Fatal error: atac_dnase_pipelines/modules/sys.bds, line 143, pos 2. Exec failed.

Hi,
I am trying to run ATAC-seq pipeline. At the step of   bds atac.bds...  error like that:
Fatal error: /root/atac_dnase_pipelines/modules/sys.bds, line 143, pos 2. Exec failed.
Exit value : 1
Command    :  hostname -f 1> /root/data/12/cmd_-4215330719029919960
git.bds, line 4 :	include "sys.bds"
sys.bds, line 4 :	include "string.bds"
sys.bds, line 21 :	init_base()
sys.bds, line 24 :	void init_base() {
sys.bds, line 29 :		hostname 	= get_hostname()
sys.bds, line 175 :	string get_hostname() {
sys.bds, line 176 :		return get_stdout("hostname -f").replace("\n","")
sys.bds, line 140 :	string get_stdout( string cmd ) {
sys.bds, line 143 :		sys $cmd 1> $cmd_

Please post a full error log. Did you run pipeline in a docker container?
Jin
On Sun, Nov 5, 2017 at 10:49 PM, yeouyang<EMAIL_ADDRESS>wrote:

Hi,
I am trying to run ATAC-seq pipeline. At the step of bds atac.bds... error
like that:
Fatal error: /root/atac_dnase_pipelines/modules/sys.bds, line 143, pos 2.
Exec failed.
Exit value : 1
Command : hostname -f 1> /root/data/12/cmd_-4215330719029919960
git.bds, line 4 : include "sys.bds"
sys.bds, line 4 : include "string.bds"
sys.bds, line 21 : init_base()
sys.bds, line 24 : void init_base() {
sys.bds, line 29 : hostname = get_hostname()
sys.bds, line 175 : string get_hostname() {
sys.bds, line 176 : return get_stdout("hostname -f").replace("\n","")
sys.bds, line 140 : string get_stdout( string cmd ) {
sys.bds, line 143 : sys $cmd 1> $cmd_
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hostname: Name or service not known
Fatal error: /root/atac_dnase_pipelines/modules/sys.bds, line 143, pos 2. Exec failed.
Exit value : 1
Command    :  hostname -f 1> /root/data/12/cmd_-4215330719029919960
git.bds, line 4 :	include "sys.bds"
sys.bds, line 4 :	include "string.bds"
sys.bds, line 21 :	init_base()
sys.bds, line 24 :	void init_base() {
sys.bds, line 29 :		hostname 	= get_hostname()
sys.bds, line 175 :	string get_hostname() {
sys.bds, line 176 :		return get_stdout("hostname -f").replace("\n","")
sys.bds, line 140 :	string get_stdout( string cmd ) {
sys.bds, line 143 :		sys $cmd 1> $cmd_
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
Not in container, and all things is here.

Can you try the following command lines for debugging info?
$ hostname
$ hostname -f
$ cat /etc/hosts
Jin
On Sun, Nov 5, 2017 at 11:34 PM, yeouyang<EMAIL_ADDRESS>wrote:

hostname: Name or service not known
Fatal error: /root/atac_dnase_pipelines/modules/sys.bds, line 143, pos 2.
Exec failed.
Exit value : 1
Command : hostname -f 1> /root/data/12/cmd_-4215330719029919960
git.bds, line 4 : include "sys.bds"
sys.bds, line 4 : include "string.bds"
sys.bds, line 21 : init_base()
sys.bds, line 24 : void init_base() {
sys.bds, line 29 : hostname = get_hostname()
sys.bds, line 175 : string get_hostname() {
sys.bds, line 176 : return get_stdout("hostname -f").replace("\n","")
sys.bds, line 140 : string get_stdout( string cmd ) {
sys.bds, line 143 : sys $cmd 1> $cmd_
Creating checkpoint file: Config or command line option disabled
checkpoint file creation, nothing done.
Not in container, and all things is here.
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Can you modify module/sys.bds and try again?
Replace
string get_hostname() {
return get_stdout("hostname -f").replace("\n","")
}
with
string get_hostname() {
out := get_stdout("hostname -f || true").replace("\n","")
if (out.startsWith("hostname: ")) return "unknown"
else return out
}
Please let me know if this works so that I can make a hot fix for it.
Thanks,
Jin
On Sun, Nov 5, 2017 at 11:42 PM, Jin<EMAIL_ADDRESS>wrote:

Can you try the following command lines for debugging info?
$ hostname
$ hostname -f
$ cat /etc/hosts
Jin
On Sun, Nov 5, 2017 at 11:34 PM, yeouyang<EMAIL_ADDRESS>wrote:

