While running the "PrepareAnnotationRefseq" function from the customProDB package in R, I ran into a problem due to a compatibility issue of the curl version. I am currently using curl version 4.3.2. The error report I got is:
PrepareAnnotationRefseq(genome='mm39',CDSfasta="geneseq.fasta",pepfasta="proteinseq.fasta", annotation_path, dbsnp = NULL, splice_matrix=FALSE, ClinVar=FALSE)
In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) : Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x55822c7f3b70): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
This could be a trivial problem for an expert in R, however with my current skill set I am unable to resolve this after looking for a solution on several forums and R groups. I would be very grateful if you could kindly shed some light on this issue. Perhaps a patch file that can fix the problem.
It's easy to read the manual. Why can't you do it?
If verify value is set to 1:
From 7.28.1 to 7.65.3: setting it to 1 made curl_easy_setopt() return an error and leaving the flag untouched.
Use 2.
When CURLOPT_SSL_VERIFYHOST is 2, that certificate must indicate that the server is the server to which you meant to connect, or the connection fails. Simply put, it means it has to have the same name in the certificate as is in the URL you operate against.
But why do you touch it? The default value for this option is 2 and is suitable for most cases of libcurl usage.
Related
I am not an admin so I can't change the scopes. I can send slackr_bot messages to a channel I set up in the creation of the app in UI but doing the below does not work. Has anyone found a solution to this?
I created a txt file called: test.txt
Within that txt file it looks like this:
api_token: xxxxxxxxxxxx
channel: #channel_name
username: myusername
incoming_webhook_url: https://hooks.slack.com/services/xxxxxxxxxxx/xxxxxxxxxxxxx
Then I want to simply send a message but eventually I would like to run the function
ggslackr(qplot(mpg, wt, data=mtcars))
slackr_setup(config_file = "test.txt")
my_message <- paste("I'm sending a Slack message at", Sys.time(), "from my R script.")
slackr_msg(my_message, channel = "#channel_name", as_user=F)
Here is the error message:
Error: Join columns must be present in data.
x Problem with `id`.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
In structure(vars, groups = group_vars, class = c("dplyr_sel_vars", :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Edit #2:
Okay, I learned some things regarding packages. If I had to do this over, I'd have gone to their github repo and read the issue tracker.
The reason is that it appears that slackr has a few issues related to changes in Slack's API.
And also since there has been a large updating of R (version 4.x) a lot of packages got broken.
My sense is that our issue is with a line of code inside a slackr function (slackr_util.r--iirc) that calls a dplyr join that is looking for a particular id that does not exist.
So, I'm going to watch the issue tracker and see what comes of it.
Edit: Try slackr_bot(my_message,channel = "#general")
worked as advertised!
But ggslackr continues to fail.
I'm having the same issue. I've found in another thread a debugging start:
`rlang::last_error()`
When I run that,
Backtrace:
1. slackr::slackr_msg(my_message, channel = "#general")
5. slackr::slackr_chtrans(channel)
6. slackr::slackr_ims(api_token)
8. dplyr:::left_join.data.frame(users, ims, by = "id", copy = TRUE)
9. dplyr:::join_mutate(...)
10. dplyr:::join_cols(...)
11. dplyr:::standardise_join_by(by, x_names = x_names, y_names = y_names)
12. dplyr:::check_join_vars(by$y, y_names)
So, step 8 there is a join effort by id, which I suppose this implies that 'id' is missing.
yet, if I run from github issue tracker : slackr::slackrSetup(echo=TRUE) I get the following:
{
"SLACK_CHANNEL": ["#general"],
"SLACK_USERNAME": ["slackr_brian"],
"SLACK_ICON_EMOJI": ["NA"],
"SLACK_INCOMING_URL_PREFIX": ["https://hooks.xxxxxxx"],
"SLACK_API_TOKEN": ["token secret"]
}
I'm not sure where to go from here as the issue tracker conversation makes mention of confirming webhooks going to the correct channel and becomes very user specific.
So, that's as far as I have gotten.
I'm using the package: IBrokers. It works well for me when I request historical data. Also the call to reqAccountUpdates() works well.
I am having problems with this script:
# myscript.r
.libPaths("rpackages")
library(IBrokers)
tws2 = twsConnect(2)
print('Attempting BUY')
mytkr = twsFuture("ES","GLOBEX","201412")
myorderid = sample(1001:3001, 1)
IBrokers:::.placeOrder(tws2, mytkr, twsOrder(myorderid, "BUY", "1", "MKT"))
twsDisconnect(tws2)
Sometimes the above script works okay. Usually though it fails. When it fails, it seems to connect okay.
