I am copying some VCL rules from this handy template and running on the latest stable Varnish4. However this section of the VCL:
vcl 4.0;
sub vcl_init {
# ...
# Normalize query arguments
set req.url = std.querysort(req.url);
}
^
Returns this error:
-- Logs begin at Tue 2016-03-15 10:44:31 UTC, end at Tue 2016-03-15 13:02:10 UTC. --
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: Message from VCC-compiler:
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: Symbol not found: 'std.querysort' (expected type STRING_LIST):
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: ('/etc/varnish/test.vcl' Line 55 Pos 23)
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: set req.url = std.querysort(req.url);
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: ----------------------#############----------
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: Running VCC-compiler failed, exited with 2
Mar 15 13:02:10 ip-172-31-10-46 reload-vcl[18044]: VCL compilation failed
Should I include a mod or define std somehow?
Yes! I stumbled on the answer inside another answer. Adding import std; at the top of the script stopped the error.
vcl 4.0;
import std;
sub vcl_init {
# ...
# Normalize query arguments
set req.url = std.querysort(req.url);
}
Related
Once more I'm encountering an error in my snakemake workflow that doesn't make any sense to me.
This is the error I get:
[Thu Jan 25 10:47:00 2018] Building DAG of jobs...
[Thu Jan 25 10:47:01 2018] Provided cores: 24
[Thu Jan 25 10:47:01 2018] Rules claiming more threads will be scaled down.
[Thu Jan 25 10:47:01 2018] Job counts:
[Thu Jan 25 10:47:01 2018] count jobs
[Thu Jan 25 10:47:01 2018] 1 merging_seurat
[Thu Jan 25 10:47:01 2018] 1
[Thu Jan 25 10:47:01 2018] Job 0: --- Merging samples using seurat.
Error in setClass("Snakemake", slots = c(input = "list", output = "list", :
unused argument(s) (slots = c(input = "list", output = "list", params = "list", wildcards = "list", threads = "numeric", log = "list", resources = "list", config = "list", rule = "character"))
Execution halted
[Thu Jan 25 10:47:02 2018] Error in rule merging_seurat:
[Thu Jan 25 10:47:02 2018] jobid: 0
[Thu Jan 25 10:47:02 2018] output: merging_seurat/12_top10_heatmap_all_wilcox.pdf, merging_seurat/13_top10_heatmap_all_roc.pdf, merging_seurat/merging_seurat.RData
[Thu Jan 25 10:47:02 2018] RuleException:
[Thu Jan 25 10:47:02 2018] CalledProcessError in line 372 of .../snakemake_pipeline/Snakefile:
[Thu Jan 25 10:47:02 2018] Command ' set -euo pipefail; Rscript .../snakemake_pipeline/scripts/.snakemake.jv8ijpiw.merging_seurat.R ' returned non-zero exit status 1
[Thu Jan 25 10:47:02 2018] File ".../snakemake_pipeline/Snakefile", line 372, in __rule_merging_seurat
[Thu Jan 25 10:47:02 2018] File ".../tools/anaconda3/envs/Seurat/lib/python3.5/concurrent/futures/thread.py", line 55, in run
[Thu Jan 25 10:47:02 2018] Will exit after finishing currently running jobs.
[Thu Jan 25 10:47:02 2018] Exiting because a job execution failed. Look above for error message
[Thu Jan 25 10:47:02 2018] Complete log: .../snakemake_6/.snakemake/log/2018-01-25T104700.498155.snakemake.log
This is the rule in question:
rule merging_seurat:
input: expand("{sample}/molecule_count/counts_wide.tsv", sample=config["samples"]),
output: "merging_seurat/12_top10_heatmap_all_wilcox.pdf",
"merging_seurat/13_top10_heatmap_all_roc.pdf",
"merging_seurat/merging_seurat.RData"
message: "--- Merging samples using seurat."
script: "scripts/merging_seurat.R"
Here we have the top of the R script that is still executed:
sink('merging_seurat/output.txt')
print(installed.packages())
print(sessionInfo())
sink()
And these are the following lines in the R script that are not executed anymore:
library('Seurat')
library('dplyr')
library('org.Hs.eg.db')
Because I logged the packages that are available, I know that the three packages that should be loaded are also installed so it shouldn't fail because of that. In fact, commenting these lines out doesn't change anything, the script still breaks and the log message that should come right after loading the packages is not written to the log file.