hostname: Name or service not known
Fatal error: /root/atac_dnase_pipelines/modules/sys.bds, line 143, pos
2. Exec failed.
Exit value : 1
Command : hostname -f 1> /root/data/12/cmd_-4215330719029919960
git.bds, line 4 : include "sys.bds"
sys.bds, line 4 : include "string.bds"
sys.bds, line 21 : init_base()
sys.bds, line 24 : void init_base() {
sys.bds, line 29 : hostname = get_hostname()
sys.bds, line 175 : string get_hostname() {
sys.bds, line 176 : return get_stdout("hostname -f").replace("\n","")
sys.bds, line 140 : string get_stdout( string cmd ) {
sys.bds, line 143 : sys $cmd 1> $cmd_
Creating checkpoint file: Config or command line option disabled
checkpoint file creation, nothing done.
Not in container, and all things is here.
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Sorry for late. I tried your advice, and error like this:
hostname: Name or service not known
== git info
Latest git commit		: 05a35648a5883f4383ad83db9d2c5c126aaf7aac (Mon Nov 6 07:50:02 2017)
== configuration file info
Hostname			:
Configuration file		:
Environment file		: /root/atac_dnase_pipelines/default.env
== parallelization info
No parallel jobs		: false
Maximum # threads 		: 8
== cluster/system info
Walltime (general)		: 5h50m
Max. memory (general)		: 7G
Force to use a system		: local
Process priority (niceness)	: 0
Retiral for failed tasks	: 0
Submit tasks to a cluster queue	:
Unlimited cluster mem./walltime	: false
Java temporary directory		: ${TMPDIR}
Info: Environments module not found on your system (e.g. /etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info
Conda env. 			:
Conda env. for python3		:
Conda bin. directory		:
Shell cmd. for init.		:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3)	:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin.		: TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len.		: 60
Cluster task delay			: 0
== output directory/title info
Output dir.			: /root/data/12/out
Title (prefix)			: 12
== species settings
Species				:
Species file			:
Species name (WashU browser)	:
Ref. genome seq. fasta		:
Chr. sizes file			:
Black list bed			:
Ref. genome seq. dir.		:
== ENCODE accession settings
ENCODE experiment accession	:
ENCODE award RFA			:
ENCODE assay category		:
ENCODE assay title		:
ENCODE award				:
ENCODE lab				:
ENCODE assembly genome		:
ENCODE alias prefix		: KLAB_PIPELINE
ENCODE alias suffix		:
== report settings
URL root for output directory	:
Genome coord. for browser tracks	:
== align multimapping settings
alignments reported for multimapping	: 0
== align bowtie2 settings
Bowtie2 index			:
Replacement --score-min for bowtie2	:
Walltime (bowtie2)		: 47h
Max. memory (bowtie2)		: 12G
Extra param. (bowtie2)		:
== adapter trimmer settings
Maximum allowed error rate for cutadapt	: 0.10
Minimum trim. length for cutadapt -m	: 5
Walltime (adapter trimming)		: 23h
Max. memory (adapter trimming)		: 12G
== postalign bam settings
MAPQ reads rm thresh.		: 30
Rm. tag reads with str.		:
No dupe removal in filtering raw bam	: false
Walltime (bam filter)		: 23h
Max. memory (bam filter)	: 12G
Dup marker				: picard
Use sambamba markdup (instead of picard)	: false
== postalign bed/tagalign settings
Max. memory for UNIX shuf			: 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf			: 12G
User-defined cross-corr. peak strandshift	: -1
Extra parameters for cross-corr. analysis	:
== callpeak macs2 settings
Genome size (hs,mm)		:
Walltime (macs2)		: 23h
Max. memory (macs2)		: 15G
Extra parameters for macs2 callpeak		:
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck	: false
== callpeak etc settings
of top peaks to pick up in peak files	: 500000
== IDR settings
Append IDR threshold to IDR out_dir	: false
== ATAQC settings
TSS enrichment bed		:
DNase bed for ataqc		:
Promoter bed for ataqc		:
Enhancer bed for ataqc		:
Reg2map for ataqc			:
Reg2map_bed for ataqc		:
Roadmap metadata for ataqc	:
Max. memory for ATAQC			: 20G
Walltime for ATAQC			: 47h
== atac pipeline settings
Type of pipeline			: atac-seq
Align only				: false
reads to subsample replicates (0 if no subsampling)	: 0
reads to subsample for cross-corr. analysis 	: 25000000
No pseudo replicates			: false
No ATAQC (advanced QC report)		: false
No Cross-corr. analysis			: false
Use CSEM for alignment			: false
Smoothing window for MACS2		: 150
DNase Seq				: false
IDR threshold				: 0.1
Force to use ENCODE3 parameter set	: false
Force to use ENCODE parameter set	: false
Disable genome browser tracks	: false
p-val thresh. for overlapped peaks	: 0.01
MACS2 p-val thresh. for peaks	: 0.01
MACS2 p-val thresh. for BIGWIGs		: 0.01
Enable IDR on called peaks	: false
Automatically find/trim adapters	: false
== checking atac parameters ...
00:00:00.249	Error (/root/atac_dnase_pipelines/modules/align_bowtie2.bds, line 41, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)

Can you try the following commands for more debugging info?
$ cat /root/atac_dnase_pipelines/default.env
Did you install genome data (
https://github.com/kundajelab/atac_dnase_pipelines#genome-data) and specify
species in the command line (e.g. -species hg38)?
Jin
On Mon, Nov 6, 2017 at 12:28 AM, yeouyang<EMAIL_ADDRESS>wrote:

Sorry for late. I tried your advice, and error like this:
hostname: Name or service not known
== git info
Latest git commit : 05a3564
https://github.com/kundajelab/atac_dnase_pipelines/commit/05a35648a5883f4383ad83db9d2c5c126aaf7aac
(Mon Nov 6 07:50:02 2017)
== configuration file info
Hostname :
Configuration file :
Environment file : /root/atac_dnase_pipelines/default.env
== parallelization info
No parallel jobs : false
Maximum # threads : 8
== cluster/system info
Walltime (general) : 5h50m
Max. memory (general) : 7G
Force to use a system : local
Process priority (niceness) : 0
Retiral for failed tasks : 0
Submit tasks to a cluster queue :
Unlimited cluster mem./walltime : false
Java temporary directory : ${TMPDIR}
Info: Environments module not found on your system (e.g.
/etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info
Conda env. :
Conda env. for python3 :
Conda bin. directory :
Shell cmd. for init. : export PATH=/root/atac_dnase_
pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_
dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3) : export PATH=/root/atac_dnase_
pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_
dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has
finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info
Output dir. : /root/data/12/out
Title (prefix) : 12
== species settings
Species :
Species file :
Species name (WashU browser) :
Ref. genome seq. fasta :
Chr. sizes file :
Black list bed :
Ref. genome seq. dir. :
== ENCODE accession settings
ENCODE experiment accession :
ENCODE award RFA :
ENCODE assay category :
ENCODE assay title :
ENCODE award :
ENCODE lab :
ENCODE assembly genome :
ENCODE alias prefix : KLAB_PIPELINE
ENCODE alias suffix :
== report settings
URL root for output directory :
Genome coord. for browser tracks :
== align multimapping settings
alignments reported for multimapping : 0
== align bowtie2 settings
Bowtie2 index :
Replacement --score-min for bowtie2 :
Walltime (bowtie2) : 47h
Max. memory (bowtie2) : 12G
Extra param. (bowtie2) :
== adapter trimmer settings
Maximum allowed error rate for cutadapt : 0.10
Minimum trim. length for cutadapt -m : 5
Walltime (adapter trimming) : 23h
Max. memory (adapter trimming) : 12G
== postalign bam settings
MAPQ reads rm thresh. : 30
Rm. tag reads with str. :
No dupe removal in filtering raw bam : false
Walltime (bam filter) : 23h
Max. memory (bam filter) : 12G
Dup marker : picard
Use sambamba markdup (instead of picard) : false
== postalign bed/tagalign settings
Max. memory for UNIX shuf : 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf : 12G
User-defined cross-corr. peak strandshift : -1
Extra parameters for cross-corr. analysis :
== callpeak macs2 settings
Genome size (hs,mm) :
Walltime (macs2) : 23h
Max. memory (macs2) : 15G
Extra parameters for macs2 callpeak :
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck : false
== callpeak etc settings
of top peaks to pick up in peak files : 500000
== IDR settings
Append IDR threshold to IDR out_dir : false
== ATAQC settings
TSS enrichment bed :
DNase bed for ataqc :
Promoter bed for ataqc :
Enhancer bed for ataqc :
Reg2map for ataqc :
Reg2map_bed for ataqc :
Roadmap metadata for ataqc :
Max. memory for ATAQC : 20G
Walltime for ATAQC : 47h
== atac pipeline settings
Type of pipeline : atac-seq
Align only : false
reads to subsample replicates (0 if no subsampling) : 0 reads to
subsample for cross-corr. analysis : 25000000
No pseudo replicates : false
No ATAQC (advanced QC report) : false
No Cross-corr. analysis : false
Use CSEM for alignment : false
Smoothing window for MACS2 : 150
DNase Seq : false
IDR threshold : 0.1
Force to use ENCODE3 parameter set : false
Force to use ENCODE parameter set : false
Disable genome browser tracks : false
p-val thresh. for overlapped peaks : 0.01
MACS2 p-val thresh. for peaks : 0.01
MACS2 p-val thresh. for BIGWIGs : 0.01
Enable IDR on called peaks : false
Automatically find/trim adapters : false
== checking atac parameters ...
00:00:00.249 Error (/root/atac_dnase_pipelines/modules/align_bowtie2.bds,
line 41, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or
.1.bt2l)
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I have install hg19 and built index.
Get hostname with the following command:
$ hostname -f

Configure environment per hostname:
[hostname1]
...

Use the same environment for multiple hostnames:
[hostname2, hostname3, ...]
...

Using group
[hostname1, hostname2, ... : group]
[group]
...

Using an asterisk in hostnames (IMPORTANT: only one * is allowed in hostnames)

[host*name1]

[hostname2, hostname3]
Stanford Kundaje group clusters (out of SGE)
[vayu, mitra, durga]
conda_env	= bds_atac
conda_env_py3	= bds_atac_py3
conda_bin_dir	= /software/miniconda3/bin
species_file	= $script_dir/species/kundaje.conf
unlimited_mem_wt= true 		# unlimited max. memory and walltime on Kundaje clusters
nice 		= 20
nth 		= 3
Stanford Kundaje group clusters (controlled with SGE)
[nandi, kali, amold, wotan, kadru, surya, indra]
conda_env	= bds_atac
conda_env_py3	= bds_atac_py3
conda_bin_dir	= /software/miniconda3/bin
species_file	= $script_dir/species/kundaje.conf
unlimited_mem_wt= true 		# unlimited max. memory and walltime on Kundaje clusters
system 		= sge
nice 		= 20
nth 		= 3
Stanford SCG4
[scg*.stanford.edu, scg*.local, carmack.stanford.edu, crick.stanford.edu]
conda_env	= bds_atac
conda_env_py3	= bds_atac_py3
conda_bin_dir   = /ifs/scratch/leepc12/sw/miniconda3/bin
species_file	= $script_dir/species/scg.conf
nth		= 4		# number of threads for each pipeline
system		= sge		# force to use SGE (Sun Grid Engine) on SCG3/4 even though a user doesn't explicitly specify SGE on command line with 'bds -s sge atac.bds ...'
cluster_task_delay = 10 	# for NFS delayed write
Stanford Sherlock clusters
[sherlock*.stanford.edu, sh-.local, sh-.int, sh-ln*.stanford.edu]
conda_env	= bds_atac
conda_env_py3	= bds_atac_py3
conda_bin_dir   = /scratch/users/leepc12/bds_pipeline_software/miniconda3/bin
species_file	= $script_dir/species/sherlock.conf
nth		= 4		# number of threads for each pipeline
system		= slurm
cluster_task_delay = 30		# for NFS delayed write
default
[default]
conda_env	= bds_atac
conda_env_py3	= bds_atac_py3
conda_bin_dir   =
species_file	= /root/data/bds_pipeline_genome_data/bds_atac_species.conf	# DEF_SPECIES_FILE: DO NOT MODIFY THIS COMMENT (install_genome_data.sh WILL NOT WORK).

