Last updated on 2024-11-29 09:49:08 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.4.1 | 24.20 | 260.35 | 284.55 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.4.1 | 16.19 | 160.70 | 176.89 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.4.1 | 482.00 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.4.1 | 625.65 | ERROR | |||
| r-devel-windows-x86_64 | 2.4.1 | 21.00 | 225.00 | 246.00 | ERROR | |
| r-patched-linux-x86_64 | 2.4.1 | 23.69 | 287.33 | 311.02 | OK | |
| r-release-linux-x86_64 | 2.4.1 | 23.68 | 285.81 | 309.49 | OK | |
| r-release-macos-arm64 | 2.4.1 | 127.00 | OK | |||
| r-release-macos-x86_64 | 2.4.1 | 289.00 | OK | |||
| r-release-windows-x86_64 | 2.4.1 | 24.00 | 261.00 | 285.00 | OK | |
| r-oldrel-macos-arm64 | 2.4.1 | 159.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.4.1 | 334.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.4.1 | 31.00 | 354.00 | 385.00 | OK |
Version: 2.4.1
Check: examples
Result: ERROR
Running examples in ‘assignR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jointP
> ### Title: Joint probability of origin
> ### Aliases: jointP
>
> ### ** Examples
>
> # load hydrogen isotope data for human hair in North America
> d = subOrigData(group = "Modern human", mask = naMap, genplot = FALSE)
788 samples are found from 347 sites
788 samples from 347 sites in the transformed dataset
>
> # rescale from environmental isoscape to tissue isoscape
> r = calRaster(d, d2h_lrNA, naMap, genplot = FALSE)
---------------------------------------
------------------------------------------
rescale function uses linear regression model,
the summary of this model is:
-------------------------------------------
--------------------------------------
Call:
lm(formula = tissue.iso ~ isoscape.iso[, 1], weights = tissue.iso.wt)
Weighted Residuals:
Min 1Q Median 3Q Max
-12.9453 -1.9445 -0.2398 1.4902 10.6126
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -43.890651 0.717638 -61.16 <2e-16 ***
isoscape.iso[, 1] 0.466743 0.009139 51.07 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 2.718 on 786 degrees of freedom
Multiple R-squared: 0.7684, Adjusted R-squared: 0.7681
F-statistic: 2608 on 1 and 786 DF, p-value: < 2.2e-16
>
> # four unknown-origin examples
> id = c("A", "B", "C", "D")
> d2H = c(-110, -90, -105, -102)
> un = data.frame(id, d2H)
>
> # posterior probabilities
> pp = pdRaster(r, un, mask = naMap, genplot = FALSE)
>
> # joint probability for individuals of common origin
> jointP(pp)
Error in options(scipen = p) : invalid 'scipen'
Calls: jointP -> options
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(assignR)
knownOrig database version 0.2, 4352 samples from 1986 sites.
>
> test_check("assignR")
trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
Content type 'application/zip' length 5393557 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_processing.R:90:3'): (code run outside of `test_that()`) ───────
Error in `options(scipen = p)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::capture_output(...) at test_processing.R:84:1
2. │ └─testthat::capture_output_lines(code, print, width = width)
3. │ └─testthat:::eval_with_output(code, print = print, width = width)
4. │ ├─withr::with_output_sink(path, withVisible(code))
5. │ │ └─base::force(code)
6. │ └─base::withVisible(code)
7. └─assignR::jointP(asn) at test_processing.R:90:3
8. └─base::options(scipen = p) at test_processing.R:90:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘assignR.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/boundary-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6000 bytes
Input file size = 6858 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5234
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 = 5234
Output IDAT size = 5234 bytes (766 bytes decrease)
Output file size = 5312 bytes (1546 bytes = 22.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/isoscape-1.png
672x302 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20005 bytes
Input file size = 20107 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16960
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 = 16960
Output IDAT size = 16960 bytes (3045 bytes decrease)
Output file size = 17038 bytes (3069 bytes = 15.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/knownOrig_sites-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55847 bytes
Input file size = 55997 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45425
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 = 45425
Output IDAT size = 45425 bytes (10422 bytes decrease)
Output file size = 45503 bytes (10494 bytes = 18.74% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdData-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdNoTrans-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-1.png
576x460 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21999 bytes
Input file size = 22881 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20834
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 20818
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 = 1 f = 0 IDAT size = 20818
Output IDAT size = 20818 bytes (1181 bytes decrease)
Output file size = 20896 bytes (1985 bytes = 8.68% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-2.png
576x460 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15124 bytes
Input file size = 15214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12910
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 = 12910
Output IDAT size = 12910 bytes (2214 bytes decrease)
Output file size = 12988 bytes (2226 bytes = 14.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/pdRaster-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19842 bytes
Input file size = 19944 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15488
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 = 15488
Output IDAT size = 15488 bytes (4354 bytes decrease)
Output file size = 15566 bytes (4378 bytes = 21.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45494 bytes
Input file size = 45632 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072
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 = 36072
Output IDAT size = 36072 bytes (9422 bytes decrease)
Output file size = 36150 bytes (9482 bytes = 20.78% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-2.png
480x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15390 bytes
Input file size = 16260 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14490
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 = 14490
Output IDAT size = 14490 bytes (900 bytes decrease)
Output file size = 14568 bytes (1692 bytes = 10.41% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15671 bytes
Input file size = 15761 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12575
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 = 12575
Output IDAT size = 12575 bytes (3096 bytes decrease)
Output file size = 12653 bytes (3108 bytes = 19.72% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/srIso-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19318 bytes
Input file size = 19420 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15435
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 = 15435
Output IDAT size = 15435 bytes (3883 bytes decrease)
Output file size = 15513 bytes (3907 bytes = 20.12% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_Honly-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17290 bytes
Input file size = 17392 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12412
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 = 12412
Output IDAT size = 12412 bytes (4878 bytes decrease)
Output file size = 12490 bytes (4902 bytes = 28.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_multi-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15055 bytes
Input file size = 15145 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11376
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 = 11376
Output IDAT size = 11376 bytes (3679 bytes decrease)
Output file size = 11454 bytes (3691 bytes = 24.37% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/polygons-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14202 bytes
Input file size = 14292 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10738
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 = 10738
Output IDAT size = 10738 bytes (3464 bytes decrease)
Output file size = 10816 bytes (3476 bytes = 24.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11660 bytes
Input file size = 11750 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10513
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 = 10513
Output IDAT size = 10513 bytes (1147 bytes decrease)
Output file size = 10591 bytes (1159 bytes = 9.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11643 bytes
Input file size = 11733 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10521
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 = 10521
Output IDAT size = 10521 bytes (1122 bytes decrease)
Output file size = 10599 bytes (1134 bytes = 9.67% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24075 bytes
Input file size = 24177 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19269
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 = 19269
Output IDAT size = 19269 bytes (4806 bytes decrease)
Output file size = 19347 bytes (4830 bytes = 19.98% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27126 bytes
Input file size = 27240 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20394
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 = 20394
Output IDAT size = 20394 bytes (6732 bytes decrease)
Output file size = 20472 bytes (6768 bytes = 24.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8482 bytes
Input file size = 8572 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7470
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 = 7470
Output IDAT size = 7470 bytes (1012 bytes decrease)
Output file size = 7548 bytes (1024 bytes = 11.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8617 bytes
Input file size = 8707 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7455
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 = 7455
Output IDAT size = 7455 bytes (1162 bytes decrease)
Output file size = 7533 bytes (1174 bytes = 13.48% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8685 bytes
Input file size = 8775 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7561
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 = 7561
Output IDAT size = 7561 bytes (1124 bytes decrease)
Output file size = 7639 bytes (1136 bytes = 12.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8745 bytes
Input file size = 8835 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7592
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 = 7592
Output IDAT size = 7592 bytes (1153 bytes decrease)
Output file size = 7670 bytes (1165 bytes = 13.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8526 bytes
Input file size = 8616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7453
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 = 7453
Output IDAT size = 7453 bytes (1073 bytes decrease)
Output file size = 7531 bytes (1085 bytes = 12.59% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8849 bytes
Input file size = 8939 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7815
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 = 7815
Output IDAT size = 7815 bytes (1034 bytes decrease)
Output file size = 7893 bytes (1046 bytes = 11.70% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8945 bytes
Input file size = 9035 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7816
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 = 7816
Output IDAT size = 7816 bytes (1129 bytes decrease)
Output file size = 7894 bytes (1141 bytes = 12.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9050 bytes
Input file size = 9140 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7964
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 = 7964
Output IDAT size = 7964 bytes (1086 bytes decrease)
Output file size = 8042 bytes (1098 bytes = 12.01% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9127 bytes
Input file size = 9217 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7956
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 = 7956
Output IDAT size = 7956 bytes (1171 bytes decrease)
Output file size = 8034 bytes (1183 bytes = 12.83% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9079 bytes
Input file size = 9169 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7937
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 = 7937
Output IDAT size = 7937 bytes (1142 bytes decrease)
Output file size = 8015 bytes (1154 bytes = 12.59% decrease)
Quitting from lines 285-286 [jointP] (assignR.Rmd)
Error: processing vignette 'assignR.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘assignR.Rmd’
SUMMARY: processing the following file failed:
‘assignR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(assignR)
knownOrig database version 0.2, 4352 samples from 1986 sites.
