for global variable
  ‘group’
plotPDiffFromEventObjList: no visible binding for global variable
  ‘seq3’
plotPDiffFromEventObjList: no visible binding for global variable
  ‘prob3’
plotVolcano: no visible binding for global variable ‘deltapsi’
plotVolcano: no visible binding for global variable ‘Pdiff’
plotVolcano: no visible binding for global variable ‘EVENT’
plotVolcano: no visible binding for global variable ‘GENE’
plotVolcanoFDR: no visible binding for global variable ‘deltapsi’
plotVolcanoFDR: no visible binding for global variable ‘invertedFDR’
plotVolcanoFDR: no visible binding for global variable ‘EVENT’
plotVolcanoFDR: no visible binding for global variable ‘GENE’
plotVolcanoFstat: no visible binding for global variable ‘deltapsi’
plotVolcanoFstat: no visible binding for global variable ‘Fstat’
plotVolcanoFstat: no visible binding for global variable ‘EVENT’
plotVolcanoFstat: no visible binding for global variable ‘GENE’
preparePieForVastToolsCOMPLEX: no visible binding for global variable
  ‘name’
preparePieForVastToolsCOMPLEX: no visible binding for global variable
  ‘y’
Undefined global functions or variables:
  EVENT Fstat GENE Pdiff deltapsi group invertedFDR labA labB name
  prob3 psis samples seq3 value variable y
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'plotIndividualDensitiesList.Rd':
  \examples lines wider than 100 characters:
     testGroups[[length(testGroups)+1]] <- list(name = "GroupA", samples = c("ERR2598266", "ERR2598267", "ERR2598268"), color = "#FF9AA2")
     testGroups[[length(testGroups)+1]] <- list(name = "GroupB", samples = c("ERR2598270", "ERR2598307", "ERR2598351"), color = "#FFB7B2")
     plotIndividualDensitiesList(eventID = "HsaEX0019479", npoints = 500, psitable = psiTable, qualtable = qualTable, groupList = testGroups ... [TRUNCATED]

Rd file 'plotVolcano.Rd':
  \examples lines wider than 100 characters:
     testGroups[[length(testGroups)+1]] <- list(name = "GroupA", samples = c("ERR2598266", "ERR2598267", "ERR2598268"), color = "#FF9AA2")
     testGroups[[length(testGroups)+1]] <- list(name = "GroupB", samples = c("ERR2598270", "ERR2598307", "ERR2598351"), color = "#FFB7B2")
     volcanoTable <- prepareTableVolcano(psitable = psiTable, qualtable = qualTable, npoints = 500, colsA = colsGroupA, colsB = colsGroupB,  ... [TRUNCATED]
     plotVolcano(betasTable = volcanoTable, labA = groupA, labB = groupB, basalColor = "#89C0AE", interestColor = "#E69A9C")

Rd file 'prepareTableVolcano.Rd':
  \examples lines wider than 100 characters:
     testGroups[[length(testGroups)+1]] <- list(name = "GroupA", samples = c("ERR2598266", "ERR2598267", "ERR2598268"), color = "#FF9AA2")
     testGroups[[length(testGroups)+1]] <- list(name = "GroupB", samples = c("ERR2598270", "ERR2598307", "ERR2598351"), color = "#FFB7B2")
     prepareTableVolcano(psitable = psiTable, qualtable = qualTable, npoints = 500, colsA = colsGroupA, colsB = colsGroupB, labA = groupA, l ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [3s/3s] 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 ... [5s/5s] OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2810/betAS_20230103191407/betAS.Rcheck/00check.log’
for details.






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 BiocCheck('betAS_0.99.0.tar.gz')

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─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: betAS
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpZedC2U/filebf1e4608f96a/betAS
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpZedC2U/filebf1e1ec72738
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2810/betAS_20230103191407/betAS.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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 4.1.0 to 4.3.0.
* 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...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 betAS...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 62 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* 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; 268 lines (7%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 1365 lines
      (37%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES

See the betAS.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 betAS_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘betAS’ ...
** using staged installation
** R
** 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 (betAS)