MethylDackel core dump Ubintu 18.04 (problem happend again in issue #95)

Hi @dpryan79
First, I have no idea why I cannot re-open my previous issue so I'm writing problem here.
(I'm sorry for that)
As you suggested in closed issue #95(https://github.com/dpryan79/MethylDackel/issues/95#issue-619857769) I have tested 0.5.1 but still in the same problem
This is the full backtrace of GDB
Thread 2 "MethylDackel" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffff263f700 (LWP 29417)]
cust_mplp_auto (iter=iter@entry=0x7fffec004e70, _tid=_tid@entry=0x7ffff263ee84, _pos=_pos@entry=0x7ffff263ee88, n_plp=n_plp@entry=0x7ffff263ee94, plp=plp@entry=0x7fffec056280) at pileup.c:288
288	        if (iter->pos[i] == iter->min) {
(gdb) bt full
#0  cust_mplp_auto (iter=iter@entry=0x7fffec004e70, _tid=_tid@entry=0x7ffff263ee84, _pos=_pos@entry=0x7ffff263ee88, n_plp=n_plp@entry=0x7ffff263ee94, plp=plp@entry=0x7fffec056280) at pileup.c:288
        i = 0
        ret = 0
        new_min =<PHONE_NUMBER>3709551615
#1  0x000055555555f101 in extractCalls (foo=0x7fffffffde60) at extract.c:391
        config = 0x7fffffffde60
        hdr = 0x7fffec003fc0
        iter = 0x7fffec004e70
        ret = <optimized out>
        tid = 0
        pos = 0
        i = <optimized out>
        seqlen = 1000012
        type = <optimized out>
        rv = <optimized out>
        o = <optimized out>
        bedIdx = 0
        n_plp = 0
        strand = <optimized out>
        direction = <optimized out>
        nmethyl = <optimized out>
        nunmethyl = <optimized out>
        nOff = <optimized out>
        nVariant = <optimized out>
        localBin = 0
        localPos = 0
        localEnd = 1000001
        localTid = 0
        localPos2 = 0
        lastPos = 0
        nVariantPositions = 0
        plp = 0x7fffec056280
        seq = 0x7ffff1d4a010 'N' <repeats 200 times>...
        base = 65 'A'
        context = "HG"
        tnc = <optimized out>
        data = 0x7fffec056250
        lastCpG = 0x0
        lastCHG = 0x0
        os = 0x7fffec000b60
        os_CpG = 0x7fffec000b80
        os_CHG = 0x7fffec000ba0
        os_CHH = 0x7fffec000bc0
---Type <return> to continue, or q <return> to quit---
        fai = 0x7fffec001db0
        bai = 0x7fffec0050a0
        fp = 0x7fffec013a70
        __PRETTY_FUNCTION__ = "extractCalls"
#2  0x00007ffff7c29669 in start_thread (arg=<optimized out>) at pthread_create.c:479
        ret = <optimized out>
        pd = <optimized out>
        unwind_buf = {cancel_jmp_buf = {{jmp_buf = {140737260025600, -269718404055552016,<PHONE_NUMBER>46494,<PHONE_NUMBER>46495,<PHONE_NUMBER>46496,<PHONE_NUMBER>23744,<PHONE_NUMBER>75873520,<PHONE_NUMBER>00975856},
              mask_was_saved = 0}}, priv = {pad = {0x0, 0x0, 0x0, 0x0}, data = {prev = 0x0, cleanup = 0x0, canceltype = 0}}}
        not_first_call = 0
#3  0x00007ffff7614323 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95
No locals.

If you have pre-compiled binary of stable version, can you let me know?
Thanks.

@tahuh Please use a 0.4 release

@dpryan79
I have use 0.4 release as you suggested and still have same problem.
The GDB trace keep saying  if (iter->pos[i] == iter->min) in pileup.c  is wrong.
My guess is iter->pos[i] is some invalid behavior(maybe iter->pos is not allocated).
Does regions with empty reads can cause this problem?
Since I have removed reads aligned on low mappabiltity regions from my bam file generating empty region in genome.
Version Check
MethylDackel: A tool for processing bisulfite sequencing alignments.
Version: 0.4.0 (using HTSlib version 1.10.2-51-g0bff7c1)
Usage: MethylDackel <command> [options]

Commands:
    mbias    Determine the position-dependent methylation bias in a dataset,
             producing diagnostic SVG images.
    extract  Extract methylation metrics from an alignment file in BAM/CRAM
             format.
    mergeContext   Combine single Cytosine metrics from 'MethylDackel extract' into
             per-CpG/CHG metrics.
    perRead  Generate a per-read methylation summary.

Error message in GDB
Starting program: /usr/local/bin/MethylDackel extract --CHG --CHH --cytosine_report /synbiodata/reference/ensemble/GRCh37/Homo_sapiens.GRCh37.dna.primary_assembly.fa AJS-EM20.sort.bam
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
writing to prefix:'AJS-EM20.sort'
[New Thread 0x7ffff69d6700 (LWP 16684)]

Thread 2 "MethylDackel" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffff69d6700 (LWP 16684)]
cust_mplp_auto (iter=iter@entry=0x7ffff00644b0, _tid=_tid@entry=0x7ffff69d5e84, _pos=_pos@entry=0x7ffff69d5e88, n_plp=n_plp@entry=0x7ffff69d5e94, plp=plp@entry=0x7ffff0063870) at pileup.c:288
288	        if (iter->pos[i] == iter->min) {
(gdb) bt full
#0  cust_mplp_auto (iter=iter@entry=0x7ffff00644b0, _tid=_tid@entry=0x7ffff69d5e84, _pos=_pos@entry=0x7ffff69d5e88, n_plp=n_plp@entry=0x7ffff69d5e94, plp=plp@entry=0x7ffff0063870) at pileup.c:288
        i = 0
        ret = 0
        new_min =<PHONE_NUMBER>3709551615
#1  0x000055555555e671 in extractCalls (foo=0x7fffffffdf10) at extract.c:385
        config = 0x7fffffffdf10
        hdr = 0x7ffff00162a0
        iter = 0x7ffff00644b0
        ret = <optimized out>
        tid = 0
        pos = 0
        i = <optimized out>
        seqlen = 1000012
        type = <optimized out>
        rv = <optimized out>
        o = <optimized out>
        bedIdx = 0
        n_plp = 0
        strand = <optimized out>
        direction = <optimized out>
        nmethyl = <optimized out>
        nunmethyl = <optimized out>
        nOff = <optimized out>
        nVariant = <optimized out>
        localBin = 0
        localPos = 0
        localEnd = 1000001
        localTid = 0
        localPos2 = 0
        lastPos = 0
        nVariantPositions = 0
        plp = 0x7ffff0063870
        seq = 0x7ffff588c010 'N' <repeats 200 times>...
        base = 65 'A'
        context = "HG"
        tnc = <optimized out>
        data = 0x7ffff0063840
        lastCpG = 0x0
        lastCHG = 0x0
        os = 0x7ffff0000b60
        os_CpG = 0x7ffff0000b80
        os_CHG = 0x7ffff0000ba0
        os_CHH = 0x7ffff0000bc0
---Type <return> to continue, or q <return> to quit---
        fai = 0x7ffff0001db0
        bai = 0x7ffff0017380
        fp = 0x7ffff0013880
        __PRETTY_FUNCTION__ = "extractCalls"
#2  0x00007ffff7c29669 in start_thread (arg=<optimized out>) at pthread_create.c:479
        ret = <optimized out>
        pd = <optimized out>
        unwind_buf = {cancel_jmp_buf = {{jmp_buf = {140737330898688, -5472056830547680361,<PHONE_NUMBER>46718,<PHONE_NUMBER>46719,<PHONE_NUMBER>46720,<PHONE_NUMBER>96832,<PHONE_NUMBER>625456023,<PHONE_NUMBER>859426711},
              mask_was_saved = 0}}, priv = {pad = {0x0, 0x0, 0x0, 0x0}, data = {prev = 0x0, cleanup = 0x0, canceltype = 0}}}
        not_first_call = 0
#3  0x00007ffff7893323 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95
No locals.
(gdb)

@tahuh Can you privately make that BAM file available? That will make the cause of this easier to debug. I suspect there's a buffer overflow in the code somewhere that's triggering this.

@dpryan79
Sorry for late reply.
Due to the large file size of the bam file I have (~37.5G), I can not directly transfer data for you.
Is there any options that you suggest?

@tahuh Can you reproduce this with a subset of the data? Maybe a single chromosome or even a couple megabases in it?

I'm also experiencing this issue for a toy dataset that contains subsampled reads from chromosome 22 with only chr22.fasta as reference (MethylDackel 0.5.1 from Bioconda on Debian 9, version 0.4.0 runs just fine).
I uploaded the test data here: https://uni-muenster.sciebo.de/s/gwAgkrO8JxhszLP
Thanks for developing MethylDackel, I hope that test data helps reproducing the error!

I can completely reproduce this with the binary distributed by conda, but oddly enough it doesn't happen with a regular local build. I'll make a new conda-built binary locally and track down the cause of this.

Any update on this? Also encountering this same issue..

Seems to potentially be an issue with HTSlib 10.2

@robertamezquita
I tried as you mentioned and it works fine for me too.
I'm wondering why htslib 1.10 does not work but any way, I'm fine with this.

@robertamezquita
I tried as you mentioned and it works fine for me too.
I'm wondering why htslib 1.10 does not work but any way, I'm fine with this.

How do I specify the HTSlib to use? I used the bioconda dist installation. Running into the same error on the HTSlib 1.10.
Do I need to uninstall the bioconda dist and do a local install of MethylDackel?

@mmark27
I had compiled from the source and specified the htslib version (htslib-1.9) I wanted to use.
You do not have to uninstall the bioconda but try docker instead.
I made my own docker container and was successful.
@dpryan79  Do you have any plan of publishing MethylDackel on DockerHub?

Hi all.
Thanks for providing this resource. I'm at the same issue --environment built from conda, bam file is produced with bwameth.
$MethylDackel --version
0.5.1 (using HTSlib version 1.10.2))

At runtime all I get to screen is
$ MethylDackel extract refGenome.fasta  fileprefix.bam
writing to prefix:'fileprefix'
Segmentation fault (core dumped)

If it will help make things easier to work with, I cut down my dataset to a subset with 100K paired-end reads (the bamfile is now only 25M). I'm happy to share it, but I'm working with a rather experimental reference genome, so that might just make things more complicated. Are there any tests I can run that might be helpful?

I had compiled from the source and specified the htslib version (htslib-1.9) I wanted to use.