>
> test_check("assignR")
trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
Content type 'application/zip' length 5393557 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_processing.R:90:3'): (code run outside of `test_that()`) ───────
Error in `options(scipen = p)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::capture_output(...) at test_processing.R:84:1
2. │ └─testthat::capture_output_lines(code, print, width = width)
3. │ └─testthat:::eval_with_output(code, print = print, width = width)
4. │ ├─withr::with_output_sink(path, withVisible(code))
5. │ │ └─base::force(code)
6. │ └─base::withVisible(code)
7. └─assignR::jointP(asn) at test_processing.R:90:3
8. └─base::options(scipen = p) at test_processing.R:90:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘assignR.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/boundary-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6000 bytes
Input file size = 6858 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5234
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 = 5234
Output IDAT size = 5234 bytes (766 bytes decrease)
Output file size = 5312 bytes (1546 bytes = 22.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/isoscape-1.png
672x302 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20005 bytes
Input file size = 20107 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16960
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 = 16960
Output IDAT size = 16960 bytes (3045 bytes decrease)
Output file size = 17038 bytes (3069 bytes = 15.26% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/knownOrig_sites-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55847 bytes
Input file size = 55997 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45425
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 = 45425
Output IDAT size = 45425 bytes (10422 bytes decrease)
Output file size = 45503 bytes (10494 bytes = 18.74% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdData-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdNoTrans-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-1.png
576x460 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21999 bytes
Input file size = 22881 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20834
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 20818
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 = 1 f = 0 IDAT size = 20818
Output IDAT size = 20818 bytes (1181 bytes decrease)
Output file size = 20896 bytes (1985 bytes = 8.68% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-2.png
576x460 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15071 bytes
Input file size = 15161 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12868
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 = 12868
Output IDAT size = 12868 bytes (2203 bytes decrease)
Output file size = 12946 bytes (2215 bytes = 14.61% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/pdRaster-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20010 bytes
Input file size = 20112 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15599
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 = 15599
Output IDAT size = 15599 bytes (4411 bytes decrease)
Output file size = 15677 bytes (4435 bytes = 22.05% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45494 bytes
Input file size = 45632 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072
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 = 36072
Output IDAT size = 36072 bytes (9422 bytes decrease)
Output file size = 36150 bytes (9482 bytes = 20.78% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-2.png
480x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15390 bytes
Input file size = 16260 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14490
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 = 14490
Output IDAT size = 14490 bytes (900 bytes decrease)
Output file size = 14568 bytes (1692 bytes = 10.41% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15671 bytes
Input file size = 15761 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12575
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 = 12575
Output IDAT size = 12575 bytes (3096 bytes decrease)
Output file size = 12653 bytes (3108 bytes = 19.72% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/srIso-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19318 bytes
Input file size = 19420 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15435
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 = 15435
Output IDAT size = 15435 bytes (3883 bytes decrease)
Output file size = 15513 bytes (3907 bytes = 20.12% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_Honly-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17290 bytes
Input file size = 17392 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12412
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 = 12412
Output IDAT size = 12412 bytes (4878 bytes decrease)
Output file size = 12490 bytes (4902 bytes = 28.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_multi-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15055 bytes
Input file size = 15145 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11376
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 = 11376
Output IDAT size = 11376 bytes (3679 bytes decrease)
Output file size = 11454 bytes (3691 bytes = 24.37% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/polygons-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14202 bytes
Input file size = 14292 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10738
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 = 10738
