revdep/problems.md

In wilkelab/cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'

dce

• Version: 1.10.0
• GitHub: https://github.com/cbg-ethz/dce
• Source code: https://github.com/cran/dce
• Date/Publication: 2023-10-24
• Number of recursive dependencies: 324

Run revdepcheck::revdep_details(, "dce") for more info

Newly broken

• checking examples ... ERROR ``` Running examples in ‘dce-Ex.R’ failed The error most likely occurred in:

  Name: get_pathway_info

  Title: Dataframe containing meta-information of pathways in database

  Aliases: get_pathway_info

  ** Examples

  head(get_pathway_info(database_list = c("kegg"))) ... 11. │ └─graphite::pathways(query_species, database) 12. │ └─graphite:::loadData(paste(species, database, sep = "-")) 13. │ └─graphite:::archivePath(name) 14. │ └─graphite:::archiveDir() 15. │ └─base::stop("error creating directory: ", d) 16. └─base::.handleSimpleError(...) 17. └─purrr (local) h(simpleError(msg, call)) 18. └─cli::cli_abort(...) 19. └─rlang::abort(...) Execution halted ```

In both

• checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: doc 3.5Mb

• checking R code for possible problems ... NOTE plot_network: no visible binding for global variable ‘.’ Undefined global functions or variables: .

• checking data for non-ASCII characters ... NOTE Note: found 3 marked UTF-8 strings

multiWGCNA

• Version: 1.0.0
• GitHub: NA
• Source code: https://github.com/cran/multiWGCNA
• Date/Publication: 2023-10-24
• Number of recursive dependencies: 175

Run revdepcheck::revdep_details(, "multiWGCNA") for more info

Newly broken

• checking examples ... ERROR ``` Running examples in ‘multiWGCNA-Ex.R’ failed The error most likely occurred in:

  Name: cleanDatExpr

  Title: cleanDatExpr

  Aliases: cleanDatExpr

  ** Examples

  library(ExperimentHub) ... 'lattice', 'learnr', 'lpSolve', 'markdown', 'mgcv', 'nlme', 'plyr', 'ragg', 'reticulate', 'rnaturalearth', 'rpart', 's2', 'sass', 'scales', 'shiny', 'sp', 'spatial', 'stringi', 'stringr', 'survival', 'systemfonts', 'terra', 'testthat', 'textshaping', 'tinytex', 'units', 'vroom', 'waldo', 'wk', 'xml2' loading from cache Error: failed to load resource name: EH8223 title: Astrocyte Ribotag SummarizedExperiment reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection Execution halted ```

In both

• checking R code for possible problems ... NOTE bidirectionalBestMatches: no visible binding for global variable ‘mod1’ bidirectionalBestMatches: no visible binding for global variable ‘mod2’ bidirectionalBestMatches: no visible binding for global variable ‘overlap’ coexpressionLineGraph: no visible binding for global variable ‘Var1’ coexpressionLineGraph: no visible binding for global variable ‘value’ coexpressionLineGraph: no visible binding for global variable ‘Var2’ computeOverlapsFromWGCNA: no visible binding for global variable ‘mod1’ computeOverlapsFromWGCNA: no visible binding for global variable ‘mod2’ continuousFlowPlot: no visible global function definition for ‘ulist’ ... ‘Zsum’ preservationComparisonPlot: no visible binding for global variable ‘trait’ preservationComparisonPlot: no visible binding for global variable ‘Module’ topNGenes: no visible binding for global variable ‘kWithin’ Undefined global functions or variables: Correlation Expression Gene Module Sample Status Var1 Var2 Zscore Zsum error kWithin layout_with_fr log10Pvalue mod1 mod2 overlap p.adj stratum trait ulist uniqueSortedData value zScoreMatrix

ORFik

• Version: 1.22.1
• GitHub: https://github.com/Roleren/ORFik
• Source code: https://github.com/cran/ORFik
• Date/Publication: 2023-12-08
• Number of recursive dependencies: 156

Run revdepcheck::revdep_details(, "ORFik") for more info

Newly broken

• checking examples ... ERROR ``` Running examples in ‘ORFik-Ex.R’ failed The error most likely occurred in:

  Name: download.SRA.metadata

  Title: Downloads metadata from SRA

  Aliases: download.SRA.metadata

  ** Examples

  Originally on SRA

  download.SRA.metadata("SRP226389") Downloading metadata from: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=9232220,9232221,9232222,9232223,9232224,9232225&rettype=fasta&retmode=xml Error in open.connection(x, "rb") : HTTP error 429. Calls: download.SRA.metadata ... read_xml.character -> read_xml.connection -> open -> open.connection Execution halted ```

In both

• checking whether package ‘ORFik’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 See ‘/Users/clauswilke/github/cowplot/revdep/checks.noindex/ORFik/new/ORFik.Rcheck/00install.out’ for details.

• checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

• checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: R 1.0Mb doc 5.6Mb

• checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’ ‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’ See the note in ?`:::` about the use of this operator.

• checking R code for possible problems ... NOTE DEG.plot.static: no visible binding for global variable ‘Regulation’ DEG.plot.static: no visible binding for global variable ‘meanCounts’ DEG.plot.static: no visible binding for global variable ‘LFC’ DTEG.plot: no visible binding for global variable ‘Regulation’ DTEG.plot: no visible binding for global variable ‘rna’ DTEG.plot: no visible binding for global variable ‘rfp’ QCplots: no visible binding for global variable ‘leaders’ QCplots: no visible binding for global variable ‘trailers’ QCstats.plot: no visible binding for global variable ‘variable’ QCstats.plot: no visible binding for global variable ‘sample_total’ ... start2 startCodonCoverage startRegionRelative subtitle sum.count sum_per_gene sum_txNorm te trailers uniprotswissprot upstream_kozak_strength utr3_len utr5_len value var_txNorm variable widths windowMean windowSD zscore Consider adding importFrom("base", "length") importFrom("graphics", "frame") importFrom("stats", "df") importFrom("utils", "browseURL", "head") to your NAMESPACE file.

wilkelab/cowplot documentation built on Jan. 28, 2024, 11:19 a.m.