@tahuh , can you elaborate on what that entails? So far I have done the following:

cloned htslib_1.11 and installed with ./configure --prefix=[PATH_HTS]
gone back to my MethylDackel repo clone and typed the following:
$ make install CFLAGS="-I/[PATH_HTS]"  LIBS="-L/[PATH_HTS]"
and I get fatal error: bigWig.h: No such file or directory

From that I understood that I needed to install libBigwig, so I cloned libBigwig, and in that directory typed make install prefix=[PATH_BIGWIG], and checked to make sure that [PATH_BIGWIG]/lib/libBigWig.a was indeed present.
I then went back to the MethylDackel repo folder and typed make LIBBIGWIG="[PATH_BIGWIG]/lib/libBigWig.a"
and I get fatal error: htslib/sam.h: No such file or directory, which means I can't get to the make install step to specify the htslib path. At this point, I'm stuck on how to actually build MethylDackel; can anyone see where I went wrong?

@Blosberg
To be clear, I have created a docker image for MethylDackel.
You can find the docker file here .

To be clear, I have created a docker image for MethylDackel.
You can find the docker file here .

Thanks for that. My alternative solution was to specify htslib=1.9 in my conda recipe. Specifying 1.11 lead to some strange behaviour with MethylDackel being built as Version: 0.3.0 (using HTSlib version 1.2.1) --which I didn't want to trust, but 1.9 seems to have resolved it. Thanks for your help.

Hi all,
Running into a similar issue trying to update Methyldackel to version 1.5.1 - (https://github.com/nf-core/methylseq/pull/185) see CI nextflow log:
Command executed:

  MethylDackel extract     genome.fa SRR389222_sub1.sorted.markDups.bam
  MethylDackel mbias   genome.fa SRR389222_sub1.sorted.markDups.bam SRR389222_sub1.sorted.markDups --txt > SRR389222_sub1.sorted.markDups_methyldackel.txt

Command exit status:
  139

Command output:
  (empty)

Command error:
  writing to prefix:'SRR389222_sub1.sorted.markDups'
  .command.sh: line 2:    27 Segmentation fault      (core dumped) MethylDackel extract genome.fa SRR389222_sub1.sorted.markDups.bam

I tried downgrading htslib to 1.9 as suggested here, but then my environment won't build - CI conda log here or a more readable output from mamba:
Problem: package methyldackel-0.5.1-h4eb3cf5_0 requires htslib >=1.10.2,<1.11.0a0, but none of the providers can be installed

We previously had Methyldackel 0.5.0 working fine, before I start downgrading all the packages in the environment again in an effort to get it back to a working state I wondered if any progress had been made on tracking down this error?
Cheers,
Phil

@ewels Is that CI run on Ubuntu 20.04 and are the commands and input files available somewhere (this being nf-core, I guess I should really know that the answer is "of course the files are available!")? I have Ubuntu 18.04 locally, but could update the system if needed.
What happens if you downgrade MethylDackel to 0.4.0? The options should be identical, so it should be a drop-in replacement. That version predates some large contributed changes that seem to at least sometimes be the cause of segfaults (though I still have yet to track down exactly why/where).

Of course the files are available! 😆
Trying with downgrading just MethylDackel now (see CI test).
The last PR to be merged had tests passing here and that was with MethylDackel 0.5.0 (see env). So there's something odd going on here, either a change in 0.5.1 or more likely a change in a dependency / something upstream as I changed a bunch of other packages in the problematic PR...

In HTSlib 1.10, __bam_mplp_t acquired some extra fields (see samtools/htslib@eb2334e6e895982ba280dedc1a3884547089fd43), so you would need to apply the following to work with current HTSlib (the struct tag renaming is required for 1.11 onwards):
diff --git a/pileup.c b/pileup.c
index 95ec767..b718b16 100644
--- a/pileup.c
+++ b/pileup.c
@@ -34,7 +34,7 @@ typedef struct {
 KHASH_MAP_INIT_STR(olap_hash, lbnode_t *)
 typedef khash_t(olap_hash) olap_hash_t;

-struct __bam_plp_t {
+struct bam_plp_s {
     mempool_t *mp;
     lbnode_t *head, *tail;
     int32_t tid, pos, max_tid, max_pos;
@@ -51,8 +51,9 @@ struct __bam_plp_t {
     int (*plp_destruct )(void *data, const bam1_t *b, bam_pileup_cd *cd);
 };

-struct __bam_mplp_t {
+struct bam_mplp_s {
     int n;
+    int32_t min_tid, *tid;
     uint64_t min, *pos;
     bam_plp_t *iter;
     int *n_plp;

You could I suppose wrap that in #if HTS_VERSION >= 101000 etc to keep it working with both older and newer HTSlib, but really trying to keep up with changes in HTSlib's internal structs is a fool's errand.
I didn't look into why you have your own pileup routines here, but if you were lucky the newer plp constructor stuff or other flexibility improvements might mean you didn't need to do that anymore; otherwise, it would be better to duplicate the pileup code entirely so that you were decoupled from changes in HTSlib's internal pileup code.
(The OP could not reopen their previous issue due to isaacs/github#583).

@jmarshall I think you've nicely pin-pointed the cause. I need to refresh my memory about exactly why I was doing what I was with pileup.c and either just redo that or fully copy the relevant portion from htslib. It's been a few years since I've looked at much depth at the code base here, so that's a good excuse to do some mental refreshing :)

@ewels Until I have a proper fix for this supporting htslib 1.10 and 1.11 I've made a new build of MethylDackel 0.5.1 pinned to htslib 1.9. That should be available in bioconda in an hour or so, can you try that with the nextflow pipeline?

Still no joy 😞
https://github.com/nf-core/methylseq/pull/185/checks?check_run_id=1935046499#step:7:111
Error executing process > 'methyldackel (SRR389222_sub1)'

Caused by:
  Process `methyldackel (SRR389222_sub1)` terminated with an error exit status (139)

Command executed:

  MethylDackel extract     genome.fa SRR389222_sub1.sorted.markDups.bam
  MethylDackel mbias   genome.fa SRR389222_sub1.sorted.markDups.bam SRR389222_sub1.sorted.markDups --txt > SRR389222_sub1.sorted.markDups_methyldackel.txt

Command exit status:
  139

Command output:
  (empty)

Command error:
  writing to prefix:'SRR389222_sub1.sorted.markDups'
  .command.sh: line 2:    26 Segmentation fault      (core dumped) MethylDackel extract genome.fa SRR389222_sub1.sorted.markDups.bam

Ah but it looks like it's building with htslib-1.10.2 still though. Did I not wait long enough?
https://github.com/nf-core/methylseq/pull/185/checks?check_run_id=1935046499#step:4:142

Looking again, I can see that methyldackel-0.5.1-hee625c5_0.tar.bz2 was used and not 0.5.1--hed50d52_1 so I'm pretty sure that this is what the issue was. I'll try restarting the jobs this evening.

Ok I tried pinning the build as well as the version but then the environment fails. I can never read the conda failures but I guess that there is a conflict in one of the other packages. I've tried removing the version pin from samtools.
Soon with Nextflow DSL2 we will move to 1 process = 1 container / environment. Going to make this stuff so much easier! 😅

Oof, I'd forgotten that the DSL1 didn't allow multiple containers, that's a real pain. I'll take this as some pressure to get things properly fixed (I originally tried the patch above, which does cause it to run through, but then the CI testing failed on it due to the output being wrong, so there's more to fix).

DSL1 does allow multiple containers, we just chose not to go that way at first with @nf-core pipelines (smaller total singularity size, ability to collect versions for all tools in a single process). But we're totally rewriting for DSL2 to have shared software wrappers and will change this approach.
After a lot of trial and error (pushing a tonne of commits and letting the CI test them all in parallel actually worked quite well) I think I got to a working environment though! Had to keep Samtools at 1.9 and preseq at v2 but managed to get everything else up to date and working now I think 🎉

Great, that's something at least.

Version 0.5.2 contains a reimplementation of the paired-end overlap detection functionality, which was the root cause of the incompatibility with htslib 1.10+. The constructor/destructor functionality pointed out by @jmarshall really helped to clean things up in this regard. Note that 0.5.2 is currently only compatible with htslib 1.11 and not earlier versions, due to https://github.com/samtools/htslib/pull/1127. I hope this issue can now be closed for good :)

Fantastic, thank you @dpryan79 !


Audio issue

Hi ,
We integrated the iOSRTC plugin 3.1.1 and observed that outgoing voice/media is fine but incoming audio is crackly . once application hits this issue even the outgoing voice/media goes bad
Note: Application code to handle the webRTC API works fine on Android and browser.
Details of setup:
iOSRTC = 3.1.1
cordova = 3.9.2
device = iOS 9.3.5
SDK : 7.3.1
Thanks.

Alas there is nothing we can do in the plugin itself to improve this.  We use libwebrtc which does the heavy lifting.  Watch the repo for the next libwebrtc update, hopefully that helps!  Cheers.


Tasks 365-374 Synthetic Data

@nrjvarshney wondering if you can help with this PR's review?

@nrjvarshney wondering if you can help with this PR's review?

@nrjvarshney, pinging to check if you have seen my earlier message?

Task 365 - It is similar to task 157. In task 157, the input is a well-formed sentence but here it is a random string.
Task 366 - I'm not sure if the string " So this is a bad example" is required in the explanation. In the definition, you could specify how an empty list looks like ("[]"). The output here is str

"output": [
                "[457, 941, 233, 137, 239]"
            ]

The order of instances should not make a difference here but if we are giving it as a string then the order also becomes important.

Task 367 - Same comment as Task 366. Also, you use "Seven and eleven" in the explanation and "7, 11" in the input. I think we should keep it consistent.

Task 368 - "Seven and eleven" comment from Task 367. It says "The output should be a list of integers that is the result of applying that logic to the input list." but the output is floating-point values also such as "0.5". Also comparing the floating-point values as strings could create problems because of rounding and number of decimal points used. Sometimes you use ".75" and "0.5" the other times. This is also a problem.

Task 369 - "In this task you ...": comma after the word "task" is missing, Add the word "then" in the sentence "If every integer in the input list is odd an empty list should be returned.": "If every integer in the input list is odd then an empty list should be returned.". + same comments as above tasks.

Will review the other tasks later.

Also, I was working on other tasks, Task 517-520. I forgot to create another branch and accidentally pushed those changes to this branch. @nrjvarshney could you review those as well? @danyaljj  Should I remove those other tasks and create a new PR or is it ok to combine them?

Reviews of tasks 517-520: https://github.com/swarooprm/CSE576HW/pull/13

Thank you, all!


Add "create" tag for sheet versions

Currently, if we create sheets from a template we still end up with an "import" tag, which is technically wrong. Should use a "create" tag instead.
Remember to also update the docs regarding this.
Spec

Add from_template argument to SampleSheetIO.import_isa()

Boolean, default=False

Update SheetTemplateCreateForm.save()

Set from_template to True in import_isa() call

If from_template=True, set tags = ['CREATE']

Else tags = ['IMPORT'] (the current implementation)

Update samplesheets template tags

In TAG_COLORS, add "CREATE": "info"

Update tests

In TestSheetTemplateCreateFormView.test_post_batch(), add check for ISATab object and that its tags value is ['CREATE']

No need to do this in loop for every template, once after the loop on ISATab.objects.first() should be enough

In UI tests TestSheetVersionListView, test for import badge visibility

No need to test CREATE badge here since the code is so simple

(We should add template tag tests for samplesheets, but that's something for a different issue...)