Output IDAT size = 10738 bytes (3464 bytes decrease)
Output file size = 10816 bytes (3476 bytes = 24.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11684 bytes
Input file size = 11774 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10526
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 = 10526
Output IDAT size = 10526 bytes (1158 bytes decrease)
Output file size = 10604 bytes (1170 bytes = 9.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11626 bytes
Input file size = 11716 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10490
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 = 10490
Output IDAT size = 10490 bytes (1136 bytes decrease)
Output file size = 10568 bytes (1148 bytes = 9.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24086 bytes
Input file size = 24188 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19244
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 = 19244
Output IDAT size = 19244 bytes (4842 bytes decrease)
Output file size = 19322 bytes (4866 bytes = 20.12% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27102 bytes
Input file size = 27216 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20416
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 = 20416
Output IDAT size = 20416 bytes (6686 bytes decrease)
Output file size = 20494 bytes (6722 bytes = 24.70% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8482 bytes
Input file size = 8572 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7470
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 = 7470
Output IDAT size = 7470 bytes (1012 bytes decrease)
Output file size = 7548 bytes (1024 bytes = 11.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8617 bytes
Input file size = 8707 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7455
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 = 7455
Output IDAT size = 7455 bytes (1162 bytes decrease)
Output file size = 7533 bytes (1174 bytes = 13.48% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8685 bytes
Input file size = 8775 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7561
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 = 7561
Output IDAT size = 7561 bytes (1124 bytes decrease)
Output file size = 7639 bytes (1136 bytes = 12.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8745 bytes
Input file size = 8835 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7592
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 = 7592
Output IDAT size = 7592 bytes (1153 bytes decrease)
Output file size = 7670 bytes (1165 bytes = 13.19% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8526 bytes
Input file size = 8616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7453
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 = 7453
Output IDAT size = 7453 bytes (1073 bytes decrease)
Output file size = 7531 bytes (1085 bytes = 12.59% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8849 bytes
Input file size = 8939 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7815
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 = 7815
Output IDAT size = 7815 bytes (1034 bytes decrease)
Output file size = 7893 bytes (1046 bytes = 11.70% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8945 bytes
Input file size = 9035 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7816
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 = 7816
Output IDAT size = 7816 bytes (1129 bytes decrease)
Output file size = 7894 bytes (1141 bytes = 12.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9050 bytes
Input file size = 9140 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7964
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 = 7964
Output IDAT size = 7964 bytes (1086 bytes decrease)
Output file size = 8042 bytes (1098 bytes = 12.01% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9127 bytes
Input file size = 9217 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7956
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 = 7956
Output IDAT size = 7956 bytes (1171 bytes decrease)
Output file size = 8034 bytes (1183 bytes = 12.83% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9079 bytes
Input file size = 9169 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7937
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 = 7937
Output IDAT size = 7937 bytes (1142 bytes decrease)
Output file size = 8015 bytes (1154 bytes = 12.59% decrease)
Quitting from lines 285-286 [jointP] (assignR.Rmd)
Error: processing vignette 'assignR.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘assignR.Rmd’
SUMMARY: processing the following file failed:
‘assignR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.4.1
Check: examples
Result: ERROR
Running examples in ‘assignR-Ex.R’ failed
The error most likely occurred in:
> ### Name: jointP
> ### Title: Joint probability of origin
> ### Aliases: jointP
>
> ### ** Examples
>
> # load hydrogen isotope data for human hair in North America
> d = subOrigData(group = "Modern human", mask = naMap, genplot = FALSE)
788 samples are found from 347 sites
788 samples from 347 sites in the transformed dataset
>
> # rescale from environmental isoscape to tissue isoscape
> r = calRaster(d, d2h_lrNA, naMap, genplot = FALSE)
---------------------------------------
------------------------------------------
rescale function uses linear regression model,
the summary of this model is:
-------------------------------------------
--------------------------------------
Call:
lm(formula = tissue.iso ~ isoscape.iso[, 1], weights = tissue.iso.wt)
Weighted Residuals:
Min 1Q Median 3Q Max
-12.9453 -1.9445 -0.2398 1.4902 10.6126
