I am trying to use the biomaRt package to access the data from Ensembl, however I got error message when using the useDataset() function. My codes are shown below.
library(httr)
listMarts()
ensembl = useMart("ENSEMBL_MART_ENSEMBL")
listDatasets(ensemble)
ensembl = useDataset("hsapiens_gene_ensembl",mart = ensemble)
When I type useDataset function i got error message like this:
> ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)
Ensembl site unresponsive, trying asia mirror
Error in textConnection(text, encoding = "UTF-8") :
invalid 'text' argument
and sometimes another different error message showed as:
> ensembl = useDataset("hsapiens_gene_ensembl",mart = ensembl)
Ensembl site unresponsive, trying asia mirror
Error in textConnection(bmResult) : invalid 'text' argument
it seems like that the mirror automatically change to asia OR useast OR uswest, but the error message still shows up over and over again, and i don't know what to do.
So if anyone could help me with this? I will be very grateful for any help or suggestion.
Kind regards Riley Qiu, Dongguan, China
TF v.0.11 (I know it is old but I need this one)
I try to configure output this way:
value = "${concat(aws_lambda_function.lambda.*.arn, [""])}"
The error message is
Error reading config for output FUNCTION_ARN: parse error at 1:46 :
expected expression but found "["
What am I doing wrong, how to fix that?
Reason: [""] don't work for v11.
Solution:
value = "${element(concat(aws_lambda_function.lambda.*.arn, list("")), 0)}"
I'm receiving a notification that advised the below script is not PEP-8:
example_var = print('whoa')
Output:
[E] invalid syntax.
It's showing that the error is a result of the first parentheses in the print statement, but nothing looks off to me.
example_var = print('whoa')
example_var
I have the following function that works fine as long as I give it a valid command to execute. As soon as I give it a non-existent command, the script is interrupted with an error message.
#!/usr/bin/lua
function exec_com(com)
local ok,res=pcall(function() return io.popen(com) end)
if ok then
local tmp=res:read('*a')
res:close()
return ok,tmp
else
return ok,res
end
end
local st,val=exec_com('uptime')
print('Executed "uptime" with status:'..tostring(st)..' and value:'..val)
st,val=exec_com('zzzz')
print('Executed "zzzz" with status:'..tostring(st)..' and value:'..val)
When I run the script above I get the following output:
Executed "uptime" with status:true and value: 18:07:38 up 1 day, 23:00, 3 users, load average: 0.37, 0.20, 0.20
sh: zzzz: command not found
Executed "zzzz" with status:true and value:
You can clearly see above that pcall() function still reported success when executing "zzzz" which is odd.
Can someone help me devise a way to catch an exception when executing a non-existent or ill-formed Linux command using Lua script? Thanks.
Edit: Restated my request after getting the clarification that pcall() works as expected, and the problem is due to popen() failing to throw an error.
I use a method which is similar to your "temporary workaround" but which gives you more information:
local cmd = "uptime"
local f = io.popen(cmd .. " 2>&1 || echo ::ERROR::", "r")
local text = f:read "*a"
if text:find "::ERROR::" then
-- something went wrong
print("error: " .. text)
else
-- all is fine!!
print(text)
end
If you look at io.popen(), you'll see that it'll always return a file handle.
Starts program prog in a separated process and returns a file handle
that you can use to read data from this program (if mode is "r", the
default) or to write data to this program (if mode is "w").
Since, a file handle returned is still a valid value for lua, the pcall(), your local function inside the pcall is returning a true value (and an error is not being propagated); thereby, giving you a true status and no output.
I have come up with my own temporary workaround that pipes the error to /dev/null and determines the success/failure of executed command based on the text received from io.popen():read('*a') command.
Here is my new code:
#!/usr/bin/lua
function exec_com(com)
local res=io.popen(com..' 2>/dev/null')
local tmp=res:read('*a')
res:close()
if string.len(tmp)>0 then
return true,tmp
else
return false,'Error executing command: '..com
end
end
local st,val=exec_com('uptime')
print('Executed "uptime" with status:'..tostring(st)..' and value:'..val)
st,val=exec_com('cat /etc/shadow')
print('Executed "cat /etc/shadow" with status:'..tostring(st)..' and value:'..val)
And the corresponding output is now correct:
Executed "uptime" with status:true and value: 00:10:11 up 2 days, 5:02, 3 users, load average: 0.01, 0.05, 0.19
Executed "cat /etc/shadow" with status:false and value:Error executing command: cat /etc/shadow
In my example above I am creating a "generic" error description. This is an intermediate fix and I am still interested in seeing alternative solutions that can return a more meaningful error message describing why the command failed to execute.
Rather than taking the time reading the whole file into a variable, why not just check if the file is empty with f:read(0)?
Local f = io.popen("NotExist")
if not f:read(0) Then
for l in st:lines() do
print(l)
end
else
error("Command Does Not Exist")
end
From the lua Manual:
As a special case, io.read(0) works as a test for end of file: It returns an empty string if there is more to be read or nil otherwise.
I want to run parallel computing in Linux.
After i managed to do so in Windows i need to run the function below in Linux. I changed the package doSnow to doMC that suppose to work in Linux but i get an error related to mclapply.
Code:
foreachFunc = function(Data) {
RowFunction<-function(d)
{
(chisq.test(d)$p.value)}
P<-as.matrix(apply(Data,1,RowFunction))
return(P)}
library(doMC)
library(foreach)
number_of_cpus=4
cl<-makeCluster(number_of_cpus)
registerDoMC(cl)
Chunks<-c(1:NROW(Data_new))%%4
P<-foreach(i=0:3, .combine=rbind, mc.cores=4) %dopar% {
foreachFunc(Data_new[Chunks==i, ])}
stopCluster(cl)
Error:
Error in mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, :
(list) object cannot be coerced to type 'integer'
Read vignette("gettingstartedMC"). I can reproduce your error like this:
number_of_cpus=4
cl<-makeCluster(number_of_cpus)
registerDoMC(cl)
P<-foreach(i=0:3) %dopar% i
#Error in mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, :
# (list) object cannot be coerced to type 'integer'
stopCluster(cl)
This works as expected:
registerDoMC(cores=4)
P<-foreach(i=0:3) %dopar% i
Explanation: registerDoMC expects an integer value for its first argument. You gave it a list, i.e. the return object of makeCluster.