Cleanup of existing code

Rename TestSheetTemplateCreateFormView to TestSheetTemplateCreateView
Delete unused ISATAB_TAGS from samplesheets.models

Done by @gromdimon.


fix: only send Digest challenge when realm is known

Based on testing, AMT (v12) refuses to respond to unknown Digest challenge with blank realm. This patch prevents such challenge to be sent allowing normal Digest challenge flow to continue.

@joko-sastriawan can you cover the if statement with additional unit test?


fix mega_genmsg to compile

while trying to build executables for the Native POSIX portion of the FreeRTPS demo, I found that the messages generated by mega_genmsg.py for rcl_interfaces didn't compile. This fixes it.

This isn't part of the binary packaging right? +1

Indeed.

look, I can even start a CI job for this, except it won't run any tests.
http://ci.ros2.org/job/freertps/19/


DataTable rowexpansioncell passthrough overriding classes instead of adding

when passing:
      :pt="{         rowexpansioncell: 'bg-red-500',       }"       :ptOptions="{ mergeSections: true, mergeProps: true }"
to the dataTable, the rowexpansioncell classes are being overridden instead of added to:
before:

after:

https://stackblitz.com/edit/ka1dqv?file=src%2FApp.vue

when passing:  :pt="{ rowexpansioncell: 'bg-red-500', }" :ptOptions="{ mergeSections: true, mergeProps: true }" to the dataTable, the rowexpansioncell classes are being overridden instead of added to:
before:  after:
https://stackblitz.com/edit/ka1dqv?file=src%2FApp.vue

The same issue we just discovered when trying to merge the numberinput globally using the usePassThrough composable. I suspect there is a problem when merging class arrays here
https://stackblitz.com/edit/nhbhmy?file=src%2Fmain.js


:bug: Use "and" to chain some conditions for more accuracy

See https://github.com/konveyor/rulesets/issues/41

I assume that this is same behavior that was non-explicit in windup? if so /LGTM


imprv: dependabot reveal.js

https://youtrack.weseek.co.jp/issue/GW-7711

reveal.js v3.5.0 resolved by v3.9.2

Reveal.js updated to v4 and adjusted the breaking changes, merged to master in https://github.com/weseek/growi/pull/5603


Pipeline step registration fails in Aurelia router 0.10.4.

Current version of plugin (0.1.6) causes application startup failure do to the following error:
Unhandled promise rejection Error: Pipeline steps can only be added to the root router
    at RouterConfiguration.exportToRouter (http://localhost:9000/jspm_packages/github/aurelia/router@0.10.4/aurelia-router.js:896:17)
    at Router.configure (http://localhost:9000/jspm_packages/github/aurelia/router@0.10.4/aurelia-router.js:963:26)
    at Function.AddFluxPipelineStep (http://localhost:9000/jspm_packages/github/tfrydrychewicz/aurelia-flux@0.1.6/router.js:19:14)
    at y.configure (http://localhost:9000/jspm_packages/github/tfrydrychewicz/aurelia-flux@0.1.6/index.js:14:31)
    at http://localhost:9000/jspm_packages/github/aurelia/framework@0.14.0/aurelia-framework.js:25:34
    at run (http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/es6.promise.js:91:43)
    at http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/es6.promise.js:105:11
    at module.exports (http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/$.invoke.js:6:25)
    at queue.(anonymous function) (http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/$.task.js:40:9)
    at Number.run (http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/$.task.js:27:7)
    at listner (http://localhost:9000/jspm_packages/npm/core-js@0.9.18/modules/$.task.js:31:9)

I just noticed that the version I tested against was actually 0.1.5. I need to retest with 0.1.6.

I'm seeing the same problem. Was working fine before update to jspm@beta and latest Aurelia.

I'll get down to that during the weekend. Thanks for reporting on that :)

That was an issue with aurelia-framework. It's been fixed with 0.14.1. Could you please give it a try with 0.14.1?

Working nicely again.  Thanks for the pointer to the latest framework version.

@stevies my pleasure :)


IntelliJ: importing multi-module project with artifact transforms fails because sub-module jar does not exist

Expected Behavior

When having a multi-module project with project dependencies and these dependencies must be transformed using artifact transforms then ./gradlew build will build the project dependencies first and finally call the artifact transform with the produced jar artifact as input.
The same should happen when importing such a project into IntelliJ which asks the Gradle Tooling API for the dependencies of a project.
Current Behavior

Currently the import into IntelliJ fails, because Gradle does not seem to build the project dependencies before calling the artifact transforms when asking the Gradle Tooling API about dependency information.
The artifact transform receives a File object pointing to a non-existing jar file which usually causes a NoSuchFileException once the file needs to be opened in the artifact transform code.
IntelliJ / Gradle output:
Warning:root project 'gradle-multimodule-artifact-transform-intellij-bug': Unable to resolve additional project configuration.
Details: org.gradle.api.artifacts.ResolveException: Could not resolve all dependencies for configuration ':runtimeClasspath'.
Caused by: org.gradle.api.internal.artifacts.transform.TransformException: Failed to transform artifact 'lib-1.jar (project :lib-1)' to match attributes {artifactType=java-classes-directory, org.gradle.category=library, org.gradle.dependency.bundling=external, org.gradle.jvm.version=11, org.gradle.libraryelements=jar, org.gradle.usage=java-runtime, processed=true}.
Caused by: org.gradle.api.internal.artifacts.transform.TransformException: Execution failed for Unzip: /some-path/gradle-multimodule-artifact-transform-intellij-bug/lib-1/build/libs/lib-1.jar.
Caused by: java.nio.file.NoSuchFileException: /some-path/gradle-multimodule-artifact-transform-intellij-bug/lib-1/build/libs/lib-1.jar

Context

I'll try to transform a java-library project dependency (jar) into an unpacked directory and during that process removing some annotated java source (the jar contains sources as well) and finally compile the modified sources again.
In addition the artifact transform generates a second artifact (directory) which contains JavaScript compiled from the modified java sources + classes.
This is a proof of concept plugin that tries to make Googles Java to Closure compiler usable with Gradle by reusing most of Gradle's infrastructure (artifact transforms, continuous build, build cache).
Steps to Reproduce

You can reproduce the issue with the example Unzip artifact transform provided by Gradle samples and a multi module project having one or two library project dependencies.
build.gradle
import java.nio.file.Files
import java.util.zip.ZipEntry
import java.util.zip.ZipException
import java.util.zip.ZipFile

import org.gradle.api.artifacts.transform.TransformParameters

abstract class Unzip implements TransformAction<TransformParameters.None> {
    @InputArtifact
    abstract Provider<FileSystemLocation> getInputArtifact()

    @Override
    void transform(TransformOutputs outputs) {
        def input = inputArtifact.get().asFile
        def unzipDir = outputs.dir(input.name)
        println "transforming: " + input + " into " + unzipDir
        unzipTo(input, unzipDir)
    }

    private static void unzipTo(File zipFile, File unzipDir) {
        // implementation...
        new ZipFile(zipFile).withCloseable { zip ->
            def outputDirectoryCanonicalPath = unzipDir.canonicalPath
            for (entry in zip.entries()) {
                unzipEntryTo(unzipDir, outputDirectoryCanonicalPath, zip, entry)
            }
        }
    }

    private static unzipEntryTo(File outputDirectory, String outputDirectoryCanonicalPath, ZipFile zip, ZipEntry entry) {
        def output = new File(outputDirectory, entry.name)
        if (!output.canonicalPath.startsWith(outputDirectoryCanonicalPath)) {
            throw new ZipException("Zip entry '${entry.name}' is outside of the output directory")
        }
        if (entry.isDirectory) {
            output.mkdirs()
        } else {
            output.parentFile.mkdirs()
            zip.getInputStream(entry).withCloseable { Files.copy(it, output.toPath()) }
        }
    }
}

plugins {
    id 'java'
}

repositories {
    jcenter()
}

def processed = Attribute.of('processed', Boolean)
def artifactType = Attribute.of('artifactType', String)

dependencies {

    attributesSchema {
        attribute(processed)
    }

    artifactTypes.getByName("jar") {
        attributes.attribute(processed, false);
    }

    registerTransform(Unzip) {
        from.attribute(artifactType, 'jar').attribute(processed, false)
        to.attribute(artifactType, 'java-classes-directory').attribute(processed, true)
    }

    implementation project(':lib-1')
    implementation project(':lib-2')
}

configurations.all {
    afterEvaluate {
        if (canBeResolved) {
            attributes.attribute(processed, true)
        }
    }
}

settings.gradle
rootProject.name = 'gradle-multimodule-artifact-transform-intellij-bug'

include ':lib-1'
include ':lib-2'

Your Environment

Mac OS 10.13.6, Java 11, IntelliJ 2019.2.1

I created https://youtrack.jetbrains.com/issue/IDEA-223152 to track this problem on the IDEA side, since it doesn't seem that Gradle can do anything about it.

Oh this is really IDE dependent? I would have assumed that the Gradle Tooling API would hide the Gradle artifact transforms, so that the IDE just takes the dependencies artifacts (transformed or not transformed) Gradle provides.
Personally I would consider artifact transformation as a build internal.
Have you verified if the issue does not exist in Eclipse and maybe Netbeans?