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -43.890651 0.717638 -61.16 <2e-16 ***
isoscape.iso[, 1] 0.466743 0.009139 51.07 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 2.718 on 786 degrees of freedom
Multiple R-squared: 0.7684, Adjusted R-squared: 0.7681
F-statistic: 2608 on 1 and 786 DF, p-value: < 2.2e-16
>
> # four unknown-origin examples
> id = c("A", "B", "C", "D")
> d2H = c(-110, -90, -105, -102)
> un = data.frame(id, d2H)
>
> # posterior probabilities
> pp = pdRaster(r, un, mask = naMap, genplot = FALSE)
>
> # joint probability for individuals of common origin
> jointP(pp)
Error in options(scipen = p) : invalid 'scipen'
Calls: jointP -> options
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 2.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(assignR)
knownOrig database version 0.2, 4352 samples from 1986 sites.
>
> test_check("assignR")
trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
Content type 'application/zip' length 5393557 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_processing.R:90:3'): (code run outside of `test_that()`) ───────
Error in `options(scipen = p)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::capture_output(...) at test_processing.R:84:1
2. │ └─testthat::capture_output_lines(code, print, width = width)
3. │ └─testthat:::eval_with_output(code, print = print, width = width)
4. │ ├─withr::with_output_sink(path, withVisible(code))
5. │ │ └─base::force(code)
6. │ └─base::withVisible(code)
7. └─assignR::jointP(asn) at test_processing.R:90:3
8. └─base::options(scipen = p) at test_processing.R:90:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘assignR.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/boundary-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6000 bytes
Input file size = 6858 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5234
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 = 5234
Output IDAT size = 5234 bytes (766 bytes decrease)
Output file size = 5312 bytes (1546 bytes = 22.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/isoscape-1.png
672x302 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20005 bytes
Input file size = 20107 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16960
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 = 16960
Output IDAT size = 16960 bytes (3045 bytes decrease)
Output file size = 17038 bytes (3069 bytes = 15.26% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/knownOrig_sites-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55757 bytes
Input file size = 55907 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45351
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 = 45351
Output IDAT size = 45351 bytes (10406 bytes decrease)
Output file size = 45429 bytes (10478 bytes = 18.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdData-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdNoTrans-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-1.png
576x460 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21986 bytes
Input file size = 22868 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20812
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 20791
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 = 1 f = 0 IDAT size = 20791
Output IDAT size = 20791 bytes (1195 bytes decrease)
Output file size = 20869 bytes (1999 bytes = 8.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-2.png
576x460 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14717 bytes
Input file size = 14807 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12660
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 = 12660
Output IDAT size = 12660 bytes (2057 bytes decrease)
Output file size = 12738 bytes (2069 bytes = 13.97% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/pdRaster-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19545 bytes
Input file size = 19647 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15277
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 = 15277
Output IDAT size = 15277 bytes (4268 bytes decrease)
Output file size = 15355 bytes (4292 bytes = 21.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45570 bytes
Input file size = 45708 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36113
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 = 36113
Output IDAT size = 36113 bytes (9457 bytes decrease)
Output file size = 36191 bytes (9517 bytes = 20.82% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-2.png
480x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15400 bytes
Input file size = 16270 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14496
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 = 14496
Output IDAT size = 14496 bytes (904 bytes decrease)
Output file size = 14574 bytes (1696 bytes = 10.42% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15671 bytes
Input file size = 15761 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12575
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 = 12575
Output IDAT size = 12575 bytes (3096 bytes decrease)
Output file size = 12653 bytes (3108 bytes = 19.72% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/srIso-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19318 bytes
Input file size = 19420 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15435
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 = 15435
Output IDAT size = 15435 bytes (3883 bytes decrease)
Output file size = 15513 bytes (3907 bytes = 20.12% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_Honly-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17290 bytes
Input file size = 17392 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12412
