CRAN Package Check Results for Package dartR

Last updated on 2024-12-25 03:50:05 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.9.7 1.08 1.89 2.97 ERROR
r-devel-linux-x86_64-debian-gcc 2.9.7 53.02 344.17 397.19 ERROR
r-devel-linux-x86_64-fedora-clang 2.9.7 763.45 ERROR
r-devel-linux-x86_64-fedora-gcc 2.9.7 716.41 ERROR
r-devel-windows-x86_64 2.9.7 75.00 463.00 538.00 ERROR
r-patched-linux-x86_64 2.9.7 85.33 555.18 640.51 NOTE
r-release-linux-x86_64 2.9.7 74.24 556.46 630.70 NOTE
r-release-macos-arm64 2.9.7 237.00 NOTE
r-release-macos-x86_64 2.9.7 368.00 NOTE
r-release-windows-x86_64 2.9.7 71.00 571.00 642.00 NOTE
r-oldrel-macos-arm64 2.9.7 250.00 NOTE
r-oldrel-macos-x86_64 2.9.7 569.00 OK
r-oldrel-windows-x86_64 2.9.7 100.00 777.00 877.00 OK

Additional issues

0len gcc-UBSAN

Check Details

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-clang

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-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-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 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