Run revdepcheck::revdep_details(, "dce")
for more info
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 ```
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
Run revdepcheck::revdep_details(, "multiWGCNA")
for more info
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 ```
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
Run revdepcheck::revdep_details(, "ORFik")
for more info
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 ```
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.
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