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 = 12412
Output IDAT size = 12412 bytes (4878 bytes decrease)
Output file size = 12490 bytes (4902 bytes = 28.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_multi-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15055 bytes
Input file size = 15145 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11376
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 = 11376
Output IDAT size = 11376 bytes (3679 bytes decrease)
Output file size = 11454 bytes (3691 bytes = 24.37% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/polygons-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14204 bytes
Input file size = 14294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10741
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 = 10741
Output IDAT size = 10741 bytes (3463 bytes decrease)
Output file size = 10819 bytes (3475 bytes = 24.31% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11661 bytes
Input file size = 11751 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10498
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 = 10498
Output IDAT size = 10498 bytes (1163 bytes decrease)
Output file size = 10576 bytes (1175 bytes = 10.00% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11645 bytes
Input file size = 11735 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10524
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 = 10524
Output IDAT size = 10524 bytes (1121 bytes decrease)
Output file size = 10602 bytes (1133 bytes = 9.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24092 bytes
Input file size = 24194 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19260
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 = 19260
Output IDAT size = 19260 bytes (4832 bytes decrease)
Output file size = 19338 bytes (4856 bytes = 20.07% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27122 bytes
Input file size = 27236 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20473
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 = 20473
Output IDAT size = 20473 bytes (6649 bytes decrease)
Output file size = 20551 bytes (6685 bytes = 24.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8482 bytes
Input file size = 8572 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7470
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 = 7470
Output IDAT size = 7470 bytes (1012 bytes decrease)
Output file size = 7548 bytes (1024 bytes = 11.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8617 bytes
Input file size = 8707 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7455
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 = 7455
Output IDAT size = 7455 bytes (1162 bytes decrease)
Output file size = 7533 bytes (1174 bytes = 13.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8685 bytes
Input file size = 8775 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7561
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 = 7561
Output IDAT size = 7561 bytes (1124 bytes decrease)
Output file size = 7639 bytes (1136 bytes = 12.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8745 bytes
Input file size = 8835 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7592
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 = 7592
Output IDAT size = 7592 bytes (1153 bytes decrease)
Output file size = 7670 bytes (1165 bytes = 13.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8526 bytes
Input file size = 8616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7453
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 = 7453
Output IDAT size = 7453 bytes (1073 bytes decrease)
Output file size = 7531 bytes (1085 bytes = 12.59% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8849 bytes
Input file size = 8939 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7815
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 = 7815
Output IDAT size = 7815 bytes (1034 bytes decrease)
Output file size = 7893 bytes (1046 bytes = 11.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8945 bytes
Input file size = 9035 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7816
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 = 7816
Output IDAT size = 7816 bytes (1129 bytes decrease)
Output file size = 7894 bytes (1141 bytes = 12.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9050 bytes
Input file size = 9140 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7964
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 = 7964
Output IDAT size = 7964 bytes (1086 bytes decrease)
Output file size = 8042 bytes (1098 bytes = 12.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9127 bytes
Input file size = 9217 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7956
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 = 7956
Output IDAT size = 7956 bytes (1171 bytes decrease)
Output file size = 8034 bytes (1183 bytes = 12.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9079 bytes
Input file size = 9169 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7937
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 = 7937
Output IDAT size = 7937 bytes (1142 bytes decrease)
Output file size = 8015 bytes (1154 bytes = 12.59% decrease)
Quitting from lines 285-286 [jointP] (assignR.Rmd)
Error: processing vignette 'assignR.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘assignR.Rmd’
SUMMARY: processing the following file failed:
‘assignR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.4.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [42s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(assignR)
knownOrig database version 0.2, 4352 samples from 1986 sites.
