CRAN Package Check Results for Package dnapath

Last updated on 2024-05-02 09:51:29 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.7.4	34.80	272.50	307.30	NOTE
r-devel-linux-x86_64-debian-gcc	0.7.4	28.21	195.22	223.43	NOTE
r-devel-linux-x86_64-fedora-clang	0.7.4			408.45	ERROR
r-devel-linux-x86_64-fedora-gcc	0.7.4			302.33	ERROR
r-devel-windows-x86_64	0.7.4	31.00	232.00	263.00	NOTE
r-patched-linux-x86_64	0.7.4	34.97	252.71	287.68	NOTE
r-release-linux-x86_64	0.7.4	34.28	260.00	294.28	NOTE
r-release-macos-arm64	0.7.4			121.00	NOTE
r-release-windows-x86_64	0.7.4	33.00	236.00	269.00	NOTE
r-oldrel-macos-arm64	0.7.4			117.00	ERROR
r-oldrel-macos-x86_64	0.7.4			198.00	NOTE
r-oldrel-windows-x86_64	0.7.4	41.00	314.00	355.00	NOTE

Additional issues

noSuggests

Check Details

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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-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-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-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: /data/gannet/ripley/R/packages/tests-clang/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: /data/gannet/ripley/R/packages/tests-clang/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) Quitting from lines at lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd) Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics: Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible types. ℹ `x$entrezgene_id` is a <double>. ℹ `y$entrezgene_id` is a <character>. --- failed re-building ‘introduction_to_dnapath.Rmd’ --- re-building ‘package_data.Rmd’ using rmarkdown Quitting from lines at lines 268-273 [unnamed-chunk-20] (package_data.Rmd) Error: processing vignette 'package_data.Rmd' failed with diagnostics: Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible types. ℹ `x$entrezgene_id` is a <double>. ℹ `y$entrezgene_id` is a <character>. --- 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-devel-linux-x86_64-fedora-clang

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: /data/gannet/ripley/R/packages/tests-devel/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: /data/gannet/ripley/R/packages/tests-devel/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) Quitting from lines at lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd) Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics: Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible types. ℹ `x$entrezgene_id` is a <double>. ℹ `y$entrezgene_id` is a <character>. --- failed re-building ‘introduction_to_dnapath.Rmd’ --- re-building ‘package_data.Rmd’ using rmarkdown Quitting from lines at lines 268-273 [unnamed-chunk-20] (package_data.Rmd) Error: processing vignette 'package_data.Rmd' failed with diagnostics: Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible types. ℹ `x$entrezgene_id` is a <double>. ℹ `y$entrezgene_id` is a <character>. --- 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-devel-linux-x86_64-fedora-gcc

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

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

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