Finally, this is the command that I use to run snakemake:
snakemake --use-conda \
--latency-wait 90 \
--rerun-incomplete \
--keep-going \
--timestamp \
--cluster-config SGE.json \
--cluster "qsub -cwd -N {cluster.name} -l h_vmem={cluster.h_vmem},h_stack=256M -o {cluster.stdout}{cluster.name}.o -e {cluster.stderr}{cluster.name}.e -m {cluster.mailtype} -M {cluster.mailuser}" \
-j 8 \
--directory .../snakemake_6
Does anybody have a clue what the error message could mean? unused argument of the snakemake R object is strange because I'm calling multiple parameters later on in the script.
What is even more strange is that I have another R script that works with different packages but has very similar first lines runs fine. I remember that in the beginning I had the same problem with that script (same error message) but don't remember how I solved it.
Any help is well appreciated.
Good day,
Hoping for the kind help of anyone here, thanks in advance.
I have T.csh which looks like this:
#! /bin/csh
set a="01 02 03 04 05 06 07 08 09 10 11 12 13"
set b="14 15 16 17 18 19 20 21 22 23 24 25"
set c="01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25"
set X = `grep $1 EOL.txt | head -n1 | cut -d- -f1`
printf "$X\n$2\n$3\nYYYY\n1\nN\n"
The variables a,b and c are optionally used as the 3rd argument in the printf line. The problem is, whenever I try to run the script, it showed undefined variable. These set command lines are working whenever I assigned them interactively, but inside the script, it seems to not work. Perhaps I need to initialize it but could not figure out how. Just new to this programming thing, I hope someone here can help me. Thanks a lot in advance.
Here are the sample execution and error for your reference:
CAT-46{bc2}40>set a="01 02 03 04 05 06 07 08 09 10 11 12 13"
CAT-46{bc2}41>./T.csh 4773 XXXX.XX "$a"
62
XXXX.XX
01 02 03 04 05 06 07 08 09 10 11 12 13
82869
1
N
CAT-46{bc2}42>unset a
CAT-46{bc2}43>./T.csh 4773 XXXX.XX "$a"
a: Undefined variable
CAT-46{bc2}44>
If i set the variables manually,it's OK, but when I called for it from the script, its flagging undefined variable error.
Mike
I post another answer because a comment is too short. Look at the following.
I have a script named /tmp/T.csh:
#!/bin/csh
set a="blah"
echo $a
My shell is bash; I type /tmp/T.csh: result is blah (csh executed the script).
Still in bash; I type unset a; /tmp/T.csh $a: result is the same.
Still in bash; I type . /tmp/T.csh: no result (bash executed the script).
I type csh; now I am in csh.
I type /tmp/T.csh: result is blah (of course).
I type /tmp/T.csh $a: "a: Undefined variable"
set a = something
/tmp/T.csh $a: blah
echo $a: something
unset a
echo $a: "a: Undefined variable"
I replicated all you did; hope this helps.
You get an error for what you wrote on the command line, not for the content of your script. Even a simple echo, as you can see here above, gives an error if you on the command line refer to a variable which does not exist.
prompt> unset a
prompt> ./T.csh 4773 XXXX.XX "$a"
The first command, "unset a", deletes the variable. In the second command you try to read the variable (on the command line!). That is why csh complains.
I have a huge dataframe that looks something like this:
Insider Trading Relationship Date \
SEC Form 4
Nov 16 04:06 PM Silverman Gene Director Nov 14
Oct 27 07:00 AM RAKOLTA JOHN JR Director Oct 26
Nov 16 04:09 PM LEIGHTON F THOMSON Chief Executive Officer Nov 15
Nov 02 04:20 PM Blumofe Robert EVP Platform Nov 01
Oct 28 04:03 PM MCCONNELL RICK M President Prods & Development Oct 28
I'm trying to change the index dtype into a datetime dtype via this code
pd.to_datetime(df2.index, format = '%b %d %I:%M %p')
but it's yielding the error:
Traceback (most recent call last):
File "<pyshell#126>", line 1, in <module>
pd.to_datetime(df2.index, format = '%b %d %I:%M %p')
File "C:\Python27\lib\site-packages\pandas\util\decorators.py", line 91, in wrapper
return func(*args, **kwargs)
File "C:\Python27\lib\site-packages\pandas\tseries\tools.py", line 420, in to_datetime
return _convert_listlike(arg, box, format, name=arg.name)
File "C:\Python27\lib\site-packages\pandas\tseries\tools.py", line 407, in _convert_listlike
raise e
Is there a way I can find the index of where the error is occurring?