>
> test_check("assignR")
trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
Content type 'application/zip' length 5393557 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_processing.R:90:3'): (code run outside of `test_that()`) ───────
Error in `options(scipen = p)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::capture_output(...) at test_processing.R:84:1
2. │ └─testthat::capture_output_lines(code, print, width = width)
3. │ └─testthat:::eval_with_output(code, print = print, width = width)
4. │ ├─withr::with_output_sink(path, withVisible(code))
5. │ │ └─base::force(code)
6. │ └─base::withVisible(code)
7. └─assignR::jointP(asn) at test_processing.R:90:3
8. └─base::options(scipen = p) at test_processing.R:90:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘assignR.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/boundary-1.png
288x288 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6000 bytes
Input file size = 6858 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5234
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 = 5234
Output IDAT size = 5234 bytes (766 bytes decrease)
Output file size = 5312 bytes (1546 bytes = 22.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/isoscape-1.png
672x302 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20005 bytes
Input file size = 20107 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16960
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 = 16960
Output IDAT size = 16960 bytes (3045 bytes decrease)
Output file size = 17038 bytes (3069 bytes = 15.26% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/knownOrig_sites-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 55757 bytes
Input file size = 55907 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45351
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 = 45351
Output IDAT size = 45351 bytes (10406 bytes decrease)
Output file size = 45429 bytes (10478 bytes = 18.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdData-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/birdNoTrans-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26118 bytes
Input file size = 26232 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20149
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 = 20149
Output IDAT size = 20149 bytes (5969 bytes decrease)
Output file size = 20227 bytes (6005 bytes = 22.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-1.png
576x460 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21986 bytes
Input file size = 22868 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20812
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 20791
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 = 1 f = 0 IDAT size = 20791
Output IDAT size = 20791 bytes (1195 bytes decrease)
Output file size = 20869 bytes (1999 bytes = 8.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/calRaster-2.png
576x460 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14956 bytes
Input file size = 15046 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12819
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 = 12819
Output IDAT size = 12819 bytes (2137 bytes decrease)
Output file size = 12897 bytes (2149 bytes = 14.28% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/pdRaster-1.png
576x345 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19675 bytes
Input file size = 19777 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15352
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 = 15352
Output IDAT size = 15352 bytes (4323 bytes decrease)
Output file size = 15430 bytes (4347 bytes = 21.98% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45570 bytes
Input file size = 45708 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36113
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 = 36113
Output IDAT size = 36113 bytes (9457 bytes decrease)
Output file size = 36191 bytes (9517 bytes = 20.82% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-2.png
480x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15400 bytes
Input file size = 16270 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14496
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 = 14496
Output IDAT size = 14496 bytes (904 bytes decrease)
Output file size = 14574 bytes (1696 bytes = 10.42% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15671 bytes
Input file size = 15761 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12575
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 = 12575
Output IDAT size = 12575 bytes (3096 bytes decrease)
Output file size = 12653 bytes (3108 bytes = 19.72% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/srIso-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19318 bytes
Input file size = 19420 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15435
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 = 15435
Output IDAT size = 15435 bytes (3883 bytes decrease)
Output file size = 15513 bytes (3907 bytes = 20.12% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_Honly-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17290 bytes
Input file size = 17392 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12412
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 = 12412
Output IDAT size = 12412 bytes (4878 bytes decrease)
Output file size = 12490 bytes (4902 bytes = 28.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/Dp_multi-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15055 bytes
Input file size = 15145 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11376
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 = 11376
Output IDAT size = 11376 bytes (3679 bytes decrease)
Output file size = 11454 bytes (3691 bytes = 24.37% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/polygons-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14204 bytes
Input file size = 14294 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10741
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 = 10741
Output IDAT size = 10741 bytes (3463 bytes decrease)
Output file size = 10819 bytes (3475 bytes = 24.31% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11658 bytes
Input file size = 11748 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10496
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 = 10496