Bump protobuf 1.2.0, and re-generate

ping @dperny @wk8 @stevvooe ptal

Hmf.. looks like protobuf 1.2.x is not backward compatible, and no longer allows using things as map keys;
remotes/remotes.go:73:17:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
remotes/remotes.go:69:49:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
remotes/remotes.go:60:14:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
remotes/remotes.go:49:21:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
remotes/remotes.go:23:16:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
agent/exec/dockerapi/executor.go:42:17:warning: invalid map key type github.com/docker/swarmkit/api.PluginDescription (unconvert)
agent/agent.go:394:14:warning: invalid map key type github.com/docker/swarmkit/api.Peer (unconvert)
manager/state/store/memory.go:583:6:warning: cannot compare oldN.GetMeta().Version != meta.Version (operator != not defined for github.com/docker/swarmkit/api.Version) (unconvert)
manager/allocator/cnmallocator/portallocator.go:41:25:warning: invalid map key type github.com/docker/swarmkit/api.PortConfig (unconvert)
manager/scheduler/scheduler.go:469:25:warning: cannot compare node.Meta.Version != nodeInfo.Meta.Version (operator != not defined for github.com/docker/swarmkit/api.Version) (unconvert)
manager/scheduler/scheduler.go:381:32:warning: invalid map key type commonSpecKey (unconvert)
manager/scheduler/nodeinfo.go:53:39:warning: invalid map key type versionedService (unconvert)
manager/scheduler/nodeinfo.go:39:21:warning: invalid map key type versionedService (unconvert)
manager/orchestrator/task.go:77:53:warning: cannot compare *s.SpecVersion == *t.SpecVersion (operator == not defined for github.com/docker/swarmkit/api.Version) (unconvert)
manager/orchestrator/restart/restart.go:366:43:warning: cannot compare *replacementTask.SpecVersion != restartInfo.specVersion (operator != not defined for github.com/docker/swarmkit/api.Version) (unconvert)
manager/orchestrator/restart/restart.go:231:52:warning: cannot compare *t.SpecVersion != restartInfo.specVersion (operator != not defined for github.com/docker/swarmkit/api.Version) (unconvert)
manager/dispatcher/dispatcher.go:710:8:warning: cannot compare task.Status == *status (operator == not defined for github.com/docker/swarmkit/api.TaskStatus) (unconvert)
remotes/remotes.go:23:12:error: invalid map key type api.Peer (vet)
remotes/remotes.go:49:17:error: invalid map key type api.Peer (vet)
remotes/remotes.go:60:10:error: invalid map key type api.Peer (vet)
remotes/remotes.go:69:45:error: invalid map key type api.Peer (vet)
remotes/remotes.go:73:13:error: invalid map key type api.Peer (vet)
manager/state/store/memory.go:583:29:error: invalid operation: oldN.GetMeta().Version != meta.Version (struct containing []byte cannot be compared) (vet)
agent/exec/dockerapi/executor.go:42:13:error: invalid map key type api.PluginDescription (vet)
manager/allocator/cnmallocator/portallocator.go:41:21:error: invalid map key type api.PortConfig (vet)
agent/exec/dockerapi/executor.go:42:13:error: invalid map key type api.PluginDescription (vet)
manager/allocator/cnmallocator/portallocator.go:41:21:error: invalid map key type api.PortConfig (vet)
manager/state/store/memory.go:583:29:error: invalid operation: oldN.GetMeta().Version != meta.Version (struct containing []byte cannot be compared) (vet)
remotes/remotes.go:23:12:error: invalid map key type api.Peer (vet)
remotes/remotes.go:49:17:error: invalid map key type api.Peer (vet)
remotes/remotes.go:60:10:error: invalid map key type api.Peer (vet)
remotes/remotes.go:69:45:error: invalid map key type api.Peer (vet)
remotes/remotes.go:73:13:error: invalid map key type api.Peer (vet)
remotes/remotes_test.go:15:15:error: invalid map key type api.Peer (vet)
remotes/remotes_test.go:86:11:error: invalid operation: next == peers[0] (struct containing []byte cannot be compared) (vet)
remotes/remotes_test.go:98:11:error: invalid operation: next != peers[0] (struct containing []byte cannot be compared) (vet)
remotes/remotes_test.go:254:8:error: invalid operation: p == peers[0] (struct containing []byte cannot be compared) (vet)
remotes/remotes_test.go:311:11:error: invalid operation: peer == peers[0] (struct containing []byte cannot be compared) (vet)
remotes/remotes_test.go:15:15:error: too many errors (vet)

See the discussion on https://github.com/golang/protobuf/issues/594

In general, the proto specification does not formally define what equality means for protos. Since comparability is undefined, and using protos as map keys requires comparability, then that means using protos as map keys is undefined behavior. The fact that proto3 structs were comparable before was unfortunate because it gave the illusion that this was the case when it wasn't.

I see some mention here https://github.com/gogo/protobuf/issues/275 of adding option (gogoproto.goproto_unrecognized) = false;

Ok, looking much better with that option set; only see this failure;
manager/allocator/network.go:186::error: Entry.Errorf format %s has arg nc.ingressNetwork.Spec.Annotations of wrong type github.com/docker/swarmkit/api.Annotations (vet)
make: *** [check] Error 1
Exited with code 2

Hm.. not out of the woods yet
--- FAIL: TestIsStateDirty (0.07s)
panic: unexpected field type in StoreSnapshot [recovered]
	panic: unexpected field type in StoreSnapshot

goroutine 42 [running]:
testing.tRunner.func1(0xc0005f1600)
	/usr/local/go/src/testing/testing.go:792 +0x6a7
panic(0x1344980, 0x1641540)
	/usr/local/go/src/runtime/panic.go:513 +0x1b9
github.com/docker/swarmkit/manager.(*Manager).IsStateDirty(0xc0000ba4e0, 0x15214e0, 0xc0000ba4e0, 0x1659ec0)
	/home/circleci/.go_workspace/src/github.com/docker/swarmkit/manager/dirty.go:48 +0xa53
github.com/docker/swarmkit/manager.TestIsStateDirty(0xc0005f1600)
	/home/circleci/.go_workspace/src/github.com/docker/swarmkit/manager/dirty_test.go:56 +0x715
testing.tRunner(0xc0005f1600, 0x1521598)
	/usr/local/go/src/testing/testing.go:827 +0x163
created by testing.(*T).Run
	/usr/local/go/src/testing/testing.go:878 +0x651
FAIL	github.com/docker/swarmkit/manager	0.376s

Looks like the bump was taken care of in https://github.com/docker/swarmkit/pull/2886
I'll open a PR for the remaining changes (could be useful)


only set mark as read if we have focus

It seems if we call try to do a GetThreadNonblock in the background, we could mark a thread as read. Only set markAsRead if we are focused.

What's the status of this PR?


StatefulSet not starting when watchNamespace is * and the MongoDb Resource is in another namespace

This issue is copy paste of https://github.com/mongodb/helm-charts/issues/104. The PR https://github.com/mongodb/helm-charts/pull/102 mentioned was deployed in the version 0.7.3 of the helm chart but we still get the issue.

I'm not sure if this is a problem with the chart or with the operator but I've installed the community-operator to the "operators" namespace via chart with watchNamespace set to "*" and created a MongoDB resource in the "test" namespace.

The mongodb statefulset is created but isn't starting with the following error message:
create Pod mongodb-0 in StatefulSet mongodb failed error: pods "mongodb-0" is forbidden: error looking up service account test/mongodb-database: serviceaccount "mongodb-database" not found

A temporary fix for this: I copied the service account "mongodb-database" to the other namespace with the secret it is referencing.


Users can't see Virtual Network and Security Group names

Bug Report
Version of OpenNebula

[ ] 5.2.2
[ ] 5.4.0
[ ] 5.4.1
[ ] 5.4.2
[ ] 5.4.3
[ ] 5.4.4
[ ] 5.4.5
[ ] 5.4.6
[ ] 5.4.7
[ ] 5.4.8
[ ] 5.4.9
[ ] 5.4.10
[ ] 5.4.11
[X] 5.4.12
[X] 5.4.13
[ ] 5.4.14
[ ] 5.4.15
[ ] Development build

Component

[ ] Authorization (LDAP, x509 certs...)
[ ] Command Line Interface (CLI)
[ ] Contextualization
[ ] Documentation
[ ] Federation and HA
[ ] Host, Clusters and Monitorization
[ ] KVM
[ ] Networking
[ ] Orchestration (OpenNebula Flow)
[ ] Packages
[ ] Scheduler
[ ] Storage & Images
[X] Sunstone
[ ] Upgrades
[ ] User, Groups, VDCs and ACL
[ ] vCenter

Description

In fresh install normal users (not members of oneadmin group) see only ID and Group fields in Virtual Netwroks and Security Groups tables.
Expected Behavior
Users shoud be able to see network name
Actual Behavior
Users see only ID and Group
How to reproduce

Create group
Create user
Make user admin for a group
Login as user and check Network -> Virtual Networks

Same thing in VM instantiate dialog when chosing network.

Progress Status

[ ] Branch created
[ ] Code committed to development branch
[ ] Testing - QA
[ ] Documentation
[ ] Release notes - resolved issues, compatibility, known issues
[ ] Code committed to upstream release/hotfix branches
[ ] Documentation committed to upstream release/hotfix branches

Please check this option, in your sunstone view:
https://github.com/OpenNebula/one/blob/5c072dae4ce3323579aa4d96b0f329e79101f8d3/src/sunstone/etc/sunstone-views/kvm/user.yaml#L739

vnet-tab on /etc/one/sunstone-views/user.yaml is:
    vnets-tab:
        panel_tabs:
            vnet_info_tab: true
            vnet_ar_list_tab: true
            vnet_leases_tab: true
            vnet_sg_list_tab: true
            vnet_vr_list_tab: true
            vnet_clusters_tab: false
        table_columns:
            - 0         # Checkbox
            - 1         # ID
            - 2         # Owner
            - 3         # Group
            - 4         # Name
            - 5         # Reservation
            - 6         # Cluster
            #- 7         # Bridge
            - 8         # Leases
            #- 9         # VLAN ID
            #- 10         # Labels
            #- 11        # Search data
        actions:

But in groupadmin.yaml there is only ID and Name:
    vnets-tab:
        panel_tabs:
            vnet_info_tab: false
            vnet_ar_list_tab: false
            vnet_leases_tab: true
            vnet_sg_list_tab: true
            vnet_vr_list_tab: false
            vnet_clusters_tab: false
        table_columns:
            - 0         # Checkbox
            - 1         # ID
            #- 2        # Name
            #- 3        # Owner
            - 4         # Group
            #- 5        # Reservation
            #- 6        # Cluster
            #- 7        # Bridge
            #- 8        # Leases
            #- 9        # VLAN ID
            #- 10       # Labels
            #- 11       # Search data
        actions:

That's the reason?

yep, just uncoment those lines

Ok, that fixed the problem. But why it was commented? I didn't touch this files so it's from package.

Seems it was a bug that's already fixed in this commit:
https://github.com/OpenNebula/one/commit/7f26f26b0c0732bbfd766d5b6097dbc7ff7d12e3#diff-f3b3a7813d42de86acd0b42590e3f144
The changes will be applied only for new releases (currently release-5.6-beta1 and release-5.5.80)

Well, it's still same problem for security groups: https://github.com/OpenNebula/one/blob/master/src/sunstone/etc/sunstone-views/kvm/groupadmin.yaml#L787
And also users has much more "true" in actions for vnets and secgroups than groupadmins. Is it intended for some reason?
For now I see that groupadmin is very restricted, at least with network stuff.

Please, these questions are for our forum. This is not a bug or a new feature.
Forum


Fix background for empty cell

Fix -fx-background for empty cell
Before:

After:

Codecov Report

Merging #102 (296a35a) into master (ebb25ee) will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #102   +/-   ##
=========================================
  Coverage     57.91%   57.91%
  Complexity      506      506
=========================================
  Files           104      104
  Lines          1965     1965
  Branches        226      226
=========================================
  Hits           1138     1138
  Misses          761      761
  Partials         66       66

Continue to review full report at Codecov.