It seems I can set errors to coerce which would just return a Nan as the date, but I would like to avoid that.
Thanks!
You are right, just finish the logic. Set to coerce and filter the index against all values being isnull() to find all the incorrect indices.
Exemple examples\activemq\activemq-camel-blueprint fails after being updated. My own blueprint bundles also fails in the same conditions.
karaf#root> features:install examples-activemq-camel-blueprint
karaf#root> >>>> ActiveMQ-Blueprint-Example set body: Fri Sep 12 18:11:16 CEST 2014
>>>> ActiveMQ-Blueprint-Example set body: Fri Sep 12 18:11:18 CEST 2014
>>>> ActiveMQ-Blueprint-Example set body: Fri Sep 12 18:11:20 CEST 2014
karaf#root> stop 381
[ 381] [Resolved ] [ ] [ ] [ 80] Apache ServiceMix :: Examples :: ActiveMQ Camel Blueprint (5.1.0)
karaf#root> update 381
karaf#root> start 381
18:13:53,156 | ERROR | Thread-65 | BlueprintContainerImpl | 7 - org.apache.aries.blueprint.core - 1.4.0 | Unable to start blueprint container for bundle activemq-camel-blueprint
org.osgi.service.blueprint.container.ComponentDefinitionException: java.lang.NullPointerException
at org.apache.aries.blueprint.container.ReferenceRecipe.internalCreate(ReferenceRecipe.java:122)
at org.apache.aries.blueprint.di.AbstractRecipe$1.call(AbstractRecipe.java:79)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)[:1.7.0_45]
at org.apache.aries.blueprint.di.AbstractRecipe.create(AbstractRecipe.java:88)
at org.apache.aries.blueprint.container.BeanRecipe.setProperty(BeanRecipe.java:933)
at org.apache.aries.blueprint.container.BeanRecipe.setProperties(BeanRecipe.java:907)
at org.apache.aries.blueprint.container.BeanRecipe.setProperties(BeanRecipe.java:888)
at org.apache.aries.blueprint.container.BeanRecipe.internalCreate2(BeanRecipe.java:820)
at org.apache.aries.blueprint.container.BeanRecipe.internalCreate(BeanRecipe.java:787)
at org.apache.aries.blueprint.di.AbstractRecipe$1.call(AbstractRecipe.java:79)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)[:1.7.0_45]
at org.apache.aries.blueprint.di.AbstractRecipe.create(AbstractRecipe.java:88)
at org.apache.aries.blueprint.container.BlueprintRepository.createInstances(BlueprintRepository.java:245)
at org.apache.aries.blueprint.container.BlueprintRepository.createInstance(BlueprintRepository.java:230)
at org.apache.aries.blueprint.container.BlueprintRepository.create(BlueprintRepository.java:155)
at org.apache.aries.blueprint.container.BlueprintContainerImpl.processProcessors(BlueprintContainerImpl.java:527)
at org.apache.aries.blueprint.container.BlueprintContainerImpl.doRun(BlueprintContainerImpl.java:361)
at org.apache.aries.blueprint.container.BlueprintContainerImpl.run(BlueprintContainerImpl.java:269)
at org.apache.aries.blueprint.container.BlueprintExtender.createContainer(BlueprintExtender.java:276)
at org.apache.aries.blueprint.container.BlueprintExtender.createContainer(BlueprintExtender.java:245)
at org.apache.aries.blueprint.container.BlueprintExtender.modifiedBundle(BlueprintExtender.java:235)
at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.customizerModified(BundleHookBundleTracker.java:500)
at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.customizerModified(BundleHookBundleTracker.java:433)
at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$AbstractTracked.track(BundleHookBundleTracker.java:725)
at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.bundleChanged(BundleHookBundleTracker.java:463)
at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$BundleEventHook.event(BundleHookBundleTracker.java:422)
at org.apache.felix.framework.util.SecureAction.invokeBundleEventHook(SecureAction.java:1103)
at org.apache.felix.framework.util.EventDispatcher.createWhitelistFromHooks(EventDispatcher.java:695)
at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:483)
at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4244)
at org.apache.felix.framework.Felix.startBundle(Felix.java:1923)
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:944)
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:931)
at org.apache.karaf.shell.osgi.StartBundle.doExecute(StartBundle.java:37)
at org.apache.karaf.shell.osgi.BundlesCommand.doExecute(BundlesCommand.java:37)
