Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* preparing ‘compSPOT’:
* 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
  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    ‘compSPOT/data/example_mutations.RData’
    ‘compSPOT/data/example_regions.RData’
* building ‘compSPOT_0.99.6.tar.gz’

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 BiocCheckGitClone('compSPOT')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.6
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3079/ac6f0460cd1b612150e2e2d7c2d1e040b45476c9/compSPOT
─ 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...

─ 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/3079/ac6f0460cd1b612150e2e2d7c2d1e040b45476c9/compSPOT.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 ‘compSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compSPOT’ version ‘0.99.6’
* 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 ‘compSPOT’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] NOTE
feature.spot: no visible binding for global variable ‘Sample’
feature.spot: no visible binding for global variable ‘Chromosome’
feature.spot : Sequential: no visible binding for global variable
  ‘Count’
feature.spot : Categorical: no visible binding for global variable
  ‘Count’
group.spot: no visible binding for global variable ‘Group’
group.spot: no visible binding for global variable ‘Sample’
group.spot: no visible binding for global variable ‘Chromosome’
plot.sigspot: no visible binding for global variable ‘percent’
plot.sigspot: no visible binding for global variable ‘number’
plot.sigspot: no visible binding for global variable ‘Label’
plot.sigspot: no visible binding for global variable ‘type’
plot.sigspot: no visible binding for global variable ‘Count’
plot.sigspot: no visible binding for global variable ‘Group’
plot.spot: no visible binding for global variable ‘Hotspot’
plot.spot: no visible binding for global variable ‘Group’
plot.spot: no visible binding for global variable ‘Mutation_Count’
sig.spots : fun: no visible binding for global variable ‘Sample’
sig.spots : fun: no visible binding for global variable ‘Chromosome’
spot.rank: no visible binding for global variable ‘Chromosome’
Undefined global functions or variables:
  Chromosome Count Group Hotspot Label Mutation_Count Sample number
  percent type
* 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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'feature.spot'
  ‘regions’ ‘feature’
Documented arguments not in \usage in documentation object 'feature.spot':
  ‘features’

Undocumented arguments in documentation object 'group.spot'
  ‘pvalue’ ‘include_genes’
Documented arguments not in \usage in documentation object 'group.spot':
  ‘pval’

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.
* 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 ... [236s/236s] OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
group.spot 225.326  1.078 226.403
sig.spots    5.174  0.179   5.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [7s/7s]
 [7s/7s] 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 ... [4s/4s] OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3079/ac6f0460cd1b612150e2e2d7c2d1e040b45476c9/compSPOT.Rcheck/00check.log’
for details.






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 BiocCheck('compSPOT_0.99.6.tar.gz')

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─ BiocCheckVersion: 1.37.7
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.6
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpBWUwHw/file119a63d9240a3/compSPOT
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpBWUwHw/file119a659af1c65
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3079/ac6f0460cd1b612150e2e2d7c2d1e040b45476c9/compSPOT.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 3.5.0 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...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* 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 compSPOT...
* 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
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 4 functions greater than 50 lines.
* Checking man page documentation...
* 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; 246 lines (21%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 218 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 | 9 NOTES

See the compSPOT.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 compSPOT_0.99.6.tar.gz'
>>>>>>> 

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