I have been using this code
nutList <- gsub("_µg","",nutList, fixed = TRUE)
to remove the string "_µg" from the variable nutList for at least a year and have had no problems. Now I'm trying use document() to see where I have problems in getting ready for a package.
Error in parse(text = lines, n = -1, srcfile = srcfile) : [filename] : unexpected INCOMPLETE_STRING
nutList <- gsub("_
It appears that document() doesn't like the µ that is there. How can I modify the code so it is accepted?
Related
I am getting some weird errors, when I try to upload a data.frame to the Teradata database using td_fastload() in R.
The copy_to() method works for smaller sets without any issues, just takes a while... but td_fastload() for bigger sets don't work, here is what I am getting, what does this mean ?
my command is:
td_fastload(con, df = TEST55, table.name = "TEST55", overwrite = TRUE )
and the errors are:
Error: In value[[3L]](cond):
[tdplyr - (TDR_E1001)] Error: In value[[3L]](cond):
[tdplyr - (TDR_E1001)] Error in obtainRows(res, FALSE, params): Argument params class character differs from the required data.frame or list
In addition: Warning messages:
1: In td_fastload(con, df = TEST55, table.name = 'TEST55', overwrite = TRUE):
[tdplyr - (TDR_W1011)] Setting 'overwrite = TRUE' will drop existing table 'TEST55' and recreate it with new schema.
2: In sprintf(gettext(fmt, domain = domain, trim = trim), ...) :
one argument not used by format 'Error in obtainRows(res, FALSE, params): Argument params class character differs from the required data.frame or list
'
3: In sprintf(gettext(fmt, domain = domain, trim = trim), ...) :
one argument not used by format 'Error: In value[[3L]](cond):
[tdplyr - (TDR_E1001)] Error in obtainRows(res, FALSE, params): Argument params class character differs from the required data.frame or list```
I am getting an "error in parse`````````; attempt to use zero-length variable" when I try to knit the below.
It always occurs at line 38. Ideas?
setwd("~/Dropbox/varsel/")
library(olsrr)
simplemodel <- read.csv("~/Dropbox/varsel/Ranalyses var sel/simplemodel.csv")
model<-lm(out ~., data =simplemodel)
aicresult<- ols_step_backward_aic(model, details = TRUE)
aicresult
38 setwd("~/Dropbox/varsel/")
library(BMS)
library(dply)
swmodel<-read.csv ("~/Dropbox/causation project/sachs warner/mainvarsnomiss")
swmodelminuscol1<-select(swmodel,-1)
swbma<- bms(swmodelminuscol1, burn=100000, iter=200000, g="BRIC", mprior="uniform", nmodel=2000, mcmc="bd", user.int=FALSE)
coef(swbma, exact = TRUE)```
Here's a piece of code I'm working with:
install.package('BiocManager');BiocManager::install('UniProt.ws')
requireNamespace('UniProt.ws')
uniprot_object <- UniProt.ws::UniProt.ws(
UniProt.ws::availableUniprotSpecies(
pattern = '^Homo sapiens$')$`taxon ID`)
query_results <- try(
UniProt.ws::select(
x = uniprot_object,
keys = 'BAA08084.1',
keytype = 'EMBL/GENBANK/DDBJ',
columns = c('ENSEMBL','UNIPROTKB')))
This particular key/keytype combination is non-productive and produces the following output:
Getting mapping data for BAA08084.1 ... and ACC
error while trying to retrieve data in chunk 1:
no lines available in input
continuing to try
Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) :
attempt to set 'colnames' on an object with less than two dimensions
Of the two [eE]rrors reported only the second is a 'proper' R error object and given the use of try accordingly captured in the variable query_result.
I am, however, desperate to capture the other error bit (no lines available in input) to inform downstream programmatic processes.
After playing with a plethora of capture.output, sink, purrr::quietly, etc. options found by startpaging (googling), I continue to fail capturing that bit. How can I do that?
As #Csd suggested, you could use tryCatch. The message that you are after is printed by the message() function in R, not stop(), so try() will ignore it. To capture output from message(), use code like this:
query_results <- tryCatch(
UniProt.ws::select(
x = uniprot_object,
keys = 'BAA08084.1',
keytype = 'EMBL/GENBANK/DDBJ',
columns = c('ENSEMBL','UNIPROTKB')),
message = function(e) conditionMessage(e))
This will abort evaluation when it gets any message, and return the message in query_results. If you are doing more than debugging, you probably want the message saved, but evaluation to continue. In that case, use withCallingHandlers instead. For example,
saveMessages <- c()
query_results <- withCallingHandlers(
UniProt.ws::select(
x = uniprot_object,
keys = 'BAA08084.1',
keytype = 'EMBL/GENBANK/DDBJ',
columns = c('ENSEMBL','UNIPROTKB')),
message = function(e)
saveMessages <<- c(saveMessages, conditionMessage(e)))
When I run this version, query_results is unchanged (because the later error aborted execution), but the messages are saved:
saveMessages
[1] "Getting mapping data for BAA08084.1 ... and ACC\n"
[2] "error while trying to retrieve data in chunk 1:\n no lines available in input\ncontinuing to try\n"
Based on #user2554330 s most excellent answer, I constructed an ugly thing that does exactly what I want:
try to execute the statement
don't fail fatally
leave no ugly messages
allow me access to errors and messages
So here it is in all it's despicable glory:
saveMessages <- c()
query_results <- suppressMessages(
withCallingHandlers(
try(
UniProt.ws::select(
x = uniprot_object,
keys = 'BAA08084.1',
keytype = 'EMBL/GENBANK/DDBJ',
columns = c('ENSEMBL','UNIPROTKB')),
silent = TRUE),
message = function(e)
saveMessages <<- c(saveMessages, conditionMessage(e))))
After a bit of a gap I updated RStudio and all packages this morning.
I have a little function that I use to prettify currencies
currency <- function(n, k=FALSE) {
n <- ifelse(!k, str_c("£", comma(round(n,0))), str_c("£", comma(round(n/1000,0)),"k"))
return(n)
}
It now fails to parse - the problem is the £ sign.
Error in parse(text = lines, n = -1, srcfile = srcfile) :
[path]/plot_helpers.R:72:
25: unexpected INCOMPLETE_STRING
71: currency <- function(n, k=FALSE) {
72: n <- ifelse(!k, str_c("
^
In addition: Warning message:
In readLines(con, warn = FALSE, n = n, ok = ok, skipNul = skipNul) :
invalid input found on input connection '/home/richardc/ownCloud/prodr/R/plot_helpers.R'
However I can run the code within the editor and it works fine. What is causing readLines to fail in this way ?
After some messing about today, I realise that the problem is in devtools. To recap here is a test project testencr.prj:
library(stringr)
library(devtools)
main <- function(n) {
n <- str_c("£", n)
return(n)
}
I can run the code fine from the console, but when I use devtools it barfs on the UTF-8 character:
> devtools::load_all()
Loading testencr
Error in parse(text = lines, n = -1, srcfile = srcfile) :
/home/richardc/ownCloud/test/R/test_enc.R:6:14: unexpected INCOMPLETE_STRING
5: main <- function(n) {
6: n <- str_c("
^
In addition: There were 27 warnings (use warnings() to see them)
But when I add a specific encoding into the DESCRIPTION
Encoding: UTF-8
It is all fine (this notwithstanding the project defaults are UTF8)
Loading testencr
There were 36 warnings (use warnings() to see them)```
I was having the same problem, specifically in a Shiny app (not the rest of the time). I managed to solve it by using this unicode instead of £:
enc2utf8("\u00A3")
I would like to create a package for internal usage (not to distribute somewhere). One of my functions contains the line
if (data$unit[i] != "°C") {
It works perfectly in the script, but if I want to create the documentation for my package using document() from devtools, i get the error
Error in parse(text = lines, keep.source = TRUE, srcfile = srcfilecopy(file, path_to_my_code: unexpected INCOMPLETE_STRING
279: if (! is.na(data$unit[i]){
280: if (data$unit[i] != "
addition: Warning message:
In readLines(con, warn = FALSE, n = n, ok = ok, skipNul = skipNul) :
invalid input found on input connection 'path_to_my_code'
If I delete the °-character, document() works. But I need this character there, so this is not an option.
When using double-\ in the if-clause, my function doesn't detect °C anymore as shown here:
test <- c("mg/l", "°C")
"\\°C" %in% test
[1] FALSE
If I use tryCatch, the documentation is also not created.
Replacing "°C" by gsub(pattern = '\\\\', replacement = "", x = '\\°C') causes the function to crash at the double-\ .
How can I tell document() that everything is fine and it should just create the files?