Last updated on 2025-02-16 10:51:12 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| benthos | 12 | 3 | |
| confidence | 12 | 3 | |
| litteR | 12 | 3 | |
| spcosa | 2 | 10 | 3 |
Current CRAN status: NOTE: 12, OK: 3
Version: 1.3-8
Check: Rd files
Result: NOTE
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
39 | \code{a} in {0, 1, 2} (see details))}
| ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Current CRAN status: NOTE: 12, OK: 3
Version: 1.1-2
Check: Rd files
Result: NOTE
checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Current CRAN status: NOTE: 12, OK: 3
Version: 1.0.0
Check: Rd files
Result: NOTE
checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup?
17 | Test for natural numbers according to ISO 80000-2, that is the set {0, 1, 2, ...}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
list_duplicates.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Current CRAN status: ERROR: 2, NOTE: 10, OK: 3
Version: 0.4-2
Check: Rd files
Result: NOTE
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 0.4-2
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
CompactStratification-class.Rd: SpatialPixels-class,
SpatialPoints-class, SpatialPixelsDataFrame-class
CompactStratificationEqualArea-class.Rd: SpatialPixels-class,
SpatialPoints-class
CompactStratificationPriorPoints-class.Rd: SpatialPoints-class,
SpatialPixels-class
SamplingPattern-class.Rd: SpatialPoints-class
SamplingPatternCentroids-class.Rd: SpatialPoints-class
SamplingPatternPriorPoints-class.Rd: SpatialPoints-class
SamplingPatternPurposive-class.Rd: SpatialPoints-class
SamplingPatternRandom-class.Rd: SpatialPoints-class
SamplingPatternRandomComposite-class.Rd: SpatialPoints-class,
SpatialPointsDataFrame-class
SamplingPatternRandomSamplingUnits-class.Rd: SpatialPoints-class
stratify-methods.Rd: SpatialPixels-class, SpatialGrid-class,
SpatialPolygons-class, SpatialPoints-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.4-2
Check: examples
Result: ERROR
Running examples in ‘spcosa-Ex.R’ failed
The error most likely occurred in:
> ### Name: estimate-methods
> ### Title: Estimating Statistics
> ### Aliases: estimate-methods estimate
> ### estimate,character,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### estimate,character,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ### estimate,SamplingVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### estimate,SamplingVariance,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ### estimate,SpatialCumulativeDistributionFunction,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### estimate,SpatialMean,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### estimate,SpatialMean,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ### estimate,SpatialVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### estimate,StandardError,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### Keywords: methods
>
> ### ** Examples
>
>
> # Note: the example below requires the 'sf'-package.
> if (require(sf)) {
+ # read vector representation of the "Mijdrecht" area
+ shp <- as(st_read(
+ dsn = system.file("maps", package = "spcosa"),
+ layer = "mijdrecht"), "Spatial")
+
+ # stratify into 30 strata
+ myStratification <- stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
+
+ # random sampling of two sampling units per stratum
+ mySamplingPattern <- spsample(myStratification, n = 2)
+
+ # plot sampling pattern
+ plot(myStratification, mySamplingPattern)
+
+ # simulate data
+ # (in real world cases these data have to be obtained by field work etc.)