Output IDAT size = 10496 bytes (1162 bytes decrease)
Output file size = 10574 bytes (1174 bytes = 9.99% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11660 bytes
Input file size = 11750 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10552
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 = 10552
Output IDAT size = 10552 bytes (1108 bytes decrease)
Output file size = 10630 bytes (1120 bytes = 9.53% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24117 bytes
Input file size = 24219 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19302
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 = 19302
Output IDAT size = 19302 bytes (4815 bytes decrease)
Output file size = 19380 bytes (4839 bytes = 19.98% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/wDist2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27082 bytes
Input file size = 27196 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20443
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 = 20443
Output IDAT size = 20443 bytes (6639 bytes decrease)
Output file size = 20521 bytes (6675 bytes = 24.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8482 bytes
Input file size = 8572 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7470
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 = 7470
Output IDAT size = 7470 bytes (1012 bytes decrease)
Output file size = 7548 bytes (1024 bytes = 11.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8617 bytes
Input file size = 8707 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7455
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 = 7455
Output IDAT size = 7455 bytes (1162 bytes decrease)
Output file size = 7533 bytes (1174 bytes = 13.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8685 bytes
Input file size = 8775 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7561
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 = 7561
Output IDAT size = 7561 bytes (1124 bytes decrease)
Output file size = 7639 bytes (1136 bytes = 12.95% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8745 bytes
Input file size = 8835 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7592
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 = 7592
Output IDAT size = 7592 bytes (1153 bytes decrease)
Output file size = 7670 bytes (1165 bytes = 13.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster1-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8526 bytes
Input file size = 8616 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7453
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 = 7453
Output IDAT size = 7453 bytes (1073 bytes decrease)
Output file size = 7531 bytes (1085 bytes = 12.59% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-1.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8849 bytes
Input file size = 8939 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7815
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 = 7815
Output IDAT size = 7815 bytes (1034 bytes decrease)
Output file size = 7893 bytes (1046 bytes = 11.70% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-2.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8945 bytes
Input file size = 9035 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7816
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 = 7816
Output IDAT size = 7816 bytes (1129 bytes decrease)
Output file size = 7894 bytes (1141 bytes = 12.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-3.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9050 bytes
Input file size = 9140 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7964
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 = 7964
Output IDAT size = 7964 bytes (1086 bytes decrease)
Output file size = 8042 bytes (1098 bytes = 12.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-4.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9127 bytes
Input file size = 9217 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7956
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 = 7956
Output IDAT size = 7956 bytes (1171 bytes decrease)
Output file size = 8034 bytes (1183 bytes = 12.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/assignR.Rcheck/vign_test/assignR/vignettes/assignR_files/figure-html/qtlRaster2-5.png
480x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9079 bytes
Input file size = 9169 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7937
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 = 7937
Output IDAT size = 7937 bytes (1142 bytes decrease)
Output file size = 8015 bytes (1154 bytes = 12.59% decrease)
Quitting from lines 285-286 [jointP] (assignR.Rmd)
Error: processing vignette 'assignR.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building ‘assignR.Rmd’
SUMMARY: processing the following file failed:
‘assignR.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.4.1
Check: tests
Result: ERROR
Running 'testthat.R' [41s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(assignR)
knownOrig database version 0.2, 4352 samples from 1986 sites.
>
> test_check("assignR")
trying URL 'https://wateriso.utah.edu/waterisotopes/media/ArcGrids/CaribSr.zip'
Content type 'application/zip' length 5393557 bytes (5.1 MB)
==================================================
downloaded 5.1 MB
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_processing.R:90:3'): (code run outside of `test_that()`) ───────
Error in `options(scipen = p)`: invalid 'scipen'
Backtrace:
▆
1. ├─testthat::capture_output(...) at test_processing.R:84:1
2. │ └─testthat::capture_output_lines(code, print, width = width)
3. │ └─testthat:::eval_with_output(code, print = print, width = width)
4. │ ├─withr::with_output_sink(path, withVisible(code))
5. │ │ └─base::force(code)
6. │ └─base::withVisible(code)
7. └─assignR::jointP(asn) at test_processing.R:90:3
8. └─base::options(scipen = p) at test_processing.R:90:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 72 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'assignR.Rmd' using rmarkdown
Quitting from lines 285-286 [jointP] (assignR.Rmd)
Error: processing vignette 'assignR.Rmd' failed with diagnostics:
invalid 'scipen'
--- failed re-building 'assignR.Rmd'
SUMMARY: processing the following file failed:
'assignR.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64