Last updated on 2024-05-01 16:52:52 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 | 27.22 | 197.53 | 224.75 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.7.4 | 385.80 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.4 | 389.69 | ERROR | |||
| r-devel-windows-x86_64 | 0.7.4 | 31.00 | 232.00 | 263.00 | NOTE | |
| r-patched-linux-x86_64 | 0.7.4 | 28.51 | 255.43 | 283.94 | 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 | 38.00 | 318.00 | 356.00 | NOTE |
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