Last updated on 2025-01-03 01:48:52 CET.
| Package | FAIL | ERROR | NOTE | OK |
|---|---|---|---|---|
| dartR | 5 | 6 | 2 | |
| dartR.base | 1 | 12 | ||
| dartR.captive | 1 | 3 | 9 | |
| dartR.data | 6 | 7 | ||
| dartR.popgen | 1 | 12 | ||
| dartR.spatial | 3 | 10 | ||
| dartRverse | 13 | |||
| PopGenReport | 3 | 10 |
Current CRAN status: ERROR: 5, NOTE: 6, OK: 2
Version: 2.9.7
Check: Rd files
Result: NOTE
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
7 | {adegenet} object}
| ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
| ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
17 | code{x2@other$history[c(1,4,5)]}). [optional].}
| ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
| ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
51 | Parallel computation is implemented. The argument code{n.cores} indicates the
| ^
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-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: 2.9.7
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
gl.genleastcost.Rd: landgenreport, popgenreport, wassermann, lgrMMRR
utils.dart2genlight.Rd: adegenet
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: 2.9.7
Check: examples
Result: ERROR
Running examples in ‘dartR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gl.filter.ld
> ### Title: Filters loci based on linkage disequilibrium (LD)
> ### Aliases: gl.filter.ld
>
> ### ** Examples
>
> ## Not run:
> ##D test <- bandicoot.gl
> ##D test <- gl.filter.callrate(test,threshold = 1)
> ##D res <- gl.report.ld.map(test)
> ##D res_2 <- gl.filter.ld(x=test,ld_report = res)
> ##D res_3 <- gl.report.ld.map(res_2)
> ## End(Not run)
> if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
+ test <- gl.filter.callrate(platypus.gl, threshold = 1)
+ test <- gl.filter.monomorphs(test)
+ test <- test[,1:20]
+ report <- gl.report.ld.map(test)
+ res <- gl.filter.ld(x=test,ld_report = report)
+ }
Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 1
Completed: gl.filter.callrate
Starting gl.filter.monomorphs
Processing genlight object with SNP data
Identifying monomorphic loci
Removing monomorphic loci and loci with all missing
data
Completed: gl.filter.monomorphs
Starting gl.report.ld.map
Processing genlight object with SNP data
Calculating pairwise LD in population SEVERN_ABOVE
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: snpStats::ld(genotype_loci, genotype_loci, stats = ld_stat)
2: gl.report.ld.map(test)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.9.7
Check: examples
Result: ERROR
Running examples in ‘dartR-Ex.R’ failed
The error most likely occurred in:
> ### Name: gl.filter.ld
> ### Title: Filters loci based on linkage disequilibrium (LD)
> ### Aliases: gl.filter.ld
>
> ### ** Examples
>
> ## Not run:
> ##D test <- bandicoot.gl
> ##D test <- gl.filter.callrate(test,threshold = 1)
> ##D res <- gl.report.ld.map(test)
> ##D res_2 <- gl.filter.ld(x=test,ld_report = res)
> ##D res_3 <- gl.report.ld.map(res_2)
> ## End(Not run)
> if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
+ test <- gl.filter.callrate(platypus.gl, threshold = 1)
+ test <- gl.filter.monomorphs(test)
+ test <- test[,1:20]
+ report <- gl.report.ld.map(test)
+ res <- gl.filter.ld(x=test,ld_report = report)
+ }
Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 1
Completed: gl.filter.callrate
Starting gl.filter.monomorphs
Processing genlight object with SNP data
Identifying monomorphic loci
Removing monomorphic loci and loci with all missing
data
Completed: gl.filter.monomorphs
Starting gl.report.ld.map
Processing genlight object with SNP data
Calculating pairwise LD in population SEVERN_ABOVE
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: snpStats::ld(genotype_loci, genotype_loci, stats = ld_stat)
2: gl.report.ld.map(test)
An irrecoverable exception occurred. R is aborting now ...
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.9.7
Check: examples
Result: ERROR
Running examples in 'dartR-Ex.R' failed
The error most likely occurred in:
> ### Name: gl.filter.ld
> ### Title: Filters loci based on linkage disequilibrium (LD)
> ### Aliases: gl.filter.ld
>
> ### ** Examples
>
> ## Not run:
> ##D test <- bandicoot.gl
> ##D test <- gl.filter.callrate(test,threshold = 1)
> ##D res <- gl.report.ld.map(test)
> ##D res_2 <- gl.filter.ld(x=test,ld_report = res)
> ##D res_3 <- gl.report.ld.map(res_2)
> ## End(Not run)
> if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
+ test <- gl.filter.callrate(platypus.gl, threshold = 1)
+ test <- gl.filter.monomorphs(test)
+ test <- test[,1:20]
+ report <- gl.report.ld.map(test)
+ res <- gl.filter.ld(x=test,ld_report = report)
+ }
Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 1
Completed: gl.filter.callrate
Starting gl.filter.monomorphs
Processing genlight object with SNP data
Identifying monomorphic loci
Removing monomorphic loci and loci with all missing
data
Completed: gl.filter.monomorphs
Starting gl.report.ld.map
Processing genlight object with SNP data
Calculating pairwise LD in population SEVERN_ABOVE
Flavor: r-devel-windows-x86_64
Version: 2.9.7
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 2.9.7
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Current CRAN status: NOTE: 1, OK: 12
Version: 0.98
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 0.98
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Current CRAN status: FAIL: 1, NOTE: 3, OK: 9
Version: 0.75
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
gl.filter.parent.offspring.Rd: gl.report.rdepth,
gl.report.reproducibility
gl.report.parent.offspring.Rd: gl.report.rdepth,
gl.report.reproducibility
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: 0.75
Check: PDF version of manual
Result: FAIL
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### ** Examples
>
> require("dartR.data")
> res <- utils.assignment_2(platypus.gl, unknown = "T27")
Starting utils.assignment_2
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Assigning individual T27 against population SEVERN_ABOVE
Assigning individual T27 against population SEVERN_BELOW
Assigning individual T27 against population TENTERFIELD
Completed: utils.assignment_2
>
>
>
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed: 15.21 1.19 16.41 NA NA
> grDevices::dev.off()
null device
1
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Flavor: r-release-windows-x86_64
Current CRAN status: NOTE: 6, OK: 7
Version: 1.0.8
Check: installed package size
Result: NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 4.5Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 1, OK: 12
Version: 1.0.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 1.0.0
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Current CRAN status: NOTE: 3, OK: 10
Version: 0.78
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
gl.spatial.autoCorr.Rd: gl.propShared, gl.dist.ind
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: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 3.1
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
allel.rich.Rd: genind
allele.dist.Rd: genind
bilby.Rd: genind
gd.kosman.Rd: genind
gd.smouse.Rd: genind
genleastcost.Rd: gdistance, rSPDistance
landgenreport.Rd: gdistance, rSPDistance
null.all.Rd: genind
popgenreport.Rd: genind, import2genind, df2genind, read.fstat,
read.structure, read.genetix, read.genepop, Mercator, dismo, knitr,
adegenet, pegas, mmod
read.genetable.Rd: genind-class, adegenet, import2genind, df2genind,
read.fstat, read.structure, read.genetix, read.genepop
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