Legend - Click here to learn more
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K9 crash try attaching files

Expected behaviour
Adding attachment and browising files whit Amaze or other files manager I would like to attach a file
Actual behaviour
K9 crash when I select the files whit Amaze or other files manager (process "com.fsck.k9" stop); if I select files from stock image gallery app or stock audio library app it works fine.
Downgrading K9 to v5.008 everything works fine
Steps to reproduce
1.Create new email
2.Add attachment
3.Select a file whit Amaze or any other files manager
Environment
K-9 Mail version:
5.010
Android version:
4.0.4
Account type (IMAP, POP3, WebDAV/Exchange):
IMAP

Please provide a debug log: https://github.com/k9mail/k-9/wiki/LoggingErrors

Tanx for reply, I don't know if I'm doing right, sorry. Anyway, here's the log file

"Here" where?

alogcat.2016-05-29-09-48-48+0200.txt
Probably I made some mistake, is it ok now?

it's a SafeContentResolver issue, interesting..

additional information: my device is rooted and files manager has root exploring enabled, rom is stock ICS 4.0.4

05-29 09:47:58.000 E/AndroidRuntime( 9042): Caused by: java.lang.UnsatisfiedLinkError: Couldn't load os-compat: findLibrary returned null
05-29 09:47:58.000 E/AndroidRuntime( 9042): 	at java.lang.Runtime.loadLibrary(Runtime.java:365)
05-29 09:47:58.000 E/AndroidRuntime( 9042): 	at java.lang.System.loadLibrary(System.java:535)
05-29 09:47:58.000 E/AndroidRuntime( 9042): 	at de.cketti.safecontentresolver.Os.<clinit>(Os.java:21)

Looks like it's failing to find the native library that safe content resolver uses.
What device are you using - maybe it's not running one the supported ABIs??
https://github.com/cketti/SafeContentResolver#native-code

It's an old LG P990 also known as Optimus X2 Dual runnig stock ICS 4.0.4 rooted: I don't really know how to check if it's not running one the supported ABIs. To be honest I do not know what it is an ABIs, sorry I am completely ignorant in this regard

@ShakurGit: Please try uninstalling, then reinstalling.
Might be related to this: https://medium.com/keepsafe-engineering/the-perils-of-loading-native-libraries-on-android-befa49dce2db

just done, everything is not changed, same error. I've used F-Droid repository to reinstall

Update: I tried other file manager and with "OI File Manager" from F-Driod there are no problems. I hope this information will be useful

I can confirm this. I have tried native file manage, amaze, es explorer. All crashing k9. The only old "OI" working.
Cm11, v5.010

I have this issue too. I use the default file manager from cyanogenmod.
Motorola razri (x86) CM11
Logcat.txt

Thanks !!!


Added optional results file name change parameter

I have added the option of specifying the name of the output .trx file.
It was functionality I needed and thought others may desire it in future.
Most of the code was taken from the trx logger which ships with vstest as that also has this optional parameter.

Hi @ltnorth,
Thanks for the PR, this is a nice addition! I left a couple of comments.
One small request: I generally like to write as much as possible in functional style, and avoid having mutable state, so that we have less side effects and the code is easier to reason about.
In this case we can get rid of the parametersDictionary and testResultsDirPath fields, and just make the various methods pass that to each other, and use local variables.
I'd do it the following way:

Determine the file path in the public Initialize method based on the input dictionary. (This way we don't need the dictionary in the later parts at all.)
Make the other Initialize accept also the trxFilePath as an input parameter.
Change DeriveTrxFilePath so that it gets the dictionary and the folder path as input parameters.
Change SetDefaultTrxFilePath to get the folder path as input parameter, and make it return the default path as the return value instead of setting it on the field.

This way we won't need any of the mutable state on the class instance.
Once this is done, I'll merge and release a new version.

I find this useful and I would like to see it implemented. Remeber of #7 meanwhile releasing.

@ltnorth sorry for the late reply.
You're right, I missed the fact that ITestLoggerWithParameters derives from ITestLogger. (Btw it's pretty weird design by MS that you have to implement both methods, but then as the implementor you have to call from one of the Initialize methods into the other one. 🤔)
I think the way the framework works (here) is that if you implement ITestLoggerWithParameters, then it doesn't call the first Initialize at all.
So what I would do is simply put all the logic in the second initialize, and leave the first initialize empty (and put a descriptive comment in it saying that this is not needed).
Can you try if this works?

We could get around the second problem by passing both the TestRunDirectory and LogFileName values as one string and then breaking that up in the second Initialize, but this seems a bit hack-y.
I agree, this is very hacky, let's not do this.

Or, if it's possible, we could remove the inheritance altogether which would fix both?
I don't think this would work, I think the framework needs this class to implement the interface, otherwise it can't call the Initialize method on it, so we wouldn't receive the parameters dictionary.


Make a seperate NLog project for WPF.

Hi. Would it be possible to make a seperate NLog project for WPF, so that there's no dependency on System.Windows.Forms.dll ?

There's a pull request for this, see #497. And separate project has been created and release see NLog/NLog.Windows.Forms

The targets have been moved to NLog/NLog.Windows.Forms, and the old code removed from NLog/NLog


[FEATURE] Edit Functionality

Describe the bug
The Edit Button for the mappings does not work.
To Reproduce
In the Main Window click on one of your actions
Click on the Edit button below the actions name
Expected behavior
Window for Editing opens
Screenshots
none
Additional context
This button could get removed instead

Temporary removed edit button in edae9cf

Temporary removed edit button in edae9cf

For first productive release there will not be an edit functionality. you have to delete and reapply mappings instead

For first productive release there will not be an edit functionality. you have to delete and reapply mappings instead


Optimizations to make much faster than browscap-php for all user-agents

See this commit https://github.com/crossjoin/Browscap/commit/3a82d37cf1a0d4a1d7e0dc927860494d648baa7d and this ticket https://github.com/crossjoin/Browscap/issues/12 for more information.

Thanks. Will look into this and merge it with my changes (there are some conflicts that need to be solved).

I had to change a lot to get it working with my previous changes, but the results are amazing.
Combined it requires up to 94% less time with some slow examples!
I will have to clean up the code a bit an do some last tests. Would be nice if you can run your tests once again with the master branch after I finished it (I will let you know).
Thanks a lot for your help.

Awesome! Good to hear.
I'm happy to run it against the same test files I've been testing against once you merge everything together.

I merged the changes. Please run your test with the master branch.
Can't wait for the results...
BTW: I'll close this pull request.

Nice, I have the browscap/browscap tests running with crossjoin now, so I'll just pull down master and run there.  I'll post results in #12.

@jaydiablo @crossjoin Some time ago I created a branch in browscap/browscap for testing with this library. The branch is named test-with-crossjoin.


on_message_complete is not called

This happens for a site as simple as http://tired.com/ (retrieved with curl -i http://tired.com/).
The breakage was introduced some time after commit<PHONE_NUMBER> , and it seems to be related to content_length parsing.

HTTP/1.1 200 OK
Date: Sun, 19 Feb 2012 12:34:46 GMT
Server: Apache/2.2.9 (Debian) PHP/5.2.6-1+lenny16 with Suhosin-Patch mod_python/3.3.1 Python/2.5.2 mod_ssl/2.2.9 OpenSSL/0.9.8g mod_perl/2.0.4 Perl/v5.10.0
Last-Modified: Mon, 29 Sep 2003 08:34:25 GMT
ETag: "3d7130-b8-3c873c3fc0640"
Accept-Ranges: bytes
Content-Length: 184
Vary: Accept-Encoding
Content-Type: text/html

<TITLE>Are you tired?</TITLE>

Are you tired?

Tell <a<EMAIL_ADDRESS>why.

It's interesting, I cannot reproduce it when I'm reading it from a locally saved file, but it reproduces every time when I get it from network. I'll investigate this more and report back. I'll also try git bisect in order to find which commit changed the behavior.

Sorry. My bad. My callback function was returning the number of bytes processed, while the http_parser was halting if anything other than 0 was returned, as far as I understand.

My callback function was returning the number of bytes processed, while the http_parser was halting if anything other than 0 was returned, as far as I understand.

That's correct. You're supposed to return HPE_OK, anything else signals an error.


Add 'fmt' command to Makefile

This command will run 'black' and 'reorder-python-imports' for you

I just added a make fmt to the upgrader tool's makefile after your PR here, here's what that looks like in case it's helpful:
REORDER_PYTHON_IMPORTS := reorder-python-imports --py37-plus --separate-from-import --separate-relative
PYTHON_FILES = $(shell find baseplate_py_upgrader/ tests/ -name '*.py')

all:

lint:
	$(REORDER_PYTHON_IMPORTS) --diff-only $(PYTHON_FILES)
	black --diff baseplate_py_upgrader/
	flake8 baseplate_py_upgrader/
	mypy baseplate_py_upgrader/

fmt:
	$(REORDER_PYTHON_IMPORTS) --exit-zero-even-if-changed $(PYTHON_FILES)
	black baseplate_py_upgrader/

test:
	pytest

.PHONY: lint fmt test


French latin characters with accents like é à ô ï don't print well with Canon printers on firefox

The Canon printer driver replaces all french accent characters by a rectangle. Firefox works fine when printing a webpage but doesn't work when printing a PDF. So I think the problem comes from pdf.js . I tested it with several printers and it looks like only canon printers have this problem. Tested it on Windows 7 and 10 with France/French language pack.

As is, this issue is currently missing virtually all the required information in order to be actionable.
Please provide all of the information requested in https://github.com/mozilla/pdf.js/blob/master/.github/ISSUE_TEMPLATE.md.

Closing since this is not actionable right now and looks like a Canon-specific problem. Please provide more information to reopen.

Web Browser : Firefox 53.0.3 (and previous versions, I think)
Operating system : Windows 10 (64 bits), Windows 8 (64 bits), Windows 7 (64 bits)
pdf.js version: 1.6.467 (according to the console output)
is an extension : [I didn't understand the question. I'm using firefox to display PDFs.]
printer : Canon iP2800 series (driver version 2.75)
steps to reproduce the problem:
-print a pdf containing french accentuated characters like é à with mozilla firefox
It only does this with firefox when printing a pdf but webpages and other softwares work well.
examples : i've attached a pdf containing those characters and a scan of the print.


Beta 7 Build / DNU restore -- fails on three test projects - "Kestrel" not found

The following Test projects are affected (reference image below):

mvc\tests\WebSites\ValidationWebSite
mvc\tests\WebSites\ActionConstraintsWebSite
mvc\tests\Microsoft.AspNet.Mvc.FunctionalTests

ValidationWebSite and ActionContraintsWebsite were fixed by replacing the following in Project.json:
"Kestrel": "1.0.0-*"
with
"Microsoft.AspNet.Server.Kestrel": "1.0.0-beta7"
FunctionalTests was fixed by adding
"Microsoft.AspNet.Server.Kestrel": "1.0.0-beta7"
Note: after the above updates the build fails with timeout on one test in FunctionalTests.