Then I see this in my TWS console:
03:47:45:581 JTS-EServerSocket-290: [2:47:71:1:0:0:0:ERR] Message type -1. Socket I/O error -
03:47:45:581 JTS-EServerSocket-290: Anticipated error
jextend.d: Socket I/O error -
at jextend.sc.b(sc.java:364)
at jextend.ch.sb(ch.java:1534)
at jextend.ch.run(ch.java:1390)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:196)
at java.net.SocketInputStream.read(SocketInputStream.java:122)
at java.net.SocketInputStream.read(SocketInputStream.java:210)
at jextend.xh.d(xh.java:45)
at jextend.sc.c(sc.java:579)
at jextend.sc.r(sc.java:227)
at jextend.af.a(af.java:232)
at jextend.sc.f(sc.java:650)
at jextend.pd.a(pd.java:822)
at jextend.sc.b(sc.java:358)
... 3 more
03:47:45:583 JTS-EServerSocket-290: [2:47:71:1:0:0:0:ERR] Socket connection for client{2} has closed.
03:47:45:583 JTS-EWriter14-291: [2:47:71:1:0:0:0:ERR] Unable write to socket client{2} -
03:47:45:584 JTS-EServerSocketNotifier-288: Terminating
Can you offer any ideas on how you would wrestle with this issue?
One other piece of info:
I think the call to reqIds() may be necessary. Sometimes reqIds() would return an id not high enough. Then, I'd use it and placeOrder() would fail. So, I call reqIds() but then use Sys.time() to give me an id which is larger than the last ID I used.
Another problem may have been some code-text I copied out of a PowerPoint. Some of the code-characters may have been corrupt.
The main problem was orderid.
I need to be careful how I generate orderid.
Also I may have moused in bad characters from a powerpoint preso which had an example.
I posted some code which works in a comment in this thread.
Dan
I am facing the following error:
Microsoft VBScript runtime error '800a0005'
Invalid procedure call or argument: 'left'
/scheduler/App.asp, line 16
The line is:
point1 = left(point0,i-1)
This code works perfectly in another server, but now on another server it is showing this error. I can guess it has to do with system or IIS settings or may be something else but its nothing with code (as its works fine in another server).
If i is equal to zero then this will call Left() with -1 as the length parameter. This will result in an Invalid procedure call or argument error. Verify that i >= 0.
Just experienced this problem myself - a script running seamlessly for many months suddenly collapsed with this error. It seems that the scripting engine falls over itself for whatever reason and string functions cease being able to handle in-function calculations.
I appreciate it's been quite a while since this question was asked, but in case anyone encounters this in the future...
Replace
point1 = left(point0, i-1)
with
j = i-1
point1 = left(point0, j)
... and it will work.
Alternatively, simply re-boot the server (unfortunately, simply re-starting the WWW service won't fix it).
These Curl docs: http://curl.haxx.se/docs/manpage.html#-d list many boolean options.
How do I specify these options in a postForm call in RCurl? For example, how do I specify the --sslv3 flag?
I tried
postForm(url, .opts = list(sslv3=TRUE))
but received the error:
Warning message:
In mapCurlOptNames(names(.els), asNames = TRUE) :
Unrecognized CURL options: sslv3
Thanks in advance.
SOLUTION
Through some trial and error, I found that this works:
options(RCurlOptions = list(sslversion=3))
postForm(url)
If anyone could clarify how to translate the Curl options to the RCurl options, it would appreciated!
Curl stands for a few things http://daniel.haxx.se/docs/curl-vs-libcurl.html. The problem here is you are looking at what the curl command line tool does and instead want to ask how the libcurl library implements something.
RCurl use the libcurl library. This can be accessed via an api. The "symbols" used in the api are listed here http://curl.haxx.se/libcurl/c/symbols-in-versions.html. We can compare them to the options listed by RCurl:
library(RCurl)
cInfo <- getURL("http://curl.haxx.se/libcurl/c/symbols-in-versions.html")
cInfo <- unlist(strsplit(cInfo, "\n"))
cInfo <- cInfo[grep("CURLOPT_", cInfo)]
cInfo <- gsub("([^[\\s]]*)\\s.*", "\\1", cInfo)
cInfo <- gsub("CURLOPT_", "", cInfo)
cInfo <- tolower(gsub("_", ".", cInfo))
listCurlOptions()[!listCurlOptions()%in%cInfo]
From the above we can see that all RCurl options are derived from libcurl api symbols. The
CURLOPT_ is removed _ is replaced by . and the letters are demoted to lower case.
The question then arises as to what types the symbols represent. I usually just look at the
php library documentation to discover this. http://php.net/manual/en/function.curl-setopt.php lists
CURLOPT_SSLVERSION The SSL version (2 or 3) to use. By default PHP will try to determine this itself, although in some cases this must be set manually.
as an integer type. expecting the value 2 or 3.
Alternatively you can look at the curl_easy_setopt manual page http://curl.haxx.se/libcurl/c/curl_easy_setopt.html.
CURLOPT_SSLVERSION
Pass a long as parameter to control what version of SSL/TLS to attempt to use. The available options are:
CURL_SSLVERSION_DEFAULT
The default action. This will attempt to figure out the remote SSL protocol version, i.e. either SSLv3 or TLSv1 (but not SSLv2, which became disabled by default with 7.18.1).
CURL_SSLVERSION_TLSv1
Force TLSv1
CURL_SSLVERSION_SSLv2
Force SSLv2
CURL_SSLVERSION_SSLv3
Force SSLv3
It says we would need to pass a long with value CURL_SSLVERSION_SSLv3 to stipulate sslv3.
