Reputation: 27
if I run following code I get the error message: Error in is.na(output) || !is.character(output) : 'length = 3' in coercion to 'logical(1)'
The code was
library(rentrez)
gene_sombols <- "IL7"
organism <- "human"
query <- paste(gene_sombols, organism, sep = " ")
genes <- entrez_search(db="gene", term = query, retmax=1)
I innitinal run the following code succesffully:
genes <- entrez_search(db="gene", term = "IL7 human", retmax=1)
After I run the mal code also this previous working code does not work any more.
Any suggestions?
Best regards wbart
UPDATE: I get this Error even when I load the workspace !!! UPDATE2: I generate a new Workspace (no errror), I installed rentrez UPDATE3: I deleted all code below and generate new one. I generated a query and forced the error by viewing the result then run traceback() and sessioninfo()
# here is the code
library(rentrez)
> resul<-entrez_search(db="gene", term= query)
# only after clicking on view the error appears
> View(resul)
Error in is.na(output) || !is.character(output) :
'length = 3' in coercion to 'logical(1)'
# run traceback
> traceback()
10: .rs.explorer.objectDesc(.$object)
9: .rs.scalar(.rs.explorer.objectDesc(.$object))
8: .rs.explorer.createInspectionResult(object, context, children)
7: .rs.explorer.inspectDefault(object, context)
6: .rs.explorer.inspectObject(object[[i]], childContext)
5: FUN(X[[i]], ...)
4: lapply(indices, function(i) {
if (is.null(names) || !nzchar(names[[i]])) {
name <- sprintf("[[%i]]", i)
access <- sprintf("#[[%i]]", i)
tags <- .rs.explorer.tags$VIRTUAL
}
else {
name <- names[[i]]
access <- sprintf("#[[\"%s\"]]", name)
tags <- character()
}
childContext <- .rs.explorer.createChildContext(context,
name, access, tags)
.rs.explorer.inspectObject(object[[i]], childContext)
})
3: .rs.explorer.inspectList(object, context)
2: .rs.explorer.inspectObject(object, context)
1: .rs.rpc.explorer_begin_inspect("0e1396e2e86e48d88b07ab7585d76766",
"resul")
# run sessioninfo
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8
[3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C
[5] LC_TIME=German_Germany.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rentrez_1.2.3
loaded via a namespace (and not attached):
[1] httr_1.4.7 compiler_4.3.1 R6_2.5.1 tools_4.3.1 curl_5.2.0
[6] jsonlite_1.8.8 XML_3.99-0.16.1
Upvotes: 0
Views: 336