Thanks for noticing this


[hiredis] Support static build on Windows

Add windows support.
It currently only supports static on Windows.
Related issue #8840
Related PR #8843, #8846.
Note: All features test pass with x64-linux triplet.
All features are only supported on Unix.

/azp run

/azp run

The Related PR #9388 has been merged.
So I close this PR now.


Specify not URI parameters

For POST request to a resource I'd like to declare parameters that will be part of the request's body with similar syntax we have for URI parameters.
For example:
## Device [/devices/]

### Create a New Device [POST]

Create a new device instantiation.
Note: any previous registration with same token will be replaced.

+ Parameters
  + uuid (string, required) - One-time unique identifier
  + something_else (string) - Something else not required

This syntax will raise a warning because uuid and something_else are not specified in the URI but I want to declare them as parameters to my request body.
Am I missing some syntax declaration?

You can use the Attributes section to define them.


Typst doesn't respect my fontconfig configuration

Description
Currently, I only understand three languages.  I'm not sure if there is a reason why we don't use that feature.

I'm not sure if there is a reason why we don't use that feature.

We do:
https://github.com/typst/typst/blob/b5ef9244eb2b546b47530d40860e9e04256aafb2/crates/typst-kit/Cargo.toml#L34-L37
We have default-features = false at the workspace level because typst as a library, without typst-cli, also depends on fontdb for SVG support, but not on any system stuff.

Ah, I see... Then I guess it most likely is a limitation in fontdb.

Thanks for the quick responses. Should I report it upstream or will you take care of it?

Feel free to report it upstream, though if you know a bit of Rust ideally check first that it indeed happens with just a bare fontdb as well.

Ok, I made a small code snippet using fontdb 0.21.0 only and enabled fontconfig features and it's clear that it's a fontdb issue. It seems that fontdb enabled very basic fontconfig support may be just to load the fonts from custom folders so my hopes are not high for a quick fix. Would there be any possibility for typst to use fontconfig directly without relying on fontdb reimplementation?

Would it be possible for typst to use fontconfig directly rather than relying on fontdb?

I'm not sure whether it would be desirable to go our own ways as opposed to improving fontdb, as it is starting to become a standard in the Rust ecosystem (e.g. also used in cosmic-text, which is fairly widely used by other projects).
But independently of that, we don't currently have the development capacity to make larger changes here.

fontdb uses the fontconfig-parser crate so there's not likely.  Before any major surgery I throw your test case in the fontconfig-parser tests directory along with the expected output, run the tests and see if they pass.

Do we need a tag UpstreamToUpstream or what? 😀
Assuming I have done it correctly, I put my config in test-conf folder and cargo test shows all OK. Then, I used the examples/list_all_fonts.rs and it listed all the fonts ignoring the </rejectfont> element. If this is the correct way to test, should this be reported to fontconfig-parser then?

Worth noting that fontdb is intentionally seeking to keep fontconfig support very minimal as they want to avoid depending on the full thing (which would lead to a C dependency). But it could be worth it to open an issue upstream either way to see if their implementation, even if minimal, could be adapted to consider this setting.

Apologies for the wild goose chase — those tests don't actually test the font resolution.
Upon further inspection the fontconfig-parser example does what fontdb does and simply gets a list of directories from fontconfig and parses all the files found within.  rejectfont entries are parsed without any C dependencies but it's up to the consumer (e.g. fontdb) to actually use them.
Spitballing here — to get the filtering working the rejectfont entries should be abstracted in a platform independent way as fontdb only uses fontconfig on non-Android Linux, then passed in to load_fonts_dir_impl.
Not much for Typst to do IMO.

typst should switch to fontconfing on Linux. That's the only option. fontdb isn't designed to replace system API.

I tried font-kit and indeed it doesn't list the blacklisted fonts. Thanks for the advice


Fix problem causing scanner to get stuck

Turns out calling get_column causes tree-sitter to get stuck, if the
next token is the eof.
Fixes https://github.com/elm-tooling/elm-language-server/issues/527
Thanks to Yarith for the great examples

https://github.com/tree-sitter/tree-sitter/issues/516


Improve  solve speed for complicated equations

This PR implements a by-hand solve base on factorization of affine equation of the form:
eq = a * target + const

where target is the variable we solve for. Most PDE time-stepper are in this form as we have
eq = u.dtn - spatial(u)
# i .e
eq = dt**(-n)*target - spatial(u) +rest_of(u.dtn)

where we always solve for target to obtain the time-stepping stencil.

Updated the tti and acoustic operator (some tutos still need updating)
Added test that ensure we get the correct result (and also check speed)

FYI: solve takes ~1s on my machine for 3D TTI so=12

Merged


time, runtime: scheduled timer may never fire if GOMAXPROCS is reduced

This issue is related to #44868 (and seems to be resolved with the same fix) but I wanted to file a separate issue as the impact is different, and may help others running into the same issue.
What version of Go are you using (go version)?

$ go version
go version go1.16.2 linux/amd64

Does this issue reproduce with the latest release?
Not yet,, go1.16.3 seems fine (only tested with simple repro, not on production)
This is likely fixed by https://go-review.googlesource.com/c/go/+/300610/.
What operating system and processor architecture are you using (go env)?
linux, amd64
go env Output
$ go env
GO111MODULE="on"
GOARCH="amd64"
[..]
GOHOSTARCH="amd64"
GOHOSTOS="linux"
GOINSECURE=""
[...]
GOPROXY="https://proxy.golang.org,direct"
GOROOT="/home/user/.gimme/versions/go1.16.2.linux.amd64"
GOSUMDB="sum.golang.org"
GOTMPDIR=""
GOTOOLDIR="/home/user/.gimme/versions/go1.16.2.linux.amd64/pkg/tool/linux_amd64"
GOVCS=""
GOVERSION="go1.16.2"
[..]

What did you do?
Created a background goroutine to do some periodic work every 500ms. The background goroutine created a ticker, and used a for loop that waited on the ticker.
Concurrently, the main goroutine reduced GOMAXPROCS (based on some system config).
Repro:
https://gist.github.com/prashantv/fdd710e270244efa23ba7a3fcb45b088
This needs to be run in a loop as it happens quite infrequently, it should eventually freeze with a log like:
$ while [ true ] ; do ./stuck-timer-repro || break; done
[...]
attempt 4
========= Likely bug =======
timer 53 timed out after 10s of waiting 0

The repro happens in a few seconds on go1.16.2.
The process is then blocked waiting on the ticker's channel, and allows the process to be debugged.
What did you expect to see?
Ticker channel to receive ticks periodically, ensuring periodic work run roughly twice a second.
What did you see instead?
Ticker did not tick at all, and periodic work did not happen.
More Context
In an internal production service, we noticed some periodic work was not happening as expected. After ruling out other possibilities, the only explanation left was that the ticker was not ticking. Using /debug/pprof/goroutines, I was able to find "stuck" select calls the appropriate stacktrace; the ticker was supposed to fire every few hundred ms, but the select was stuck for many minutes (including thousands of minutes).
Using delve with a core, I discovered that the timer was added to a P that was dead. The same can be reproduced with the repro, and an example delve sessions showing the state is below:
delve debugging
wait for the stuck-docker-repro to print the "likely bug" as above before running delve

dlv attach $(pidof stuck-timer-repro)
(dlv) grs
Goroutine 1 - User: ./stuck-timer-repro.go:52 main.run (0x4a74e5)
Goroutine 2 - User: /home/user/.gimme/versions/go1.16.2.linux.amd64/src/runtime/proc.go:337 runtime.gopark (0x435985)
Goroutine 3 - User: /home/user/.gimme/versions/go1.16.2.linux.amd64/src/runtime/proc.go:337 runtime.gopark (0x435985)
Goroutine 4 - User: /home/user/.gimme/versions/go1.16.2.linux.amd64/src/runtime/proc.go:337 runtime.gopark (0x435985)
Goroutine 5 - User: /home/user/.gimme/versions/go1.16.2.linux.amd64/src/runtime/proc.go:337 runtime.gopark (0x435985)
[5 goroutines]

switch to the main goroutine so we can find the timer object
(dlv) gr 1
Switched from 0 to 1 (thread 108415)
(dlv) bt -full
0  0x0000000000435985 in runtime.gopark
at /home/user/.gimme/versions/go1.16.2.linux.amd64/src/runtime/proc.go:337
unlockf = runtime.chanparkcommit
[...]
3  0x00000000004a74e5 in main.run
at ./stuck-timer-repro.go:52
gomaxprocs = 10
goroutines = 100
wg = sync.WaitGroup {noCopy: sync.noCopy {}, state1: [3]uint32 [...]}
tickers = []*time.Ticker len: 100, cap: 100, [...]
i = 0
ti = 81
t = (*time.Ticker)(0xc0004820a0)
[...]
get information about the timer
(dlv) frame 3
(truncated)
=>  52:                                 <-t.C
(dlv) print t
*time.Ticker {
C: <-chan time.Time {
qcount: 0,
dataqsiz: 1,
buf: *[1]time.Time [
(*time.Time)(0xc000480030),
],
elemsize: 24,
closed: 0,
elemtype: *runtime._type {size: 24, ptrdata: 24, hash:<PHONE_NUMBER>, tflag: tflagUncommon|tflagExtraStar|tflagNamed|tflagRegularMemory (15), align: 8, fieldAlign: 8, kind: 25, equal: runtime.memequal_varlen, gcdata: *4, str: 9430, ptrToThis: 140736},
sendx: 0,
recvx: 0,
recvq: waitq<time.Time> {
first: *(*sudog<time.Time>)(0xc00013e000),
last: *(*sudog<time.Time>)(0xc00013e000),},
sendq: waitq<time.Time> {
first: *sudog<time.Time> nil,
last: *sudog<time.Time> nil,},
lock: runtime.mutex {
lockRankStruct: runtime.lockRankStruct {},
key: 0,},},
r: time.runtimeTimer {
pp:<PHONE_NUMBER>60,
when:<PHONE_NUMBER>42503,
period: 1000000,
f: time.sendTime,
arg: interface {}(chan time.Time) *(*interface {})(0xc0004820c8),
seq: 0,
nextwhen: 0,
status: 1,},}
print status of the p that the timer was added to, which shows the p is dead
(dlv) print (*runtime.p)(824633896960).status
4
(dlv) print (*runtime.p)(824633896960).timers
[]*runtime.timer len: 1, cap: 1, [
*{
pp:<PHONE_NUMBER>60,
when:<PHONE_NUMBER>42503,
period: 1000000,
f: time.sendTime,
arg: interface {}(chan time.Time) *(*interface {})(0xc0004820c8),
seq: 0,
nextwhen: 0,
status: 1,},

If I'm reading this issue correctly, it is already fixed.  Should we just close it?