What is the value of CURL_SSLVERSION_SSLv3? We can examine RCurl:::SSLVERSION_SSLv3
> c(RCurl:::SSLVERSION_DEFAULT, RCurl:::SSLVERSION_TLSv1, RCurl:::SSLVERSION_SSLv2, RCurl:::SSLVERSION_SSLv3)
[1] 0 1 2 3
>
So in fact the permissible values for sslversion are 0,1,2 or 3.
So the confusion in this case arose from the curl program which presumably uses the libcurl api implementing this in a binary fashion.
So the correct way in this case to use this option would be:
postForm(url, .opts = list(sslversion = 3))
or
postForm(url, .opts = list(sslv = 3))
you can use the shorter sslv as .opts is passed to mapCurlOptNames which will use pmatch
to find sslversion.
To be fair to the author of RCurl this is all explained in http://www.omegahat.org/RCurl/philosophy.html also located in /RCurl/inst/doc/philosophy.html .An excerpt reads:
Each of these and what it controls is described in the libcurl
man(ual) page for curl_easy_setopt and that is the authoritative
documentation. Anything we provide here is merely repetition or
additional explanation.
The names of the options require a slight explanation. These
correspond to symbolic names in the C code of libcurl. For example,
the option url in R corresponds to CURLOPT_URL in C. Firstly,
uppercase letters are annoying to type and read, so we have mapped
them to lower case letters in R. We have also removed the prefix
"CURLOPT_" since we know the context in which they option names are
being used. And lastly, any option names that have a _ (after we have
removed the CURLOPT_ prefix) are changed to replace the '_' with a '.'
so we can type them in R without having to quote them. For example,
combining these three rules, "CURLOPT_URL" becomes url and
CURLOPT_NETRC_FILE becomes netrc.file. That is the mapping scheme.
Try this (after reviewing examples on ?curlOptions after being referred by ?postForm:)
myOpts = curlOptions(sslv3 = TRUE)
postForm(url, .opts = myOpts)
Although I admit I thought your code should work. You may need to also post you version numbers. There is also a curlSetOpt that might be more "assertive".
I am running ruby unit tests against Chrome using watir-webdriver. Whenever a test is run and chromedriver.exe is launched output similar to below appears:
Started ChromeDriver
port=9515
version=26.0.1383.0
log=C:\Home\Server\Test\Watir\web\chromedriver.log
[5468:8796:0404/150755:ERROR:accelerated_surface_win.cc(208)] Reseting D3D device
[5468:8996:0404/150758:ERROR:textfield.h(156)] NOT IMPLEMENTED
[WARNING:..\..\..\..\flash\platform\pepper\pep_module.cpp(63)] SANDBOXED
None of this impacts the correct functioning of the tests, but as one might imagine the appearance of "ERROR" and "WARNING" might be rather confusing to, for example, parsing rules in Jenkins looking for failures. Sure I can get really fancy with regular expression in the parsing rules, but it would be really nice to turn off this verbose and unnecessary logging on the part of chromedriver.exe. I have seen many mentions of this searching for an answer. No one has come up with a solution. Yes, chromedriver possibly has a "--silent" option, but there seems to be no way to pass that to the executable. Code similar to below is supposed to work, but has zero effect as far as I can see. Any ideas?
profile = Selenium::WebDriver::Chrome::Profile.new
profile['--cant-make-any-switches-work-here-how-about-you'] = true
browser = Watir::Browser.new :chrome, :profile => profile, :switches => %w[--ignore-certificate-errors --disable-extensions --disable-popup-blocking --disable-translate--allow-file-access]
Here's help for anyone else searching
Find ...selenium\webdriver\chrome\service.rb
Path start may differ on your system
And I added "-silent" to the passed parameters .... However, this silenced everything but the error/warning messages.
def initialize(executable_path, port)
#uri = URI.parse "http://#{Platform.localhost}:#{port}"
server_command = [executable_path, " -silent", "--port=#{port}"]
#process = ChildProcess.build(*server_command)
#socket_poller = SocketPoller.new Platform.localhost, port, START_TIMEOUT
#process.io.inherit! if $DEBUG == true
end
set chromeOptions with key --log-level=3 this should shut it up
I was able to divert the hundreds, yes hundreds, of chrome driver log messages that were showing up in cucumber stdout by using the :service_log_path argument.
#browser = Watir::Browser.new :chrome, :service_log_path => 'chromedriver.out'
the '-silent', or '--silent', or ' -silent', or ' --silent' parameter suggested above did nothing when I added it to ...selenium\webdriver\chrome\service.rb. And having to tweak the gem itself is not a particularly viable solution.
I couldn't find a place to capture the chromedriver stderr and divert it to null (not to mention having to handle doing that in windows and in *nix/osx)
The driver should default to something way less verbose. In this case INFO is way too verbose as hundreds of log entries pop out as INFO, 90%+ of them identical.
At least the :service_log_path argument works most of them.
You can try -Dwebdriver.chrome.logfile="/dev/null" and/or -Dwebdriver.chrome.args="--disable-logging" to the options of java that runs selenium-server-standalone-what.ever.jar