at org.apache.karaf.shell.console.OsgiCommandSupport.execute(OsgiCommandSupport.java:38)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.commands.basic.AbstractCommand.execute(AbstractCommand.java:35)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.CommandProxy.execute(CommandProxy.java:78)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.Closure.executeCmd(Closure.java:474)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.Closure.executeStatement(Closure.java:400)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.Pipe.run(Pipe.java:108)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.Closure.execute(Closure.java:183)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.Closure.execute(Closure.java:120)[15:org.apache.karaf.shell.console:2.3.4]
at org.apache.felix.gogo.runtime.CommandSessionImpl.execute(CommandSessionImpl.java:89)
at org.apache.karaf.shell.console.jline.Console.run(Console.java:183)
at java.lang.Thread.run(Thread.java:744)[:1.7.0_45]
at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4.doRun(ShellFactoryImpl.java:144)[47:org.apache.karaf.shell.ssh:2.3.4]
at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4$1.run(ShellFactoryImpl.java:135)
at java.security.AccessController.doPrivileged(Native Method)[:1.7.0_45]
at javax.security.auth.Subject.doAs(Subject.java:356)[:1.7.0_45]
at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4.run(ShellFactoryImpl.java:133)[47:org.apache.karaf.shell.ssh:2.3.4]
Caused by: java.lang.NullPointerException
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1432)
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:72)
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1843)
at java.lang.ClassLoader.loadClass(ClassLoader.java:412)[:1.7.0_45]
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)[:1.7.0_45]
at java.lang.Class.forName0(Native Method)[:1.7.0_45]
at java.lang.Class.forName(Class.java:270)[:1.7.0_45]
at org.apache.aries.proxy.impl.interfaces.ProxyClassLoader.isInvalid(ProxyClassLoader.java:109)
at org.apache.aries.proxy.impl.interfaces.InterfaceProxyGenerator.getProxyInstance(InterfaceProxyGenerator.java:84)
at org.apache.aries.proxy.impl.AsmProxyManager.createNewProxy(AsmProxyManager.java:72)
at org.apache.aries.proxy.impl.AbstractProxyManager.createDelegatingInterceptingProxy(AbstractProxyManager.java:75)
at org.apache.aries.proxy.impl.AbstractProxyManager.createDelegatingProxy(AbstractProxyManager.java:40)
at org.apache.aries.blueprint.container.AbstractServiceReferenceRecipe.createProxy(AbstractServiceReferenceRecipe.java:338)
at org.apache.aries.blueprint.container.ReferenceRecipe.internalCreate(ReferenceRecipe.java:106)
... 50 more
Hi I've been following this article to setup FreeRADIUS Google Dual Factor Authenticator
http://www.supertechguy.com/help/security/freeradius-google-auth
Hours of testing I still can't get it to work. If my /etc/pam.d/radiusd looks like the following it works well with
the following command
radtest test test localhost 18120 testing123
#
# /etc/pam.d/radiusd - PAM configuration for FreeRADIUS
#
# We fall back to the system default in /etc/pam.d/common-*
#
#include common-auth
#include common-account
#include common-password
#include common-session
However if it looks like the following
#
# /etc/pam.d/radiusd - PAM configuration for FreeRADIUS
#
# We fall back to the system default in /etc/pam.d/common-*
#
##include common-auth
##include common-account
##include common-password
##include common-session
auth requisite pam_google_authenticator.so forward_pass
auth required pam_unix.so use_first_pass
my log file says the following and auth fails.
rad_recv: Access-Request packet from host 127.0.0.1 port 43185, id=111, length=56
User-Name = "test"
User-Password = "test"
NAS-IP-Address = 127.0.1.1
NAS-Port = 18120
Thu Sep 26 16:38:19 2013 : Info: # Executing section authorize from file /etc/freeradius/sites-enabled/default
Thu Sep 26 16:38:19 2013 : Info: +- entering group authorize {...}
Thu Sep 26 16:38:19 2013 : Info: ++[preprocess] returns ok
Thu Sep 26 16:38:19 2013 : Info: ++[chap] returns noop
Thu Sep 26 16:38:19 2013 : Info: ++[mschap] returns noop
Thu Sep 26 16:38:19 2013 : Info: ++[digest] returns noop
Thu Sep 26 16:38:19 2013 : Info: [suffix] No '#' in User-Name = "test", looking up realm NULL
Thu Sep 26 16:38:19 2013 : Info: [suffix] No such realm "NULL"
Thu Sep 26 16:38:19 2013 : Info: ++[suffix] returns noop
Thu Sep 26 16:38:19 2013 : Info: [eap] No EAP-Message, not doing EAP
Thu Sep 26 16:38:19 2013 : Info: ++[eap] returns noop
Thu Sep 26 16:38:19 2013 : Info: [files] users: Matched entry DEFAULT at line 74
Thu Sep 26 16:38:19 2013 : Info: ++[files] returns ok
Thu Sep 26 16:38:19 2013 : Info: ++[expiration] returns noop
Thu Sep 26 16:38:19 2013 : Info: ++[logintime] returns noop
Thu Sep 26 16:38:19 2013 : Info: [pap] WARNING! No "known good" password found for the user. Authentication may fail because of this.