I think it's fixed, but it would be great if someone who knows the timer code more closely can verify that https://go-review.googlesource.com/c/go/+/300610/ fixes this. I haven't been able to reproduce this, but don't know the code well enough to confirm that it's definitely fixed.
I'm not sure if this is possible or is worth doing, but I would have liked to see something like this mentioned in the 1.16.3 release notes, since it's not just that a timer doesn't fire for 2 minutes, but a timer may never fire.

Yes, it seems plausible that CL 300610 will fix this problem.
I think it's quite rare that people reduce GOMAXPROCS while a program is running; I don't think this is the kind of thing that we would normally put into the release notes.  Certainly we didn't think of this case.

@gopherbot Please open backport to 1.15 branch.

Closing this issue as it is fixed on tip and 1.16 branch.


Would love better ChefSpec Integration

I'm going to see what I can do to get all the snippets added for modern chefspec. It's a bit lacking right now.


Add lround and llround

Only difference between the existing round and these new ones is the deduced return type from lround and llround, and the explicit coersion to long and long-long.

Thanks for being so responsive!  :)
I made the patch quickly and now in hindsight think unit tests could
improve for testing the larger numbers for long and long long by using
computed large numbers based on numeric_limits::max() and min() (minus
some amount), rather than assuming that 6 billion will fit into a long (and
long long).
On Thu, Sep 13, 2018 at 12:46 PM Morwenn<EMAIL_ADDRESS>wrote:

Merged #23 https://github.com/Morwenn/static_math/pull/23 into master.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/Morwenn/static_math/pull/23#event-1844260546, or mute
the thread
https://github.com/notifications/unsubscribe-auth/ASmx7lUwirxBWFP6FIHj0MJN551w4Qnzks5uapnxgaJpZM4WnxwG
.

True enough, feel free to propose another patch if you feel like it might be a problem :)


Changes to follow Godot style guide

Hello, I've made some changes to follow the Godot style guide, mainly adding types, according to #14. Let me know what you think.

Looks good to me. Thanks for your contribution!
Note that, as far as I know there is no difference between var _dot_size := 6.0 and var _dot_size: float = 6.0 since is implicit in the 6.0 that is a float value, so just := should work the same way. Link to documentation on this matter. I'm not 100% sure about this, but is how I think it works.
Thanks again for helping with this project!


Deleting preview manifests from main folder

Signed-off-by: shivamkm07<EMAIL_ADDRESS>Part 2 of PR #82508
Reference: https://github.com/microsoft/winget-pkgs/pull/82508#issuecomment-1268735377

[x] Have you signed the Contributor License Agreement?
[x] Have you checked that there aren't other open pull requests for the same manifest update/change?
[ ] Have you validated your manifest locally with winget validate --manifest <path>?
[ ] Have you tested your manifest locally with winget install --manifest <path>?
[ ] Does your manifest conform to the 1.2 schema?

Note: <path> is the name of the directory containing the manifest you're submitting.

Microsoft Reviewers: Open in CodeFlow

cc @ryfu-msft


Need some help getting started please

Hello,
I think this TimeDimension plugin is pretty neat. However I 'm struggling with getting started with this thing.
Are there any write-ups on what a basic script in its entirety should look like? Things like what I need in my head section. I simply want to display a feature layer that changes location at different points in time.
I appreciate any help you willing to give.
Thanks!

Hey @JRosh33 ,
checkout the Leaflet TimeDimension Demos http://apps.socib.es/Leaflet.TimeDimension/examples/

Hi @trillerpfeife , I'm aware of those demos and attempted to copy and paste their code into an html file and  modify it. However, I can't even get the map div to pop up when I open it in either chrome or firefox. I'm honestly looking for just the most bare-bones example someone can give me.

@JRosh33 did you clone the examples folder?

Well cloning it did the trick. This is a good starting point. Thanks @trillerpfeife

Any idea how to prep data in a feature layer on a WMS? For example how do I specify my time attribute?


Support changing icons for non-Steam shortcuts

Possible implementation:

User boops a non-Steam icon.
Shortcut is selected from popup.
Save icon as Steam/userdata/XXXXXXXX/config/grid/APPID_icon.ext (path can actually be anywhere, but SRM and other programs unofficially save in this path already)
Add or edit the icon key in shortcuts.vdf to point to the saved icon location.

Progress done in nonsteam-icons. Requires more review/testing due to the possibility of severely messing up shortcuts.vdf.

Not working on my end with latest version


automate creation of map of SDK->API versions

Can we automate creation of the columns in this table: https://github.com/joshgav/azure-sdk-for-go/blob/a0b7692b68da4717dd98ceaa4a325afb5ed743ef/SERVICES.md, perhaps as part of profileBuilder? I think we'll need a column for each SDK version which includes supported API versions in that SDK version.
cc @marstr @sptramer

That would be pretty straight-forward. @jhendrixMSFT and I have talked a few times about how we could add a makefile or equivalent. This work item would fit in nicely with that effort.


Unexpected transformation of NamedNulls into AbstractConstants during reasoning

Hi,
I am using VLog through your Java adapter with the goal of enumerating homomorphisms, which essentially works.  However, I recognized that, during reasoning, instances of NamedNull occurring in a knowledge base will be transformed into instances of AbstractConstant.  The situation can be reproduced by means of the following steps:

Create or parse an instance kb of KnowledgeBase in which instances of NamedNull occur.
Initialize an instance reasoner of VLogReasoner with argument kb.
Call reasoner.reason().
Walk through reasoner.getInferences(), which does not contain the facts in kb anymore but rather copies of them where each instance of NamedNull is replaced by an according instance of AbstractConstant.

I already had a short conversation with @mmarx and he explained that this happens due to skolemization, and he advised me to open an issue report here.
In my humble opinion, I would rather expect the chase to be a superset of the given knowledge base.  Furthermore---please correct me if I am wrong---I interpret a constant as an object entity with a fixed, known name and a null as an object entity without a name (but which we give an internal name within implementations to make them accessible)---in that sense I find it problematic to transform nulls into constants, since a name for an object entity without a known name is just invented, which seems to be logically wrong, and further since it gets difficult to recognize which fresh abstract constant was introduced for a named null in the input.  Of course, there is an easy workaround by just using abstract constants and storing those that one considers as nulls in a set, but then the distinction between constants and nulls by the datatype is lost.
Thanks in advance for your reaction.
Best regards,
Francesco

VLog does not support named nulls in syntactic inputs. Rulewerk allows them on the Java level, since inferred facts may contain nulls. If nulls are also used in input data, Rulewerk will skolemize them for you before sending them to VLog (rather than just throwing an error).
In general, it is not recommended to use nulls in input data. They have no advantage over constants, but several disadvantages:

Nulls semantically correspond to existentially quantified variables, and therefore can (and will) change names in several situations during syntactic transformations that require variable renaming, potentially confusing users.
According to their semantics, the meaning of named nulls depends on the scope of the existential quantifier that binds them. Since this quantifier is usually implicit, it can lead to unexpected behaviour (e.g., that nulls of the same name in two different files will be renamed apart upon loading).
There is no way to refer to a specific named null in a query (since query and KB do not share quantifier scopes),  making it hard to query for features of specific nulls.

I am not sure what the resolution to this bug should be. Maybe some documentation to help users understand the expected behaviour? We could also throw an exception when users try to give nulls in inputs to VLog, but I am not really in favour of this.

I am also unsure what the solution to this bug could be.  Specifically, I think that it depends on the point of view.
For our prototypical implementation of an ABox repair approach [2], we employ the latter point of view.  As datasets we use so-called "quantified ABoxes" [1], which are essentially ABoxes with variables (anonymous individuals).  As a starting point for constructing the actual repair, we use the so-called CQ-saturation, which is essentially the chase of the ABox w.r.t. the TBox.  Exactly for this purpose we are using your code.  However, for correctness of the repair it is essential that there is a clear distinction between the constants (named individuals) and the nulls (variables, anonymous individuals).  This distinction is lost due to skolemization.
In essence, skolemization of such a quantified ABox would produce a conservative extension w.r.t. individual names, which might logically be fine if this is expected behaviour, but skolemization does not produce a logical consequence.  For instance the dataset { A(x) } where x is a null does not entail its skolemization { A(a) } where a is a fresh constant.  Since we require that a repair is a logical consequence of the input dataset, we can thus not rely on the skolemization and its chase without further ado.
As I already wrote in my first comment, I would expect that the chase is a superset of the input dataset.
Documenting this behaviour will definitely help, maybe also writing a warning message to the logger if the input contains nulls or even crashing in such cases.
As a workaround in the cases where the user expects that the chase is a logical consequence of the given dataset plus the given ruleset, either the developer using your code could take care of the transformation of nulls to constants and do the back-transformation afterwards herself/himself, or Rulewerk could maintain a map from the nulls to the according Skolem constants and do the back-transformation before the chase is returned.
--
References:
[1] Franz Baader, Francesco Kriegel, Adrian Nuradiansyah, and Rafael Peñaloza: Computing Compliant Anonymisations of Quantified ABoxes w.r.t. EL Policies. ISWC 2020. https://lat.inf.tu-dresden.de/research/papers/2020/BaKrNuPe-ISWC2020.pdf
[2] Franz Baader, Patrick Koopmann, Francesco Kriegel, and Adrian Nuradiansyah: Computing Optimal Repairs of Quantified ABoxes w.r.t. Static EL TBoxes (Extended Version). LTCS-Report 21-01. https://lat.inf.tu-dresden.de/research/reports/2021/BaKoKrNu-LTCS-21-01.pdf


Fixed path error for test Grunt task

When starting a new project (yo react-webpack), and trying to test the application right away, we got an error.
It comes from wrong path in the test Grunt task.

@Anomen thanks


Error during auth because I don't have X11 server

I'm trying to run the graph in a digital ocean droplet, so it doesn't have any GUI.
When I run auth, I get an error:
$  graph auth https://api.thegraph.com/deploy/ <token>
Error: Error storing access token with libsecret (usually gnome-keyring or ksecretservice): Error: Cannot autolaunch D-Bus without X11 $DISPLAY
    at saveAccessToken (/home/ubuntu/node/lib/node_modules/@graphprotocol/graph-cli/src/command-helpers/auth.js:70:13)

Graph CLI uses node-keytar for storing access tokens natively. On Linux this requires D-Bus and a libsecret service, which it is trying to auto-launch in your case.
You may be able to run graph auth inside dbus-launch to avoid the auto-launch/X11 problem. We do this for CI as well: https://github.com/graphprotocol/graph-cli/blob/master/.travis.yml

Let us know if it works for you. If it does, we'll add it to our docs.

python-gnomekeyring is no longer in Ubuntu 18.04, so I'm not sure how to run that step.

I am facing the same problem!

