Package check result: OK Changes to worse in reverse depends: Package: photobiologyInOut Check: dependencies in R code New result: WARNING Missing or unexported object: ‘photobiology::na_geocode’ Package: photobiologyInOut Check: examples New result: ERROR Running examples in ‘photobiologyInOut-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: read_cid_spectravue_csv > ### Title: Read File Saved by CID's SpectraVue. > ### Aliases: read_cid_spectravue_csv > > ### ** Examples > > > # read file containing a single reflectaance spectrum > > file.name <- + system.file("extdata", "cid-spectravue-Rpc-Measurements.csv", + package = "photobiologyInOut", mustWork = TRUE) > > cid_filter.spct <- + read_cid_spectravue_csv(file = file.name) Error: 'na_geocode' is not an exported object from 'namespace:photobiology' Execution halted Package: photobiologyInOut Check: R code for possible problems New result: NOTE read_spectrapen_csv: no visible global function definition for ‘na_geocode’ Undefined global functions or variables: na_geocode Package: photobiologyInOut Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘user-guide.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-4-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44897 bytes Input file size = 45035 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39772 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39772 Output IDAT size = 39772 bytes (5125 bytes decrease) Output file size = 39850 bytes (5185 bytes = 11.51% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-9-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40651 bytes Input file size = 40777 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39204 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37069 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37069 Output IDAT size = 37069 bytes (3582 bytes decrease) Output file size = 37147 bytes (3630 bytes = 8.90% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-10-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40445 bytes Input file size = 40571 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39167 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36911 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36911 Output IDAT size = 36911 bytes (3534 bytes decrease) Output file size = 36989 bytes (3582 bytes = 8.83% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-11-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40185 bytes Input file size = 40311 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38963 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36741 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36741 Output IDAT size = 36741 bytes (3444 bytes decrease) Output file size = 36819 bytes (3492 bytes = 8.66% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-13-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 41126 bytes Input file size = 41264 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39833 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37426 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37426 Output IDAT size = 37426 bytes (3700 bytes decrease) Output file size = 37504 bytes (3760 bytes = 9.11% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-14-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40817 bytes Input file size = 40943 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39539 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36955 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36955 Output IDAT size = 36955 bytes (3862 bytes decrease) Output file size = 37033 bytes (3910 bytes = 9.55% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-15-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40075 bytes Input file size = 40201 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39187 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36381 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36381 Output IDAT size = 36381 bytes (3694 bytes decrease) Output file size = 36459 bytes (3742 bytes = 9.31% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-16-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43072 bytes Input file size = 43210 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 38834 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 38834 Output IDAT size = 38834 bytes (4238 bytes decrease) Output file size = 38912 bytes (4298 bytes = 9.95% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-19-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 36847 bytes Input file size = 36973 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32803 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32803 Output IDAT size = 32803 bytes (4044 bytes decrease) Output file size = 32881 bytes (4092 bytes = 11.07% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-20-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42796 bytes Input file size = 42934 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35513 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35513 Output IDAT size = 35513 bytes (7283 bytes decrease) Output file size = 35591 bytes (7343 bytes = 17.10% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-21-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37969 bytes Input file size = 38095 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32772 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32772 Output IDAT size = 32772 bytes (5197 bytes decrease) Output file size = 32850 bytes (5245 bytes = 13.77% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-23-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38059 bytes Input file size = 38185 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32802 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32802 Output IDAT size = 32802 bytes (5257 bytes decrease) Output file size = 32880 bytes (5305 bytes = 13.89% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-25-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42063 bytes Input file size = 42201 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40363 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37834 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 37834 Output IDAT size = 37834 bytes (4229 bytes decrease) Output file size = 37912 bytes (4289 bytes = 10.16% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-27-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28720 bytes Input file size = 28834 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24999 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24999 Output IDAT size = 24999 bytes (3721 bytes decrease) Output file size = 25077 bytes (3757 bytes = 13.03% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-28-1.png 672x576 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 23527 bytes Input file size = 24409 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20637 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20637 Output IDAT size = 20637 bytes (2890 bytes decrease) Output file size = 20715 bytes (3694 bytes = 15.13% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/photobiologyInOut.Rcheck/vign_test/photobiologyInOut/vignettes/user-guide_files/figure-html/unnamed-chunk-29-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39757 bytes Input file size = 39883 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34966 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34966 Output IDAT size = 34966 bytes (4791 bytes decrease) Output file size = 35044 bytes (4839 bytes = 12.13% decrease) Quitting from lines 675-683 [unnamed-chunk-30] (user-guide.Rmd) Error: processing vignette 'user-guide.Rmd' failed with diagnostics: 'na_geocode' is not an exported object from 'namespace:photobiology' --- failed re-building ‘user-guide.Rmd’ SUMMARY: processing the following file failed: ‘user-guide.Rmd’ Error: Vignette re-building failed. Execution halted Package: photobiologyInOut Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(photobiology) Loading required package: SunCalcMeeus Documentation at https://docs.r4photobiology.info/ > library(photobiologyInOut) > > test_check("photobiology") [ FAIL 3 | WARN 0 | SKIP 4 | PASS 800 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-tuv.R:84:3', 'test-tuv.R:323:3', 'test-tuv.R:353:3', 'test-yoctopuce.R:47:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-cid.R:12:3'): Absorbance Mode ────────────────────────────────── Error: 'na_geocode' is not an exported object from 'namespace:photobiology' Backtrace: ▆ 1. └─photobiologyInOut::read_cid_spectravue_csv(file = file.name) at test-cid.R:12:3 ── Error ('test-cid.R:71:3'): Reflectance Mode ───────────────────────────────── Error: 'na_geocode' is not an exported object from 'namespace:photobiology' Backtrace: ▆ 1. └─photobiologyInOut::read_cid_spectravue_csv(file = file.name) at test-cid.R:71:3 ── Error ('test-cid.R:101:3'): Multiple Modes ────────────────────────────────── Error: 'na_geocode' is not an exported object from 'namespace:photobiology' Backtrace: ▆ 1. └─photobiologyInOut::read_cid_spectravue_csv(file = file.name) at test-cid.R:101:3 [ FAIL 3 | WARN 0 | SKIP 4 | PASS 800 ] Error: Test failures Execution halted