Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘SARC/DESCRIPTION’ ... OK
* preparing ‘SARC’:
* 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 ‘SARC_0.99.21.tar.gz’

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 BiocCheckGitClone('SARC')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.21
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3071/d62045379755eabe7fc3aade6a06a3bcfee3d3cc/SARC
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      R/.Rhistory
      tests/testthat/.Rhistory
* 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...
* Checking that provided CITATION file is correctly formatted...

─ 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/3071/d62045379755eabe7fc3aade6a06a3bcfee3d3cc/SARC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘0.99.21’
* 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 ‘SARC’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [37s/37s] NOTE
addExonsGenes: no visible global function definition for ‘metadata’
addExonsGenes: no visible global function definition for ‘metadata<-’
anovaOnCNV: no visible global function definition for ‘metadata’
anovaOnCNV: no visible global function definition for ‘metadata<-’
cnvConfidence: no visible global function definition for ‘metadata’
cnvConfidence: no visible global function definition for ‘metadata<-’
pasteExonsGenes: no visible global function definition for ‘metadata’
pasteExonsGenes: no visible global function definition for ‘metadata<-’
phDunnetonCNV: no visible global function definition for ‘metadata’
phDunnetonCNV: no visible global function definition for ‘metadata<-’
plotCovPrep: no visible global function definition for ‘metadata’
plotCovPrep: no visible global function definition for ‘metadata<-’
prepAnova: no visible global function definition for ‘metadata’
prepAnova: no visible global function definition for ‘metadata<-’
regionGrangeMake: no visible global function definition for ‘metadata’
regionGrangeMake: no visible global function definition for
  ‘metadata<-’
regionMean: no visible global function definition for ‘metadata’
regionMean: no visible global function definition for ‘metadata<-’
regionQuantiles: no visible global function definition for ‘metadata’
regionQuantiles: no visible global function definition for ‘metadata<-’
regionSet: no visible global function definition for ‘sortSeqlevels’
regionSet: no visible global function definition for ‘metadata’
regionSet: no visible global function definition for ‘metadata<-’
regionSplit: no visible global function definition for ‘metadata’
regionSplit: no visible global function definition for ‘metadata<-’
setQDplot: no visible global function definition for ‘metadata’
setQDplot: no visible global function definition for ‘metadata<-’
setupCNVplot: no visible global function definition for ‘metadata’
setupCNVplot: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  metadata metadata<- sortSeqlevels
* 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 ... WARNING
Error: package or namespace load failed for ‘SARC’ in namespaceExport(ns, exports):
 undefined exports: addExonsGenes, anovaOnCNV, cnvConfidence, pasteExonsGenes, phDunnetonCNV, plotCNV, plotCovPrep, prepAnova, regionGrangeMake, regionMean, regionQuantiles, regionSet, regionSplit, seeDist, setQDplot, setupCNVplot
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           me
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
* checking Rd \usage sections ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Calls: <Anonymous> -> find.package
Execution halted
* checking for unstated dependencies in examples ... WARNING
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Execution halted
* checking contents of ‘data’ directory ... WARNING
Output for data("test_cnv", package = "SARC"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘SARC’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
Output for data("test_cnv2", package = "SARC"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘SARC’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
Output for data("test_cov", package = "SARC"):
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called ‘SARC’
  Calls: <Anonymous> ... suppressMessages -> withCallingHandlers -> <Anonymous> -> find.package
  Execution halted
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [0s/0s]
 [0s/0s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #test SARC unit tests
  > #unit test check
  > library(testthat)
  > library(SARC)
  Error in library(SARC) : there is no package called 'SARC'
  Execution halted
* checking for unstated dependencies in vignettes ... NOTE
Error in find.package(package, lib.loc) : 
  there is no package called ‘SARC’
Execution halted
* 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 ... [3s/3s] OK
* DONE

Status: 1 ERROR, 5 WARNINGs, 3 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3071/d62045379755eabe7fc3aade6a06a3bcfee3d3cc/SARC.Rcheck/00check.log’
for details.





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 BiocCheck('SARC_0.99.21.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.21
─ sourceDir: /tmp/RtmpnrpZPK/file11aa3f5452918/SARC
─ installDir: /tmp/RtmpnrpZPK/file11aa3f29b1b7c5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3071/d62045379755eabe7fc3aade6a06a3bcfee3d3cc/SARC.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...
* 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:
      Coverage
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...
* 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 SARC...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
    Found @ in man/addExonsGenes.Rd
    Found @ in man/pasteExonsGenes.Rd
    Found @ in man/plotCNV.Rd
    Found @ in man/setupCNVplot.Rd
    Found @ in vignettes/SARC_guide.Rmd
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 11 functions greater than 50 lines.
* Checking man page documentation...
    * 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; 320 lines (11%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 579 lines
      (19%) 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...
    Maintainer is subscribed to 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 | 10 NOTES

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