R version >= 3.5.0 dependency created via package_build()
Closed this issue · 2 comments
mariev commented
Due to the changes to data serialization in saveRDS, running package_build() with R >= 3.6.0 creates an unstated dependency on R (>=3.5.0), which shows up as a warning when users install the datapackage if not manually addressed. Prior to R 3.6.0, the default serialization was version 2.
This warning can be resolved by specifying saveRDS(..., version = 2) or usethis::use_data()
remotes::install_github("FredHutch/Pantaleo733")
#> Using github PAT from envvar GITHUB_PAT
#> Downloading GitHub repo FredHutch/Pantaleo733@HEAD
#> v checking for file 'C:\Users\mvendett\AppData\Local\Temp\RtmpMltBHb\remotes6d34440d7d63\FredHutch-Pantaleo733-88c2aed66650ce95f8f7948fca532cd932455ebc/DESCRIPTION' (412ms)
#> - preparing 'Pantaleo733': (378ms)
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... v checking DESCRIPTION meta-information
#> - excluding invalid files (381ms)
#> Subdirectory 'inst/doc' contains invalid file names:
#> 'Pantaleo733_BAMA IgG_qc_report.Rmd'
#> - checking for LF line-endings in source and make files and shell scripts
#> - checking for empty or unneeded directories
#> NB: this package now depends on R (>= 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: 'Pantaleo733/data/Pantaleo733_adcc_gtl.rda' 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: 'Pantaleo733/data/Pantaleo733_adcc_luc.rda' 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: 'Pantaleo733/data/Pantaleo733_nab.rda' 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: 'Pantaleo733/data/Pantaleo733_serum_bama.rda' 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: 'Pantaleo733/data/Pantaleo733_serum_bama_standard.rda'
#> - building 'Pantaleo733_1.0.tar.gz'
#> Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
#> storing paths of more than 100 bytes is not portable:
#> 'Pantaleo733/inst/extdata/Logfiles/Pantaleo733_ADCC_GTL_qc_report_files/figure-latex/ADCC_GTL_plots1-1.pdf'
#> Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
#> storing paths of more than 100 bytes is not portable:
#> 'Pantaleo733/inst/extdata/Logfiles/Pantaleo733_ADCC_GTL_qc_report_files/figure-latex/ADCC_GTL_plots1-1.png'
#> Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
#> storing paths of more than 100 bytes is not portable:
#> 'Pantaleo733/inst/extdata/Logfiles/Pantaleo733_ADCC_GTL_qc_report_files/figure-latex/ADCC_GTL_plots2-1.pdf'
#> Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
#> storing paths of more than 100 bytes is not portable:
#> 'Pantaleo733/inst/extdata/Logfiles/Pantaleo733_ADCC_GTL_qc_report_files/figure-latex/ADCC_GTL_plots2-1.png'
#>
#>
#> Installing package into 'C:/Users/mvendett/Documents/R/win-library/4.0'
#> (as 'lib' is unspecified)
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/Los_Angeles
#> date 2020-09-10
#>
#> - Packages -------------------------------------------------------------------
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
#> backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2)
#> callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
#> curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.2)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
#> knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
#> processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
#> ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
#> rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
#> rmarkdown 2.3 2020-06-18 [2] CRAN (R 4.0.2)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
#> stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
#> withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)
#> xfun 0.16 2020-07-24 [1] CRAN (R 4.0.2)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
#>
#> [1] C:/Users/mvendett/Documents/R/win-library/4.0
#> [2] C:/Users/mvendett/Documents/R/R-4.0.2/libraryCreated on 2020-09-10 by the reprex package (v0.3.0)
slager commented
Appears addressed by the above PRs