+ myData <- as(mySamplingPattern, "data.frame")
+ myData$observation <- rnorm(n = nrow(myData), mean = 10, sd = 1)
+
+ # design-based inference
+ estimate("spatial mean", myStratification, mySamplingPattern, myData["observation"])
+ estimate("sampling variance", myStratification, mySamplingPattern, myData["observation"])
+ estimate("standard error", myStratification, mySamplingPattern, myData["observation"])
+ estimate("spatial variance", myStratification, mySamplingPattern, myData["observation"])
+ estimate("scdf", myStratification, mySamplingPattern, myData["observation"])
+ }
Loading required package: sf
Linking to GEOS 3.12.2, GDAL 3.5.3, PROJ 9.3.1; sf_use_s2() is TRUE
Reading layer `mijdrecht' from data source
`/data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/spcosa/maps'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 2 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 115796.2 ymin: 463380.5 xmax: 121670.8 ymax: 471524.6
CRS: NA
2025-02-13 15:20:45 | optimizing configuration 1
2025-02-13 15:20:46 | current objective function value: 50485.85
2025-02-13 15:20:46 | minimum objective function value: 50485.85
2025-02-13 15:20:46 | optimizing configuration 2
[gannet:2581142:0:2581142] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f92d371c000)
==== backtrace (tid:2581142) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f921bcb0144]
1 /lib64/libucs.so.0(+0x2880d) [0x7f921bcb180d]
2 /lib64/libucs.so.0(+0x289dd) [0x7f921bcb19dd]
3 [0x7f92b05b9f4d]
=================================
*** caught segfault ***
address 0x4d200276296, cause 'unknown'
Traceback:
1: .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl, "java/lang/Object"), .jnew("java/lang/String", method), j_p, j_pc, use.true.class = TRUE, evalString = simplify, evalArray = FALSE)
2: .jrcall(x, name, ...)
3: p$optimize()
4: .local(object, ...)
5: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
7: .local(object, ...)
8: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
9: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4-2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘spcosa.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-7-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29571 bytes
Input file size = 29685 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21909
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 = 21909
Output IDAT size = 21909 bytes (7662 bytes decrease)
Output file size = 21987 bytes (7698 bytes = 25.93% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-8-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32369 bytes
Input file size = 32483 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23908
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 = 23908
Output IDAT size = 23908 bytes (8461 bytes decrease)
Output file size = 23986 bytes (8497 bytes = 26.16% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-10-1.png
672x384 pixels, 8 bits/pixel, 215 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8991 bytes
Input file size = 9738 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7498
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7419
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 = 7419
Output IDAT size = 7419 bytes (1572 bytes decrease)
Output file size = 7497 bytes (2241 bytes = 23.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-11-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40069 bytes
Input file size = 40195 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29976
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 = 29976
Output IDAT size = 29976 bytes (10093 bytes decrease)
Output file size = 30054 bytes (10141 bytes = 25.23% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-16-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35456 bytes
Input file size = 35582 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26150
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 = 26150
Output IDAT size = 26150 bytes (9306 bytes decrease)
Output file size = 26228 bytes (9354 bytes = 26.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-18-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19527 bytes
Input file size = 19629 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15302
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 = 15302
Output IDAT size = 15302 bytes (4225 bytes decrease)
Output file size = 15380 bytes (4249 bytes = 21.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-20-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26615 bytes
Input file size = 26729 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21182
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 = 21182
Output IDAT size = 21182 bytes (5433 bytes decrease)
Output file size = 21260 bytes (5469 bytes = 20.46% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-1.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7412 bytes
Input file size = 8258 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6199
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 = 6199
Output IDAT size = 6199 bytes (1213 bytes decrease)
Output file size = 6277 bytes (1981 bytes = 23.99% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-2.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7399 bytes
Input file size = 8245 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6170
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 = 6170
Output IDAT size = 6170 bytes (1229 bytes decrease)
Output file size = 6248 bytes (1997 bytes = 24.22% decrease)
[gannet:2599268:0:2599268] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc)
==== backtrace (tid:2599268) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f42d403b144]
1 /lib64/libucs.so.0(+0x2880d) [0x7f42d403c80d]
2 /lib64/libucs.so.0(+0x289dd) [0x7f42d403c9dd]
3 [0x7f42eebd0c69]
=================================
*** caught segfault ***
address 0x4d20027a964, cause 'unknown'
Traceback:
1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class, .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, evalArray = FALSE, use.true.class = TRUE)
2: .J(Class, ...)
3: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer")))
4: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer")))
5: .local(object, ...)
6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
8: .local(object, ...)
9: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
10: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
11: eval(expr, envir)
12: eval(expr, envir)
13: withVisible(eval(expr, envir))
14: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
15: eval(call)
16: eval(call)
17: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
18: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
20: withRestartList(expr, restarts[-nr])
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
23: withRestartList(expr, restarts)
24: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
25: evaluate::evaluate(...)
26: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
27: in_dir(input_dir(), expr)
28: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
29: eng_r(options)
30: block_exec(params)
31: call_block(x)
32: process_group(group)
33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
34: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
35: process_file(text, output)
36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
38: vweave_rmarkdown(...)
39: engine$weave(file, quiet = quiet, encoding = enc)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
44: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa", skip = TRUE, ser_elibs = "/tmp/RtmpW5Zp2y/file271bdc92de785.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4-2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘spcosa.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-7-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29571 bytes
Input file size = 29685 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21909
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 = 21909
Output IDAT size = 21909 bytes (7662 bytes decrease)
Output file size = 21987 bytes (7698 bytes = 25.93% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-8-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32369 bytes
Input file size = 32483 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23908
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 = 23908
Output IDAT size = 23908 bytes (8461 bytes decrease)
Output file size = 23986 bytes (8497 bytes = 26.16% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-10-1.png
672x384 pixels, 8 bits/pixel, 215 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8991 bytes
Input file size = 9738 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7498
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7419
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 = 7419
Output IDAT size = 7419 bytes (1572 bytes decrease)
Output file size = 7497 bytes (2241 bytes = 23.01% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-11-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40069 bytes
Input file size = 40195 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29976
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 = 29976
Output IDAT size = 29976 bytes (10093 bytes decrease)
Output file size = 30054 bytes (10141 bytes = 25.23% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-16-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35456 bytes
Input file size = 35582 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26150
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 = 26150
Output IDAT size = 26150 bytes (9306 bytes decrease)
Output file size = 26228 bytes (9354 bytes = 26.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-18-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19527 bytes
Input file size = 19629 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15302
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 = 15302
Output IDAT size = 15302 bytes (4225 bytes decrease)
Output file size = 15380 bytes (4249 bytes = 21.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-20-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26615 bytes
Input file size = 26729 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21182
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 = 21182
Output IDAT size = 21182 bytes (5433 bytes decrease)
Output file size = 21260 bytes (5469 bytes = 20.46% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-1.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7412 bytes
Input file size = 8258 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6199
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 = 6199
Output IDAT size = 6199 bytes (1213 bytes decrease)
Output file size = 6277 bytes (1981 bytes = 23.99% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-2.png
576x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7399 bytes
Input file size = 8245 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6170
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 = 6170
Output IDAT size = 6170 bytes (1229 bytes decrease)
Output file size = 6248 bytes (1997 bytes = 24.22% decrease)
[gannet:1260319:0:1260319] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc)
==== backtrace (tid:1260319) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7efeb5113144]
1 /lib64/libucs.so.0(+0x2880d) [0x7efeb511480d]
2 /lib64/libucs.so.0(+0x289dd) [0x7efeb51149dd]
3 [0x7eff7f1d1be9]
=================================
*** caught segfault ***
address 0x4d200133b1f, cause 'unknown'
Traceback:
1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class, .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, evalArray = FALSE, use.true.class = TRUE)
2: .J(Class, ...)
3: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer")))
4: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer")))
5: .local(object, ...)
6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
8: .local(object, ...)
9: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
10: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10)
11: eval(expr, envir)
12: eval(expr, envir)
13: withVisible(eval(expr, envir))
14: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
15: eval(call)
16: eval(call)
17: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
18: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
20: withRestartList(expr, restarts[-nr])
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
23: withRestartList(expr, restarts)
24: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
25: evaluate::evaluate(...)
26: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
27: in_dir(input_dir(), expr)
28: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
29: eng_r(options)
30: block_exec(params)
31: call_block(x)
32: process_group(group)
33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
34: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
35: process_file(text, output)
36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
38: vweave_rmarkdown(...)
39: engine$weave(file, quiet = quiet, encoding = enc)
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
44: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa", skip = TRUE, ser_elibs = "/tmp/RtmpKsPH98/file1301fe482fc7cc.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.