Me too!
I get the error: ```
Could not get access token from libsecret (usually gnome-keyring or ksecretservice): Cannot autolaunch D-Bus without X11 $DISPLAY
Continuing without an access token
✖ HTTP error creating the subgraph: ECONNRESET

This issue can be circumvented by passing the access token through the CLI with --access-token <token>.

Where do I get the access token @leoyvens ?

Running graph auth https://api.thegraph.com/deploy/ <ACCESS_TOKEN>  gives the same issue
Error: Error storing access token with libsecret (usually gnome-keyring or ksecretservice): Error: Cannot autolaunch D-Bus without X11 $DISPLAY     at saveAccessToken (/home/fred/.nvm/versions/node/v10.15.1/lib/node_modules/@graphprotocol/graph-cli/src/command-helpers/auth.js:70:13)

Fixed with:
graph deploy --access-token YOUR_TOKEN \
    --debug \
    --node https://api.thegraph.com/deploy/ \
    --ipfs https://api.thegraph.com/ipfs/ \
    <GITHUB_USERNAME>/<SUBGRAPH_NAME>

This works perfectly, thanks!

Fixed with:
graph deploy --access-token YOUR_TOKEN \
    --debug \
    --node https://api.thegraph.com/deploy/ \
    --ipfs https://api.thegraph.com/ipfs/ \
    <GITHUB_USERNAME>/<SUBGRAPH_NAME>

This works perfectly, thanks!

closing as similar to https://github.com/graphprotocol/graph-tooling/issues/569


Could it use one sentence to search google?

Could it use one sentence to search google except a word?

When running runtest, all tests failed


Issue counting components

Issue originally reported by @Kryssie in Discord:
I have found a strange issue, adding multiple entities with textshape and billboard blows up the component count on the scene adding hundreds of extra components out of nowhere
I wanted to make sure I was on the current of everything before reporting it so I updated and its still happening
let a = new Entity();
a.addComponent(new Transform({position: new Vector3(7, 1, 8)});
a.addComponent(new TextShape("a"));
a.addComponent(new Billboard());
engine.addEntity(a);

let b = new Entity();
b.addComponent(new Transform({position: new Vector3(8, 1, 8)});
b.addComponent(new TextShape("b"));
b.addComponent(new Billboard());
engine.addEntity(b);

let c = new Entity();
c.addComponent(new Transform({position: new Vector3(9, 1, 8)});
c.addComponent(new TextShape("c"));
c.addComponent(new Billboard());
engine.addEntity(c);

this creates a component count of 110, if I remove one of the sections the component count is 17
the project I am working on has 2 billboard/textshapes and that creates a component count over 600 for some reason, removing one of the text shapes drops the count to around 70
it also happens (and is sometimes worse) if I use one billboard object for all the entities, not sure there is a reason to make a new one for each entity or not

Issue with SDK6


Should not this be a branch?

https://github.com/nephila/giturlparse/blob/a6b48dad230d43393227ffdf52f2099db8038622/giturlparse/tests/test_parse.py#L381
    from giturlparse import parse as giturlparse
    p = giturlparse("https://github.com/nephila/giturlparse/tree/master/changes")
    print (p.branch, p.path)
    assert p.branch == "master"
    assert p.path == "changes"

@feliam The url you're referring to in test_parse.py is https://github.com/nephila/giturlparse/blob/master/giturlparse/github.py , but you did test https://github.com/nephila/giturlparse/tree/master/changes , that is a different url.
Or am I missing something here?


Edit button does not work anymore for tasks in my challenge

I have a challenge with ~ 16 000 tasks in it - link to challenge.
Everything used to work fine with the challenge, as I have solved a number of tasks myself to make sure of it. However, recently the Edit button has stopped working for tasks. Instead of opening the task in the preferred OSM editor, it just gets stuck in loading.
The only thing I have noticed in between the last time the button was working and the time it stopped working is that the MapRoulette website was down for a day (possibly for maintenance or version update).

Thanks for the report, @imajic-unimelb . This is fixed by PR #1028 in version 3.5.2, which will likely be deployed to maproulette.org early this week.

Deployment is complete, so this should be fixed on maproulette.org now.

@nrotstan I can confirm the problem is now fixed for my challenge in maproulette.org! Thanks :)


Domain to Module Route

I want to point a domain module.com to https://domain.com/module
Any tips on how to do it properly?
This is a microsite of the domain that uses mvc (not just plain html) so I guess it's justifiable that I can just create a module for that particular microsite and point the domain to that route.

You'd achieve that through your server configuration and DNS - not through anything the package provides.


W/cr_BindingManager: Cannot call determinedVisibility()

same error with webview

You get the same error (on the same page) with Android's built-in WebView?

dear ocram,
thanks for reply, looks like something miss on my code or maybe else...
topology is not direct to main page:
apps => myserver.com => company.payment.gateway => payment.provider.checkout
I think in "company.payment.gateway" there some cookie/session that should be stored, so when another redirect to "payment.provider.checkout" its rejected...
and now I'm using chrometabs to achieve that

@ntaloventi Thank you!
Does that mean this issue is obsolete? If you switched to a solution using custom Chrome tabs, we cannot re-produce this problem anymore, I guess, and you don't mind anymore.
Custom Chrome tabs are, of course, not an equivalent solution. Sometimes they're better, sometimes they're worse. They serve slightly different purposes.
Both cookies in general and third-party cookies can be disabled with this library, but they should be enabled by default.


Fix format-modified script

Before it was only updating non-staged files.
Now it updates all modified files, staged or not.

Codecov Report

Merging #2708 into canary will decrease coverage by 0.04%.
The diff coverage is n/a.

@@            Coverage Diff            @@
##           canary   #2708      +/-   ##
=========================================
- Coverage    8.21%   8.17%   -0.05%
=========================================
  Files         260     260
  Lines       10513   10485      -28
  Branches     1341    1339       -2
=========================================
- Hits          864     857       -7
+ Misses       9591    9570      -21
  Partials       58      58

Impacted Files
Coverage Δ

src/util/dev/builder-cache.ts
39.48% <0%> (-0.42%)
:arrow_down:

src/util/get-files.ts
87.07% <0%> (+0.81%)
:arrow_up:

src/util/output/create-output.ts
29.54% <0%> (+2.46%)
:arrow_up:

src/util/dev/router.ts
80.3% <0%> (+4.58%)
:arrow_up:

src/util/metrics.ts
68.18% <0%> (+6.64%)
:arrow_up:

src/util/prefer-v2-deployment.ts
69.44% <0%> (+6.94%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 24a3b99...b8c15e6. Read the comment docs.


cloudlog: 2.6.10 -> 2.6.11

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for cloudlog is: Web based amateur radio logging application built using PHP & MySQL
meta.homepage for cloudlog is: https://www.magicbug.co.uk/cloudlog
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.6.11 with grep in /nix/store/mwdyz2hrrrjk73pnz4xp2nh6h0n5gmr3-cloudlog-2.6.11
found 2.6.11 in filename of file in /nix/store/mwdyz2hrrrjk73pnz4xp2nh6h0n5gmr3-cloudlog-2.6.11

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

cloudlog

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/mwdyz2hrrrjk73pnz4xp2nh6h0n5gmr3-cloudlog-2.6.11 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A cloudlog https://github.com/r-ryantm/nixpkgs/archive/afa11c824b219e86b7d43c5539d155a0a245b6a3.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/afa11c824b219e86b7d43c5539d155a0a245b6a3#cloudlog

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/mwdyz2hrrrjk73pnz4xp2nh6h0n5gmr3-cloudlog-2.6.11
ls -la /nix/store/mwdyz2hrrrjk73pnz4xp2nh6h0n5gmr3-cloudlog-2.6.11/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review --extra-nixpkgs-config '{ allowInsecurePredicate = x: true; }' run on x86_64-linux 1

1 package built:

cloudlog

Maintainer pings
cc @mattmelling for testing.

Result of nixpkgs-review pr 311229 run on x86_64-linux 1

1 package built:

cloudlog


Is there any plan of making an OpenCL accelerated version for non-CUDA users?

The CUDA implementation is amazing, but for systems that don't have Nvidia GPU's are there any plans of making an (expectably much slower) more general implementation?

To do that well would be a massive undertaking.  The shortcut approach is to replace the CPU's matrix operations with OpenCL accelerated versions which in theory might require minimal effort.  I plan at some point to do this to take advantage of Apple's Neural Engine and can look into doing it for OpenCL as well, but this isn't a high priority.  Contributions are always welcome.


update stream relative, fix mtd&blk stream readback before block update. decrese int use in stream to handle FS_LARGEFILE

Summary
int is not reliable when we use same code for cross platform.
replace with off_t,size_t,ssize_t should prefer.
offset int -> offset, len int -> size_t, ret int -> ssize_t
Also we should readback sector/block before operate to new sector/block,
for user only update partial case.
Impact
stream will able to support FS_LARGEFILE better cover >4GB devices.
if user use blk/mtd stream to update partial, the old data will be kept back.
Testing
CI-test, local arm-v8m prject, qemu-armv8a, ubutun sim:nsh

[Experimental Bot, please feedback here]
Yes, this PR appears to meet the NuttX requirements, although the provided information is minimal.  It would be stronger with more detail. Here's a breakdown:
Strengths:

Clear Summary of "Why": Explains the motivation for the change (cross-platform compatibility and partial update handling).
Functional Change Description: Identifies the affected code (int to off_t/size_t/ssize_t) and the readback mechanism.
Impact on User/Features: Briefly mentions improved large file support and data preservation.
Testing Performed: Lists tested platforms (CI, ARMv8-M, qemu, Ubuntu sim).

Weaknesses & Missing Information:

No Issue References: Missing links to related NuttX issues.  Even if there isn't a directly related issue, creating one beforehand is good practice.
Impact Details Lacking: The "Impact" section needs significant expansion.  While "YES" is stated for user and feature impact, the descriptions are very brief. More details are needed for all impact categories (build, hardware, documentation, security, compatibility).  Be explicit about any potential breaking changes.  For example, does the change to size_t and off_t affect any existing drivers or applications?  If documentation is required, state whether it's included in the PR.
Vague Testing Logs:  Providing actual log snippets is crucial. "CI-test" is insufficient – link to the CI run.  Include specific commands used and relevant output demonstrating the issue before the change and the corrected behavior afterward.  Quantify the improvements if possible (e.g., "Successfully wrote a 5GB file," "Partial update preserved data from previous sectors X to Y").
Build Host Details Missing: Specify your development environment in the "Testing" section as requested by the template (OS, CPU, compiler versions).

Recommendation:
While the core elements are present, this PR description needs more detail to ensure thorough review and avoid potential problems. Expand the "Impact" and "Testing" sections considerably, providing concrete examples and data.  Add issue references.  A more detailed PR will increase confidence in the changes and streamline the review process.

has the test fail:
https://github.com/apache/nuttx/actions/runs/11830852498/job/32965096269?pr=14778