Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* 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 ‘pgxRpi_0.99.5.tar.gz’

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 BiocCheckGitClone('pgxRpi')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: pgxRpi
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3120/1feb432f1c09dbf1b17ee69945b7bacbbd0b4860/pgxRpi
─ 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/3120/1feb432f1c09dbf1b17ee69945b7bacbbd0b4860/pgxRpi.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 ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘0.99.5’
* 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 ‘pgxRpi’ 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [6s/6s] NOTE
pgxSegprocess: no visible binding for global variable
  ‘followup_state_id’
pgxSegprocess: no visible binding for global variable ‘followup_time’
Undefined global functions or variables:
  followup_state_id followup_time

Found the following calls to data() loading into the global environment:
File ‘pgxRpi/R/helper_pgxFreqplot.R’:
  data(list = c(paste0(op$assembly, "_cytoband")))
File ‘pgxRpi/R/helper_pgxSegprocess.R’:
  data(list = c(paste0(genome, "_bins")))
See section ‘Good practice’ in ‘?data’.
* 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 ... 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 ... [6s/29s] OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
pgxFreqplot 2.213  0.154   8.505
pgxLoader   0.481  0.065  14.364
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/52s]
 [4s/52s] 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 ... [6s/9s] OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3120/1feb432f1c09dbf1b17ee69945b7bacbbd0b4860/pgxRpi.Rcheck/00check.log’
for details.






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 BiocCheck('pgxRpi_0.99.5.tar.gz')

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─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: pgxRpi
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpgcGP8N/file1600d1da5e429/pgxRpi
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpgcGP8N/file1600d4d09701e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3120/1feb432f1c09dbf1b17ee69945b7bacbbd0b4860/pgxRpi.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 4.2 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 recommeded fields in DESCRIPTION...
* 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 pgxRpi...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
* Checking parsed R code in R directory, 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 12 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; 414 lines (12%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 349 lines
      (10%) 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 | 7 NOTES

See the pgxRpi.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 pgxRpi_0.99.5.tar.gz'
>>>>>>> 

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