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_0.99.23.tar.gz’

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 BiocCheckGitClone('SARC')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.23
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3071/6749099bf150c497bc7c87a1cce8f6fee98c2194/SARC
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* 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 ──
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/3071/6749099bf150c497bc7c87a1cce8f6fee98c2194/SARC.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SARC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SARC’ version ‘0.99.23’
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [27s/27s] 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
Codoc mismatches from documentation object 'cnvConfidence':
cnvConfidence
  Code: function(RE, cnv, ph = FALSE, m1 = 0.2, m2 = 0.8, m3 = 1.2, m4
                 = 1.8, nameofnewdf = "CNVrank")
  Docs: function(RE, cnv, ph = FALSE, m1 = 0.2, m2 = 0.8, m3 = 1.2, m4
                 = 1.8)
  Argument names in code not in docs:
    nameofnewdf

Codoc mismatches from documentation object 'pasteExonsGenes':
pasteExonsGenes
  Code: function(RE, setup, cnv, nameofnewdf = "CNVexonsgenes")
  Docs: function(RE, setup, cnv, nameofnewdf = "cnvExonsGenes")
  Mismatches in argument default values:
    Name: 'nameofnewdf' Code: "CNVexonsgenes" Docs: "cnvExonsGenes"

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [106s/106s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plotCNV         33.707  0.371  34.078
addExonsGenes   19.283  0.433  19.720
pasteExonsGenes 13.807  0.257  14.066
setupCNVplot    13.348  0.244  13.595
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [30s/30s]
 [30s/30s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
  Loading required package: GenomeInfoDb
  > test_check(package = "SARC")
  Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 24 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_plotCNV.R:7:1'): (code run outside of `test_that()`) ───────────
  Error in `gzfile(file, "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. └─base::readRDS("tests/testthat/test1.rds") at test_plotCNV.R:7:0
   2.   └─base::gzfile(file, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 24 ]
  Error: Test failures
  Execution halted
* 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 ... [4s/4s] OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3071/6749099bf150c497bc7c87a1cce8f6fee98c2194/SARC.Rcheck/00check.log’
for details.





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 BiocCheck('SARC_0.99.23.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: SARC
─ PackageVersion: 0.99.23
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp0MrEV0/file15115624195c5/SARC
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp0MrEV0/file151156b474612
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3071/6749099bf150c497bc7c87a1cce8f6fee98c2194/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; 321 lines (11%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 583 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.

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 R CMD BUILD

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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir SARC_0.99.23.tar.gz'
>>>>>>> 

* installing *source* package ‘SARC’ ...
** 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 (SARC)