Thu Sep 26 16:38:19 2013 : Info: ++[pap] returns noop
Thu Sep 26 16:38:19 2013 : Info: Found Auth-Type = PAM
Thu Sep 26 16:38:19 2013 : Info: # Executing group from file /etc/freeradius/sites-enabled/default
Thu Sep 26 16:38:19 2013 : Info: +- entering group authenticate {...}
Thu Sep 26 16:38:19 2013 : Debug: pam_pass: using pamauth string <radiusd> for pam.conf lookup
Thu Sep 26 16:38:19 2013 : Debug: pam_pass: function pam_authenticate FAILED for <test>. Reason: Cannot make/remove an entry for the specified session
Thu Sep 26 16:38:19 2013 : Info: ++[pam] returns reject
Thu Sep 26 16:38:19 2013 : Info: Failed to authenticate the user.
Thu Sep 26 16:38:19 2013 : Info: Using Post-Auth-Type Reject
Thu Sep 26 16:38:19 2013 : Info: # Executing group from file /etc/freeradius/sites-enabled/default
Thu Sep 26 16:38:19 2013 : Info: +- entering group REJECT {...}
Thu Sep 26 16:38:19 2013 : Info: [attr_filter.access_reject] expand: %{User-Name} -> test
Thu Sep 26 16:38:19 2013 : Debug: attr_filter: Matched entry DEFAULT at line 11
Thu Sep 26 16:38:19 2013 : Info: ++[attr_filter.access_reject] returns updated
Thu Sep 26 16:38:19 2013 : Info: Delaying reject of request 0 for 1 seconds
Thu Sep 26 16:38:19 2013 : Debug: Going to the next request
Thu Sep 26 16:38:19 2013 : Debug: Waking up in 0.9 seconds.
Thu Sep 26 16:38:20 2013 : Info: Sending delayed reject for request 0
Sending Access-Reject of id 111 to 127.0.0.1 port 43185
Thu Sep 26 16:38:20 2013 : Debug: Waking up in 4.9 seconds.
Thu Sep 26 16:38:25 2013 : Info: Cleaning up request 0 ID 111 with timestamp +3
Thu Sep 26 16:38:25 2013 : Info: Ready to process requests.
I'm using Ubuntu latest
Does anyone know what the issue here?
Many Thanks
After so much internet surfing and forum hunting I manage to fix this problem. If anyone else having this issue this might help them :)
Thu Sep 26 16:38:19 2013 : Debug: pam_pass: using pamauth string <radiusd> for pam.conf lookup
Thu Sep 26 16:38:19 2013 : Debug: pam_pass: function pam_authenticate FAILED for <test>. Reason: Cannot make/remove an entry for the specified session
The above line actually means a auth fail, even though it doesn't sound like it, also it could mean that .google_authenticator file in the user's home directory isn't accessible.
FreeRadius log file not help you much with this issue, but have a look through /var/log/secure on CentOS and /var/log/auth.log in Ubuntu. This will explain which is the issue.
Issue with my system was my time was out and my random generated number by Google Dual Factor Authenticator application on my iPhone wasn't valid. I had to install NTP and change my servers time to the correct time which fixed the issue!!!!
hope this help someone else :)
The how-to on Super Tech Guy's page (http://www.supertechguy.com/help/security/freeradius-google-auth) has a typo.
DEFAULT Auth-Type := PAM
should be
DEFAULT Auth-Type = PAM
I don't know why he put a colon in there, but removing it fixed my issue.
This was after I made sure the server had the correct time (and timezone), which it didn't. So thanks for that suggestion too!