CRAN Package Check Results for Package dnapath

Last updated on 2024-04-23 03:56:43 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.7.4 35.88 198.81 234.69 NOTE
r-devel-linux-x86_64-debian-gcc 0.7.4 29.82 196.78 226.60 NOTE
r-devel-linux-x86_64-fedora-clang 0.7.4 392.21 NOTE
r-devel-linux-x86_64-fedora-gcc 0.7.4 391.98 NOTE
r-prerel-macos-arm64 0.7.4 121.00 NOTE
r-prerel-windows-x86_64 0.7.4 32.00 260.00 292.00 NOTE
r-patched-linux-x86_64 0.7.4 38.82 255.75 294.57 NOTE
r-release-linux-x86_64 0.7.4 33.42 243.22 276.64 ERROR
r-release-macos-arm64 0.7.4 117.00 ERROR
r-release-macos-x86_64 0.7.4 198.00 NOTE
r-release-windows-x86_64 0.7.4 39.00 347.00 386.00 NOTE
r-oldrel-macos-arm64 0.7.4 98.00 OK
r-oldrel-windows-x86_64 0.7.4 39.00 294.00 333.00 ERROR

Additional issues

noSuggests

Check Details

Version: 0.7.4
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'AnnotationDbi', 'reactome.db', 'biomaRt' Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.7.4
Check: C++ specification
Result: NOTE Specified C++11: please drop specification unless essential 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-prerel-macos-arm64, r-prerel-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: 0.7.4
Check: Rd metadata
Result: NOTE Invalid package aliases in Rd file 'dnapath2-package.Rd': ‘dnapath2-package’ 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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64

Version: 0.7.4
Check: Rd contents
Result: NOTE Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd': \references: ‘This optional section can contain literature or other refere...’ \seealso: ‘Optional links to other man pages’ \examples: ‘\dontrun{ ## Optional simple examples of the most impor...’ 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-prerel-macos-arm64, r-prerel-windows-x86_64, r-patched-linux-x86_64

Version: 0.7.4
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘reactome.db’ Flavors: r-prerel-macos-arm64, r-release-macos-x86_64

Version: 0.7.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-3-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 83472 bytes Input file size = 83670 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76968 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 = 76968 Output IDAT size = 76968 bytes (6504 bytes decrease) Output file size = 77046 bytes (6624 bytes = 7.92% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-7-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25119 bytes Input file size = 25233 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19956 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 = 19956 Output IDAT size = 19956 bytes (5163 bytes decrease) Output file size = 20034 bytes (5199 bytes = 20.60% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-9-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27276 bytes Input file size = 27390 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21547 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 = 21547 Output IDAT size = 21547 bytes (5729 bytes decrease) Output file size = 21625 bytes (5765 bytes = 21.05% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-12-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10479 bytes Input file size = 10569 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7984 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 = 7984 Output IDAT size = 7984 bytes (2495 bytes decrease) Output file size = 8062 bytes (2507 bytes = 23.72% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-13-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 10479 bytes Input file size = 10569 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7984 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 = 7984 Output IDAT size = 7984 bytes (2495 bytes decrease) Output file size = 8062 bytes (2507 bytes = 23.72% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-14-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 25023 bytes Input file size = 25137 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19685 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 = 19685 Output IDAT size = 19685 bytes (5338 bytes decrease) Output file size = 19763 bytes (5374 bytes = 21.38% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-15-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 69314 bytes Input file size = 69488 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55130 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 = 55130 Output IDAT size = 55130 bytes (14184 bytes decrease) Output file size = 55208 bytes (14280 bytes = 20.55% decrease) --- finished re-building ‘introduction_to_dnapath.Rmd’ --- re-building ‘package_data.Rmd’ using rmarkdown Quitting from lines at lines 126-135 [unnamed-chunk-8] (package_data.Rmd) Error: processing vignette 'package_data.Rmd' failed with diagnostics: SSL peer certificate or SSH remote key was not OK: [www.linkedomics.org] server certificate verification failed. CAfile: none CRLfile: none --- failed re-building ‘package_data.Rmd’ SUMMARY: processing the following file failed: ‘package_data.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 0.7.4
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'GENIE3', 'reactome.db' Flavor: r-release-macos-arm64

Version: 0.7.4
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘GENIE3’ Flavor: r-release-macos-arm64

Version: 0.7.4
Check: examples
Result: ERROR Running examples in ‘dnapath-Ex.R’ failed The error most likely occurred in: > ### Name: run_genie3 > ### Title: Wrapper for GENIE3 method > ### Aliases: run_genie3 > > ### ** Examples > > if(!requireNamespace("GENIE3", quietly = TRUE)) { + data(meso) + data(p53_pathways) + + # To create a short example, we subset on two pathways from the p53 pathway list, + # and will only run 5 permutations for significance testing. + pathway_list <- p53_pathways[c(8, 13)] + n_perm <- 5 + + # Use this method to perform differential network analysis. + # The parameters in run_genie3() can be adjusted using the ... argument. + # For example, the 'nTrees' parameter can be specified as shown here. + results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_genie3, + nTrees = 100) + summary(results) + + # The group-specific association matrices can be extracted using get_networks(). + nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. + + # nw_list has length 2 and contains the inferred networks for the two groups. + # The gene names are the Entrezgene IDs from the original expression dataset. + # Renaming the genes in the dnapath results to rename those in the networks. + # NOTE: The temporary directory, tempdir(), is used in this example. In practice, + # this argument can be removed or changed to an existing directory + results <- rename_genes(results, to = "symbol", species = "human", + dir_save = tempdir()) + nw_list <- get_networks(results[[1]]) # The genes (columns) will have new names. + + # (Optional) Plot the network using SeqNet package (based on igraph plotting). + # First rename entrezgene IDs into gene symbols. + SeqNet::plot_network(nw_list[[1]]) + } Warning: The `GENIE3` package must be installed to use run_genie3(). Using run_corr() instead. Error in wCorr::weightedCorr(x[, index_set[1, i]], x[, index_set[2, i]], : The vectors ‘x’, ‘y’, and ‘weights’ must all be of the same length. Calls: dnapath ... network_inference -> run_corr -> sapply -> lapply -> FUN -> <Anonymous> Execution halted Flavor: r-release-macos-arm64

Version: 0.7.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'introduction_to_dnapath.Rmd' using rmarkdown Quitting from lines at lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd) Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics: Failed to collect lazy table. Caused by error in `db_collect()`: ! Arguments in `...` must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? --- failed re-building 'introduction_to_dnapath.Rmd' --- re-building 'package_data.Rmd' using rmarkdown Quitting from lines at lines 126-135 [unnamed-chunk-8] (package_data.Rmd) Error: processing vignette 'package_data.Rmd' failed with diagnostics: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - Das empfangene Zertifikat ist abgelaufen. --- failed re-building 'package_data.Rmd' SUMMARY: processing the following files failed: 'introduction_to_dnapath.Rmd' 'package_data.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64