What was your command line to run the pipeline?
On Mon, Nov 6, 2017 at 12:41 AM, yeouyang<EMAIL_ADDRESS>wrote:

I have install hg19 and built index.
Get hostname with the following command: $ hostname -f Configure
environment per hostname: [hostname1] ... Use the same environment for
multiple hostnames: [hostname2, hostname3, ...] ... Using group [hostname1,
hostname2, ... : group] [group] ... Using an asterisk in hostnames
(IMPORTANT: only one * is allowed in hostnames) [host*name1] [hostname2,
hostname3] Stanford Kundaje group clusters (out of SGE)
[vayu, mitra, durga]
conda_env = bds_atac
conda_env_py3 = bds_atac_py3
conda_bin_dir = /software/miniconda3/bin
species_file = $script_dir/species/kundaje.conf
unlimited_mem_wt= true # unlimited max. memory and walltime on Kundaje
clusters
nice = 20
nth = 3
Stanford Kundaje group clusters (controlled with SGE)
[nandi, kali, amold, wotan, kadru, surya, indra]
conda_env = bds_atac
conda_env_py3 = bds_atac_py3
conda_bin_dir = /software/miniconda3/bin
species_file = $script_dir/species/kundaje.conf
unlimited_mem_wt= true # unlimited max. memory and walltime on Kundaje
clusters
system = sge
nice = 20
nth = 3
Stanford SCG4
[scg*.stanford.edu, scg*.local, carmack.stanford.edu, crick.stanford.edu]
conda_env = bds_atac
conda_env_py3 = bds_atac_py3
conda_bin_dir = /ifs/scratch/leepc12/sw/miniconda3/bin
species_file = $script_dir/species/scg.conf
nth = 4 # number of threads for each pipeline
system = sge # force to use SGE (Sun Grid Engine) on SCG3/4 even though a
user doesn't explicitly specify SGE on command line with 'bds -s sge
atac.bds ...'
cluster_task_delay = 10 # for NFS delayed write
Stanford Sherlock clusters
[sherlock*.stanford.edu, sh-.local, sh-.int, sh-ln*.stanford.edu]
conda_env = bds_atac
conda_env_py3 = bds_atac_py3
conda_bin_dir = /scratch/users/leepc12/bds_pipeline_software/miniconda3/
bin
species_file = $script_dir/species/sherlock.conf
nth = 4 # number of threads for each pipeline
system = slurm
cluster_task_delay = 30 # for NFS delayed write
default
[default]
conda_env = bds_atac
conda_env_py3 = bds_atac_py3
conda_bin_dir =
species_file = /root/data/bds_pipeline_genome_data/bds_atac_species.conf
DEF_SPECIES_FILE: DO NOT MODIFY THIS COMMENT (install_genome_data.sh WILL
NOT WORK).
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bds /root/atac_dnase_pipelines/atac.bds -species hg19 -4 -fastq1_1 R1.fastq.gz -fastq1_2 R2.fastq.gz

Can you remove -4 and try again? What is -4 for?
On Mon, Nov 6, 2017 at 12:45 AM, yeouyang<EMAIL_ADDRESS>wrote:

bds /root/atac_dnase_pipelines/atac.bds -species hg19 -4 -fastq1_1
R1.fastq.gz -fastq1_2 R2.fastq.gz
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Sorry, I remove -4, and still the same error. 4 is regarded as threads.

Yes, you should use -nth 4 instead of -4.
Please replace the following in modules/sys.bds
string get_stdout( string cmd ) {
rnd  := randInt()
cmd_ := "cmd_$rnd".path()
sys $cmd 1> $cmd_
ret := cmd_.read()
sys rm -f $cmd_
return rm_str_at_end(ret,"\n")
}
with
string get_stdout( string cmd ) {
rnd  := randInt()
cmd_ := "cmd_$rnd".path()
sys $cmd 1> $cmd_ || true
ret := cmd_.read()
sys rm -f $cmd_
return rm_str_at_end(ret,"\n")
}
And then try again. Please post a new full log here even if you get the
same error.
Jin
On Mon, Nov 6, 2017 at 12:51 AM, yeouyang<EMAIL_ADDRESS>wrote:

Sorry, I remove -4, and still the same error. 4 is regarded as threads.
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I do the replacement, and error like that:
`hostname: Name or service not known
== git info
Latest git commit		: 05a35648a5883f4383ad83db9d2c5c126aaf7aac (Mon Nov 6 07:50:02 2017)
== configuration file info
Hostname			:
Configuration file		:
Environment file		: /root/atac_dnase_pipelines/default.env
== parallelization info
No parallel jobs		: false
Maximum # threads 		: 4
== cluster/system info
Walltime (general)		: 5h50m
Max. memory (general)		: 7G
Force to use a system		: local
Process priority (niceness)	: 0
Retiral for failed tasks	: 0
Submit tasks to a cluster queue	:
Unlimited cluster mem./walltime	: false
Java temporary directory		: ${TMPDIR}
Info: Environments module not found on your system (e.g. /etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info
Conda env. 			:
Conda env. for python3		:
Conda bin. directory		:
Shell cmd. for init.		:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3)	:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin.		: TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len.		: 60
Cluster task delay			: 0
== output directory/title info
Output dir.			: /root/data/12/out
Title (prefix)			: 12
Reading parameters from section (default) in file(/root/atac_dnase_pipelines/default.env)...
== species settings
Species				: hg19
Species file			:
Species name (WashU browser)	: hg19
Ref. genome seq. fasta		:
Chr. sizes file			:
Black list bed			:
Ref. genome seq. dir.		:
== ENCODE accession settings
ENCODE experiment accession	:
ENCODE award RFA			:
ENCODE assay category		:
ENCODE assay title		:
ENCODE award				:
ENCODE lab				:
ENCODE assembly genome		:
ENCODE alias prefix		: KLAB_PIPELINE
ENCODE alias suffix		:
== report settings
URL root for output directory	:
Genome coord. for browser tracks	:
== align multimapping settings
alignments reported for multimapping	: 0
== align bowtie2 settings
Bowtie2 index			:
Replacement --score-min for bowtie2	:
Walltime (bowtie2)		: 47h
Max. memory (bowtie2)		: 12G
Extra param. (bowtie2)		:
== adapter trimmer settings
Maximum allowed error rate for cutadapt	: 0.10
Minimum trim. length for cutadapt -m	: 5
Walltime (adapter trimming)		: 23h
Max. memory (adapter trimming)		: 12G
== postalign bam settings
MAPQ reads rm thresh.		: 30
Rm. tag reads with str.		:
No dupe removal in filtering raw bam	: false
Walltime (bam filter)		: 23h
Max. memory (bam filter)	: 12G
Dup marker				: picard
Use sambamba markdup (instead of picard)	: false
== postalign bed/tagalign settings
Max. memory for UNIX shuf			: 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf			: 12G
User-defined cross-corr. peak strandshift	: -1
Extra parameters for cross-corr. analysis	:
== callpeak macs2 settings
Genome size (hs,mm)		:
Walltime (macs2)		: 23h
Max. memory (macs2)		: 15G
Extra parameters for macs2 callpeak		:
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck	: false
== callpeak etc settings
of top peaks to pick up in peak files	: 500000
== IDR settings
Append IDR threshold to IDR out_dir	: false
== ATAQC settings
TSS enrichment bed		:
DNase bed for ataqc		:
Promoter bed for ataqc		:
Enhancer bed for ataqc		:
Reg2map for ataqc			:
Reg2map_bed for ataqc		:
Roadmap metadata for ataqc	:
Max. memory for ATAQC			: 20G
Walltime for ATAQC			: 47h
== atac pipeline settings
Type of pipeline			: atac-seq
Align only				: false
reads to subsample replicates (0 if no subsampling)	: 0
reads to subsample for cross-corr. analysis 	: 25000000
No pseudo replicates			: false
No ATAQC (advanced QC report)		: false
No Cross-corr. analysis			: false
Use CSEM for alignment			: false
Smoothing window for MACS2		: 150
DNase Seq				: false
IDR threshold				: 0.1
Force to use ENCODE3 parameter set	: false
Force to use ENCODE parameter set	: false
Disable genome browser tracks	: false
p-val thresh. for overlapped peaks	: 0.01
MACS2 p-val thresh. for peaks	: 0.01
MACS2 p-val thresh. for BIGWIGs		: 0.01
Enable IDR on called peaks	: false
Automatically find/trim adapters	: false
== checking atac parameters ...
00:00:00.211	Error (/root/atac_dnase_pipelines/modules/align_bowtie2.bds, line 41, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)`

Sorry, please replace the following too.
Replace
string get_hostname() {
out := get_stdout("hostname -f || true").replace("\n","")
if (out.startsWith("hostname: ")) return "unknown"
else return out
}
with
string get_hostname() {
out := get_stdout("hostname -f").replace("\n","")
if (out.startsWith("hostname: ")) return "unknown"
else return out
}
Jin
On Mon, Nov 6, 2017 at 1:04 AM, Jin<EMAIL_ADDRESS>wrote:

Yes, you should use -nth 4 instead of -4.
Please replace the following in modules/sys.bds
string get_stdout( string cmd ) {
rnd  := randInt()
cmd_ := "cmd_$rnd".path()
sys $cmd 1> $cmd_
ret := cmd_.read()
sys rm -f $cmd_
return rm_str_at_end(ret,"\n")
}
with
string get_stdout( string cmd ) {
rnd  := randInt()
cmd_ := "cmd_$rnd".path()
sys $cmd 1> $cmd_ || true
ret := cmd_.read()
sys rm -f $cmd_
return rm_str_at_end(ret,"\n")
}
And then try again. Please post a new full log here even if you get the
same error.
Jin
On Mon, Nov 6, 2017 at 12:51 AM, yeouyang<EMAIL_ADDRESS>wrote:

Sorry, I remove -4, and still the same error. 4 is regarded as threads.
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hostname: Name or service not known
== git info
Latest git commit		: 05a35648a5883f4383ad83db9d2c5c126aaf7aac (Mon Nov 6 07:50:02 2017)
== configuration file info
Hostname			:
Configuration file		:
Environment file		: /root/atac_dnase_pipelines/default.env
== parallelization info
No parallel jobs		: false
Maximum # threads 		: 4
== cluster/system info
Walltime (general)		: 5h50m
Max. memory (general)		: 7G
Force to use a system		: local
Process priority (niceness)	: 0
Retiral for failed tasks	: 0
Submit tasks to a cluster queue	:
Unlimited cluster mem./walltime	: false
Java temporary directory		: ${TMPDIR}
Info: Environments module not found on your system (e.g. /etc/profile.d/modules.sh). Ignoring shell env. parameters like '-mod'.
== shell environment info
Conda env. 			:
Conda env. for python3		:
Conda bin. directory		:
Shell cmd. for init.		:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3)	:  export PATH=/root/atac_dnase_pipelines/.:/root/atac_dnase_pipelines/modules:/root/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin.		: TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len.		: 60
Cluster task delay			: 0
== output directory/title info
Output dir.			: /root/data/12/out
Title (prefix)			: 12
Reading parameters from section (default) in file(/root/atac_dnase_pipelines/default.env)...
== species settings
Species				: hg19
Species file			:
Species name (WashU browser)	: hg19
Ref. genome seq. fasta		:
Chr. sizes file			:
Black list bed			:
Ref. genome seq. dir.		:
== ENCODE accession settings
ENCODE experiment accession	:
ENCODE award RFA			:
ENCODE assay category		:
ENCODE assay title		:
ENCODE award				:
ENCODE lab				:
ENCODE assembly genome		:
ENCODE alias prefix		: KLAB_PIPELINE
ENCODE alias suffix		:
== report settings
URL root for output directory	:
Genome coord. for browser tracks	:
== align multimapping settings
alignments reported for multimapping	: 0
== align bowtie2 settings
Bowtie2 index			:
Replacement --score-min for bowtie2	:
Walltime (bowtie2)		: 47h
Max. memory (bowtie2)		: 12G
Extra param. (bowtie2)		:
== adapter trimmer settings
Maximum allowed error rate for cutadapt	: 0.10
Minimum trim. length for cutadapt -m	: 5
Walltime (adapter trimming)		: 23h
Max. memory (adapter trimming)		: 12G
== postalign bam settings
MAPQ reads rm thresh.		: 30
Rm. tag reads with str.		:
No dupe removal in filtering raw bam	: false
Walltime (bam filter)		: 23h
Max. memory (bam filter)	: 12G
Dup marker				: picard
Use sambamba markdup (instead of picard)	: false
== postalign bed/tagalign settings
Max. memory for UNIX shuf			: 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf			: 12G
User-defined cross-corr. peak strandshift	: -1
Extra parameters for cross-corr. analysis	:
== callpeak macs2 settings
Genome size (hs,mm)		:
Walltime (macs2)		: 23h
Max. memory (macs2)		: 15G
Extra parameters for macs2 callpeak		:
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck	: false
== callpeak etc settings
of top peaks to pick up in peak files	: 500000
== IDR settings
Append IDR threshold to IDR out_dir	: false
== ATAQC settings
TSS enrichment bed		:
DNase bed for ataqc		:
Promoter bed for ataqc		:
Enhancer bed for ataqc		:
Reg2map for ataqc			:
Reg2map_bed for ataqc		:
Roadmap metadata for ataqc	:
Max. memory for ATAQC			: 20G
Walltime for ATAQC			: 47h
== atac pipeline settings
Type of pipeline			: atac-seq
Align only				: false
reads to subsample replicates (0 if no subsampling)	: 0
reads to subsample for cross-corr. analysis 	: 25000000
No pseudo replicates			: false
No ATAQC (advanced QC report)		: false
No Cross-corr. analysis			: false
Use CSEM for alignment			: false
Smoothing window for MACS2		: 150
DNase Seq				: false
IDR threshold				: 0.1
Force to use ENCODE3 parameter set	: false
Force to use ENCODE parameter set	: false
Disable genome browser tracks	: false
p-val thresh. for overlapped peaks	: 0.01
MACS2 p-val thresh. for peaks	: 0.01
MACS2 p-val thresh. for BIGWIGs		: 0.01
Enable IDR on called peaks	: false
Automatically find/trim adapters	: false
== checking atac parameters ...
00:00:00.191	Error (/root/atac_dnase_pipelines/modules/align_bowtie2.bds, line 41, pos 3): Bowtie2 index (-bwt2_idx) doesn't exists! (file: .1.bt2 or .1.bt2l)

Okay, I figure it out. Please unzip the attached file and replace your modules/sys.bds with it.
sys.zip
Also, please run the following for more debugging info:
$ cat /root/data/bds_pipeline_genome_data/bds_atac_species.conf
Jin

It seems work, up to now it finished trimming adapter. Thank you, Jin!

Sounds good.


Curated Packages and cert manager are not installed in child workload cluster.

Curated Packages and cert manager are not installed in child workload cluster. Geting this error.

The Amazon EKS Anywhere Curated Packages are only available to customers with the
Amazon EKS Anywhere Enterprise Subscription

Curated packages cannot be installed as cert-manager is not present in the cluster.
This is most likely caused by an action to install curated packages at a workload
cluster. Refer to https://anywhere.eks.amazonaws.com/docs/tasks/troubleshoot/packages/
for how to resolve this issue.

This is currently the expected behavior as a manual step is required for packages to be deployed on workload clusters today. This will change in the future and the message will no longer be displayed.


Improvements to plugin validator

Spaced out the output
Put each error on its own line
Added red & green output for fail/pass
Allowed the user to specify the location, defaulting to current working directory
Exit with a non-zero exit code if there are errors (important for CI environments and command chaining)
Separated out stderr and stdout

Looks all good, from testing against the mockPlugins I can see we get the same error for all cases. I think previously we specified what was actually wrong with the plugin config which I feel could direct the user more... although this is a content issue not development so all good :)


soft pwm api questions

Current softpwm uses os cpu time, ie I think that means it shares with the system timer. At how often a timer would that get problematic?
Would it be better to use a separate hal timer? or I guess maybe a syscfg flag to choose the source?
Secondly,
soft pwm appears to attempt to utilize the pwm api 1:1, why should it get a separate device name?
https://github.com/apache/mynewt-core/blob/master/apps/pwm_test/src/main.c#L41
I would argue for the default bsps to resolve soft pwm to pwm0

I would argue for the default bsps to resolve soft pwm to pwm0

It made sense at the time having a name which tells us it is not the hardware based PWM, plus using it won't affect any other PWM device, which might happen with hw based PWM. Is this against any pattern we're following with device names? Probably, so if everyone agrees let's change it.

