Last updated on 2024-12-23 12:49:38 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| dartR | 5 | 6 | 2 |
| dartR.base | 1 | 12 | |
| dartR.captive | 3 | 10 | |
| dartR.data | 6 | 7 | |
| dartR.popgen | 1 | 1 | 11 |
| dartR.spatial | 1 | 2 | 10 |
| dartRverse | 13 | ||
| PopGenReport | 1 | 2 | 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-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-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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.9.7
Check: package dependencies
Result: ERROR
Packages required but not available: 'PopGenReport', 'raster'
Packages suggested but not available for checking:
'dismo', 'gdistance', 'hierfstat', 'leaflet', 'leaflet.minicharts',
'terra'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: 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: NOTE: 3, OK: 10
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
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: ERROR: 1, NOTE: 1, OK: 11
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘dartR.popgen-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gl.ld.haplotype
> ### Title: Visualize patterns of linkage disequilibrium and identification
> ### of haplotypes
> ### Aliases: gl.ld.haplotype
>
> ### ** Examples
>
> require("dartR.data")
> x <- platypus.gl
> x <- gl.filter.callrate(x, threshold = 1)
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
> # only the first 15 individuals because of speed during tests
> x <- gl.keep.pop(x, pop.list = "TENTERFIELD")[1:15, ]
Starting gl.keep.pop
Processing genlight object with SNP data
Checking for presence of nominated populations
Retaining only populations TENTERFIELD
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop
> x$chromosome <- as.factor(x$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1)
> x$position <- x$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
> ld_res <- gl.ld.haplotype(x,
+ chrom_name = "NC_041728.1_chromosome_1",
+ ld_max_pairwise = 10000000
+ )
Starting gl.ld.haplotype
Processing genlight object with SNP data
Calculating pairwise LD in population TENTERFIELD
Analysing chromosome NC_041728.1_chromosome_1
The maximum distance at which LD should be calculated
(ld_max_pairwise) is too short for chromosome NC_041728.1_chromosome_1 . Setting this distance to 40201976 bp
Error in loadNamespace(x) : there is no package called ‘raster’
Calls: gl.ld.haplotype ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
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: ERROR: 1, NOTE: 2, 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-windows-x86_64
Version: 0.78
Check: package dependencies
Result: ERROR
Package required but not available: ‘raster’
Packages suggested but not available for checking:
'dismo', 'gdistance', 'terra', 'PopGenReport'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 2, 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-windows-x86_64
Version: 3.1
Check: package dependencies
Result: ERROR
Packages required but not available: 'dismo', 'gdistance', 'raster'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc