I'm currently trying to loop through a searchTwitter() call for each of 21 players in the NBA to get the 100 most recent tweets about them. However, weirdly, the call was working within my for loop of lastMVPs (which is a list of the names), but then stopped after 10 loops through, which would have only been 1,000 API calls. Now the call only works when outside of the for loop. Does anyone have any idea why this is?
For example - this works:
searchTwitter("Lebron James", n = 2, lang = 'en')
But this does not:
for (name in lastMVPs) {
newitem = searchTwitter(name, n = 100, lang = 'en')
df = twListToDF(newitem)
name = df$text
tweetMatrix = cbind(tweetMatrix, name)
}
And I get the error
Error in twListToDF(newitem) : Empty list passed to twListToDF
In addition: Warning message:
In doRppAPICall("search/tweets", n, params = params, retryOnRateLimit = retryOnRateLimit, :
100 tweets were requested but the API can only return 0
Which doesn't make sense to me because how can the API be maxed out when it's already working for my call outside of the loop?
Related
We have a basic tryCatch that writes a dataframe to Google Sheets, and trys again if the first write fails for any reason:
result = tryCatch({
print('TRYING')
googlesheets4::sheet_write(data = our_df, ss = our_spreadsheet, sheet = 'our_sheetname')
}, error = function(e) {
print('ERROR, TRYING AGAIN')
googlesheets4::sheet_write(data = our_df, ss = our_spreadsheet, sheet = 'our_sheetname')
})
It is possible to generalize this code to retry the googlesheets4::sheet_write() function call for N number of tries? Is something built into base R for this or is there a good R library that handles unlimited retries of a function?
You can put it in a for loop like this.
First, I am going to define a function that often fails (as I don't have access to your Google sheet).
russian_roulette <- function(n = 6) {
revolver <- sample(1:n, 1)
if (revolver == 1) {
return("You lived")
} else {
stop("Better luck next time...")
}
}
Then you can try it as many times as you consider reasonable. You can replace my call to russian_roulette() with your call to googlesheets4::sheet_write().
NUM_TRIES <- 10
for (i in 1:NUM_TRIES) {
message(i)
result <- try({
russian_roulette()
})
if (class(result) != "try-error") {
print("Success!")
break
}
}
Output:
1
Error in russian_roulette() : Better luck next time...
2
Error in russian_roulette() : Better luck next time...
3
Error in russian_roulette() : Better luck next time...
4
Error in russian_roulette() : Better luck next time...
5
Error in russian_roulette() : Better luck next time...
6
[1] "Success!"
result
# [1] "You lived"
I don't know why you expect writing to a file to fail - depending on the reason you may want to add a Sys.sleep() call in there for a certain number of seconds after every failure.
I'm using the Academic Twitter API and I'm facing some difficulties to collect a good quantity of tweets to my database...
My script is:
tweets <- searchTwitter('ICMS + gasolina',
n = 10000,
since = '2022-08-01',
lang ="pt")
and the R return is:
Warning message:
In doRppAPICall("search/tweets", n, params = params, retryOnRateLimit = retryOnRateLimit, :
10000 tweets were requested but the API can only return 1547
I don't know if it's exactalty what I have to expect or I have anything that I can do.
Trying to cut a bunch of audio (.WAV) files into smaller samples in R. For this example, I'm using a loop to cut out 1 minute samples at 140 minutes.
For some files, the recording ends before 140 minutes due to an error in the recording device. When this occurs, an error appears -- and the loop stops. I'm trying to make it so the loop continues by using the try or tryCatch function however keep getting errors.
The code is as follows:
for(i in 1:length(AR_CD288)){
CUT_AR288_5 <- try({readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")})
FILE.OUT_AR288_5<- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible=FALSE, filename = OUT.PATH_AR288_5[i])
}
I get the following two errors from the code:
Error in readBin(con, int, n = N, size = bytes, signed = (bytes != 1), :
invalid 'n' argument
Error in writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i]) :
'object' needs to be of class 'Wave' or 'WaveMC
The loop still saves some samples into the "New files" directory, however, once the loop reaches a file <140 minutes, the loop stops.
I am very stuck! Any help would be greatly appreciated.
Cheers.
When I use try, I always do one (or both) of:
check the return value to see if it inherits "try-error", indicating that the command failed; or
add try(., silent = TRUE), indicating that I don't care if it succeeded (but this implies that I will not use its return value, either).
Try this:
for (i in seq_along(AR_CD288)) {
CUT_AR288_5 <- try({
readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")
}, silent = TRUE)
if (!inherits(CUT_AR288_5, "try_error")) {
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i])
}
}
Three notes:
I changed 1:length(.) to seq_along(.); the latter is more resilient in an automated use when it is feasible that the vector might be length 0. For example, if AR_CD288 can ever be length 2, intuitively we expect 1:length(AR_CD288) to return nothing so that the for loop will not run; unfortunately, it resolves to 1:0 which returns a vector of length 2, which will often fail (based on whatever code is operating in the loop). The use of seq_along(.) will always return a vector of length 0 with an empty input, which is what we need. (Alternatively and equivalent, seq_len(length(AR_CD288)), though that's really what seq_along is intended to do.)
If you do not add silent=TRUE (or explicitly add silent=FALSE), then you will get an error message indicating that the command failed. Unfortunately, the error message may not indicate which i failed, so you may be left in the dark as far as fixing or removing the errant file. You may prefer to add an else to the if (inherits(.,"try-error")) clause so that you can provide a clearer error, such as
if (inherits(CUT_AR288_5, "try_error")) {
warning("'readWave' failed on ", sQuote(AR_CD288[i]), call. = FALSE)
} else {
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
# ...
}
(noting that I put the "things worked" code in the else clause here ... I find it odd to do if (!...) {} else {}, seems like a double-negation :-).
The choice to wrap one function or the whole block depends on your needs: I tend to prefer to know exactly where things fail, so the will-possibly-fail functions are often individually wrapped with try so that I can react (or log/message) accordingly. If you don't need that resolution of error-detection, then you can certainly wrap the whole code-block in a sense:
for (i in seq_along(AR_CD288)) {
ret <- try({
CUT_AR288_5 <- readWave(AR_CD288[i], from = 140, to = 141, units = "minutes")
FILE.OUT_AR288_5 <- sub("\\.wav$", "_140.wav", AR_CD288)
OUT.PATH_AR288_5 <- file.path("New files", basename(FILE.OUT_AR288_5))
writeWave(CUT_AR288_5, extensible = FALSE, filename = OUT.PATH_AR288_5[i])
}, silent = TRUE)
if (inherits(ret, "try-error")) {
# do or log something
}
}
I am coding in R-studio and have a function called saveResults(). It takes:
sce - a Single Cell Experiment object.
opt - a list with five things
clusterLabels - simple dataframe with two columns
The important thing is that I receive an error stating:
Error: unexpected symbol in:
"saveResults(sce = sce, opt = opt, clusteInputs()
zhengMix"
which doesn't agree at all with the parameters I pass into the function. You can see this on the last line of the code block below: I pass in proper parameters, but I receive an error that says I have passed in clusteInputs(), and zhengMix instead of clusterLabels. I don't have a function called clusteInputs(), and zhengMix was several lines above.
# Save the clustering data
InstallAndLoadPackagesForSC3Clustering()
opt <- GetOptionInputs()
zhengMix <- FetchzhengMix(opt)
sce <- CreateSingleCellExperiment(zhengMix)
clusterLabels <- getClusterLabels(sce)
opt <- createNewDirectoriesToSaveData(opt)
saveResults <- function(sce, opt, clusterLabels){
print("Beginning process of saving results...")
maxClusters = ncol(clusterLabels)/2+1
for (n in 2:maxClusters){
savePCAasPDF(sce, opt, numOfClusters = n, clusterLabels)
saveClusterLabelsAsRDS(clusterLabels, numOfClusters = n, opt)
}
saveSilhouetteScores(sce, opt)
print("Done.")
}
saveResults(sce = sce, opt = opt, clusterLabels = clusterLabels)
Does anyone have an idea what is going on? I'm pretty stuck on this.
This isn't the best solution, but I fixed my own problem by removing the code out of the function and running it there caused no issues.
I'm using slackr to send alert messages to a Slack channel. It works great except the message format is not great and I want to improve it.
install_github("hrbrmstr/slackr")
library(slackr)
slackr_setup(channel="#alerts", username="Mark Davis",
incoming_webhook_url = "https://hooks.slack.com/services/T31P8UDAB/BCH4HKQSC/*********",
api_token = "*********", echo = F)
alert="On Monday, 2018-09-03 # 2pm Pacific..."
slackr(alert)
Here is an example of how a message from slackr looks in Slack:
Here is an example of how I'd like it to look:
slackr doesn't seem to have many options in the way of formatting. I was thinking of building an image and inserting that, but I'm having trouble building an image out of a text file using R.
Perhaps there is another api I could call that could take my text and format it for slack?
I'm open to any suggestions.
Addendum:
Slackr has an option to upload files, so my latest attempt is to create an image from the text message and upload that object.
I am able to create a png file from the text message using the magick library. I created an image with a colored background, and I simply add the message text to the image:
library(magick)
alert_picture <- image_read('alert_480x150_dark_red.png')
alert_picture=image_annotate(alert_picture, DreamCloud_Alert, size = 20, gravity = "southwest",
color = "white", location = "+10+10")
image_write(alert_picture, path = "alert_picture.png", format = "png")
The image looks pretty good (although there doesn't seem to be an easy way to bold or underline specific words in the message), but the obstacle now is that I can't get the upload command to work.
slackr_upload(filename = "alert_picture.png")
I don't get any error messages but nothing is uploaded to slack.
I got around this issue by using the httr package to execute the post image function to slack.
Thanks to Adil B. for providing the solution:
Post Image to Slack Using HTTR package in R
I am not sure this is what you meant, but I solved allowing formatting like in a regular slack message by altering the slackr_bot() function and just removing the 2 sets of 3 back-ticks at the end of the code where it says text. Then just call it slackr_bot1() or something, and then you can post formatted messages. This is the function after the back-ticks removal:
slackr_bot1 <- function(...,
channel=Sys.getenv("SLACK_CHANNEL"),
username=Sys.getenv("SLACK_USERNAME"),
icon_emoji=Sys.getenv("SLACK_ICON_EMOJI"),
incoming_webhook_url=Sys.getenv("SLACK_INCOMING_URL_PREFIX")) {
if (incoming_webhook_url == "") {
stop("No incoming webhook URL specified. Did you forget to call slackr_setup()?", call. = FALSE)
}
if (icon_emoji != "") { icon_emoji <- sprintf(', "icon_emoji": "%s"', icon_emoji) }
resp_ret <- ""
if (!missing(...)) {
# mimics capture.output
# get the arglist
args <- substitute(list(...))[-1L]
# setup in-memory sink
rval <- NULL
fil <- textConnection("rval", "w", local = TRUE)
sink(fil)
on.exit({
sink()
close(fil)
})
# where we'll need to eval expressions
pf <- parent.frame()
# how we'll eval expressions
evalVis <- function(expr) withVisible(eval(expr, pf))
# for each expression
for (i in seq_along(args)) {
expr <- args[[i]]
# do something, note all the newlines...Slack ``` needs them
tmp <- switch(mode(expr),
# if it's actually an expresison, iterate over it
expression = {
cat(sprintf("> %s\n", deparse(expr)))
lapply(expr, evalVis)
},
# if it's a call or a name, eval, printing run output as if in console
call = ,
name = {
cat(sprintf("> %s\n", deparse(expr)))
list(evalVis(expr))
},
# if pretty much anything else (i.e. a bare value) just output it
integer = ,
double = ,
complex = ,
raw = ,
logical = ,
numeric = cat(sprintf("%s\n\n", as.character(expr))),
character = cat(sprintf("%s\n\n", expr)),
stop("mode of argument not handled at present by slackr"))
for (item in tmp) if (item$visible) { print(item$value, quote = FALSE); cat("\n") }
}
on.exit()
sink()
close(fil)
# combined all of them (rval is a character vector)
output <- paste0(rval, collapse="\n")
loc <- Sys.getlocale('LC_CTYPE')
Sys.setlocale('LC_CTYPE','C')
on.exit(Sys.setlocale("LC_CTYPE", loc))
resp <- POST(url = incoming_webhook_url, encode = "form",
add_headers(`Content-Type` = "application/x-www-form-urlencoded",
Accept = "*/*"), body = URLencode(sprintf("payload={\"channel\": \"%s\", \"username\": \"%s\", \"text\": \"%s\"%s}",
channel, username, output, icon_emoji)))
warn_for_status(resp)
}
return(invisible())
}
slackr_bot1("*test* on time")