I am not saying having a syscfg (or not having one) is a good/bad idea, but I would think it would be fine in most cases. Hard to say without getting hard numbers but it is not something I would be particularly worried about. What period/frequencies are being generally used here?


all in one docker-compose.yml

someone know if this project have mage2nosql and vue-storefront in one single docker-compose.yml file?
thanks in advance,

As far as I know we don't have such configuration yet. I agree - it would be great to have it. We have to find somebody who'll be eager to prepare it :D @mkoszutowski Mateusz maybe you're the one? :) Great first contribution to the prject!


Suspender sometimes does not suspend the scans when the PV reached and went beyond threshold value

We have been using the following suspender to pause scans when the monochrmator's Bragg motor temperature rises above threshold value (120 degree C).
dcm_bragg_temp_pv = 'XF:05IDA-OP:1{Mono:HDCM-Ax:P}T-I'
PVSuspendCeil(RE, dcm_bragg_temp_pv, 120, resume_thresh=70, sleep = 10)

It has been working for some time. However, we observed two cases yesterday that the suspender did not pause the scan. The first time when it occurred, the suspender did not pause the scan and the temperature kept increasing to 140 degree C. The scan will aborted and bluesky was restarted.
The scan was then re-launched, and the suspender again did not pause the scan when it reaches 120 degree C. The scan was aborted. Not exception was thrown; the scan simply keep on running.
However, for the third time launching the scan, the suspender successfully paused the scan. The suspender was not modified during all these scans.

Are there certain conditions that may cause the suspender to fail to suspend the scans?

I can't recall whether we already spoke about this offline. Our best guess is that the suspension condition was met when the RunEngine was not presently in control of execution. The can be addressed in two ways:

Each time the RunEngine takes control of execution, check on all the "suspenders" to see if any were tripped before the RunEngine started watching. This has been done in the latest version of bluesky.
To respond as quickly as possible to suspenders, put all experimental logic into "plans" so that the RunEngine is always in control.

We will see if we can reproduce this issue when we visit SRX with the new version of bluesky. I will close this issue now -- please reopen if it reoccurs.
Thanks again for the detailed report.


err: <_rendezvous of RPC that terminated with (StatusCode.PERMISSION_DENIED, permission denied: No "settings" rights to Application)

err: <_rendezvous of RPC that terminated with (StatusCode.PERMISSION_DENIED, permission denied: No "settings" rights to Application)
I'm trying to use TTN library with sample code from @ https://github.com/TheThingsNetwork/python-app-sdk
When I call application client I'm getting error as StatusCode.Permission_denied.
using application manager client
app_client =  handler.application()
my_app = app_client.get()
print(my_app)
my_devices = app_client.devices()
print(my_devices)
May I know what is reason ?

Hi Johan,
Thanks for response, which is working now.
Actually it is a corporate proxy issues :(


Refactor codebase to async/await - auth files and chili

Closes #5145

Thank you, we'll have a look at it ASAP!

Merged manually, thank you! 🎊⚡


World map..

The GraphEq assignment (Assignment 4) gets  100 earthquakes and does draw the world map as an overlay, but anything over 100 quakes it doesnt.  The map calls seem right from the assignment and the server side looks reasonable -- dont see any limitations so far.
Was testing it with the C++ version.

Java version doesnt draw it I think. Python is behaving like C++. The setMap() with a string param should set the JSON correctly. Not sure why the number of objects seem to constrain the map drawing.


Select Discard Changes not on the window with VSCODE Running (with multi monitor)

Type: Bug
Use a Pc, with a couple of monitors
Use a Project with Git Source control
Change a file
modify it
Save it
Go to Source Control
Go to changes
Select Discard Changes
BUG*
The "Are you sure you want to discard changes in..." is  often not displayed centred in the VSCode screen, but as a old popup somewhere on one of the other screens
VS Code version: Code 1.88.0 (5c3e652f63e798a5ac2f31ffd0d863669328dc4c, 2024-04-03T13:26:18.741Z)
OS version: Windows_NT x64 10.0.22631
Modes:

System Info

Item
Value

CPUs
13th Gen Intel(R) Core(TM) i7-13850HX (28 x 2304)

GPU Status
2d_canvas: enabledcanvas_oop_rasterization: enabled_ondirect_rendering_display_compositor: disabled_off_okgpu_compositing: enabledmultiple_raster_threads: enabled_onopengl: enabled_onrasterization: enabledraw_draw: disabled_off_okskia_graphite: disabled_offvideo_decode: enabledvideo_encode: enabledvulkan: disabled_offwebgl: enabledwebgl2: enabledwebgpu: enabled

Load (avg)
undefined

Memory (System)
63.69GB (36.89GB free)

Process Argv
--crash-reporter-id f947e526-ce45-491b-9f36-a510f0ac5a67

Screen Reader
no

VM
0%

Extensions (20)

Extension
Author (truncated)
Version

vscode-eslint
dba
2.4.4

gitlens
eam
14.9.0

gitlab-workflow
Git
4.8.0

hcl
has
0.4.0

svg
joc
1.5.3

vscode-docker
ms-
1.29.0

debugpy
ms-
2024.4.0

python
ms-
2024.4.0

vscode-pylance
ms-
2024.4.1

remote-containers
ms-
0.354.0

remote-wsl
ms-
0.88.0

cmake-tools
ms-
1.17.17

vscode-jest
Ort
6.2.3

phind
phi
0.25.0

vscode-yaml
red
1.14.0

markdown-preview-enhanced
shd
0.8.13

sonarlint-vscode
Son
4.4.2

pdf
tom
1.2.2

cmake
twx
0.0.17

gitblame
wad
10.10.0

A/B Experiments
vsliv368cf:30146710
vspor879:30202332
vspor708:30202333
vspor363:30204092
vstes627:30244334
vscod805cf:30301675
binariesv615:30325510
vsaa593cf:30376535
py29gd2263:30899288
vscaac:30438847
c4g48928:30535728
azure-dev_surveyone:30548225
962ge761:30959799
pythongtdpath:30769146
welcomedialogc:30910334
pythonidxpt:30866567
pythonnoceb:30805159
asynctok:30898717
pythontestfixt:30902429
pythonregdiag2:30936856
pyreplss1:30897532
pythonmypyd1:30879173
pythoncet0:30885854
h48ei257:31000450
pythontbext0:30879054
accentitlementst:30995554
dsvsc016:30899300
dsvsc017:30899301
dsvsc018:30899302
cppperfnew:31000557
d34g3935:30971562
fegfb526:30981948
bg6jg535:30979843
ccp2r3:30993541
dsvsc020:30976470
pythonait:31006305
gee8j676:31009558
dsvsc021:30996838
g1icg217:30999571
jg8ic977:31013176

@tserhere, is this issue specific to source control modal dialogs or any modal dialogs in VS Code? You can verify that by disabling auto-save, modifying a file and then try to close it. Thanks!

That also opens in the other display. What i mean is and wanted to get the discission on going...... Vscode is showing the "legacy" behaviour of Windows, regarding to dialog boxes, when it comes to multi monitor.
Move  vscode to the non-main display. Then the fastest way to reproduce is the Menu [Help] -> About option. You will see that dialog pop up in the Main display, Rather then how more modern  applications behave. (Like the new Windows 11 Notepad ) does.
For example , type something in the famous windows notepad application, then press the close tab options and you will see that the dialog is  shown in the same screen as notepad is.
Now, you could off course consider that  vscode is "behaving by design", but i think, the desktop landscape has evolved into the expectation that popups, related to an application you use, appear on the same screen :-))
And you sure don't want to brag the notepad team that their application is more modern than vscode!

@deepak1556, could you please take a look at this one? Thank you!

Merging to https://github.com/microsoft/vscode/issues/85898


init.cpython-38-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e'))

Checks

[x] I added a descriptive title to this issue
[x] I have searched (google, github) for similar issues and couldn't find anything
[x] I have read and followed the docs and still think this is a bug

Bug
Output of python -c "import pydantic.utils; print(pydantic.utils.version_info())":
ImportError: dlopen(/Users/xxx/.local/share/virtualenvs/backend-8q-GUuhq/lib/python3.8/site-packages/pydantic/__init__.cpython-38-darwin.so, 0x0002): tried: '/Users/xxx.local/share/virtualenvs/backend-8q-GUuhq/lib/python3.8/site-packages/pydantic/__init__.cpython-38-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e'))

macOS 12.4

from pydantic import BaseModel
class BaseModel(Representation, metaclass=ModelMetaclass):
...
...

you have the wrong binary installed, this is not a but with pydantic.

if you install pydantic with just pip install pydantic and you have a recent version of pip, the correct wheel should be installed.

have same problem when installing Pydantic with Poetry
python 3.10
poetry 1.2.0

ImportError: dlopen(/Users/xxx/Library/Caches/pypoetry/virtualenvs/env/lib/python3.10/site-packages/pydantic/init.cpython-310-darwin.so, 0x0002): tried: '/Users/xxx/Library/Caches/pypoetry/virtualenvs/env/lib/python3.10/site-packages/pydantic/init.

is there correct wheel in Poetry?

Poetry shouldn't require a specific wheel.
There's definitely a wheel for python3.10 on MacOS.
If pydantic is installing and working properly with pip, the problem is with poetry.

thank you
i think the issue with poetry
in my case helped:

fully remove pydantic from env
reinstall with pip: arch -arm64 pip install "pydantic[email,dotenv]" --no-cache

ARCHFLAGS="-arch arm64" pip install pydantic  --compile --no-cache-dir


allow getting of $catchExceptions

Im working on a laravel pull request which utlises the Console\Application.
I need to set $catchExceptions to false for this, which is fine, theres a setter for it.
However ideally i should be able to save the properties current state before changing it, allowing me to restore it, which isnt currently possible as there is no getter method.
This solves that problem.

Wrong repo, and wrong branch.

This should be targeted at the 2.7 branch on symfony/symfony.


Use assert instead of enforce in std.numeric

... in order to make the code more @nogc and nothrow friendly.
And also use onOutOfMemoryError instead of allocating and throwing a new
exception when malloc fails.

Technically this is a breaking change. I have no opinion on if this should be merged or not but this should get approval from many core team members before getting merged.

All of the changes were cases of irrecoverable errors. enforce should have never been used for them.

Current coverage is 88.68% (diff: 88.88%)

Merging #4688 into master will decrease coverage by <.01%

@@             master      #4688   diff @@
==========================================
  Files           121        121
  Lines         73827      73829     +2
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits          65471      65472     +1
- Misses         8356       8357     +1
  Partials          0          0

Powered by Codecov. Last update f75eeb5...2a9faae

I would argue that any code that tries to calculate euclideanDistance of two non equal length ranges has a serious problem.

AFAIR, there were other PRs that changed enforces to asserts inside .popFront for empty ranges and they were accepted. To me the situation is analogous.

This is a breaking API change, and we need to treat it as such.

I seriously doubt anyone is relying on being able to catch bare Exceptions from std.numeric, but anyway, how would you propose to mitigate the breakage?

LGTM
Will wait for yet another one LGTM from core team before merge

For what it is worth needing to catch exceptions in math code makes it slower and annoying to use.
So I like this move, my code wants to be pure nothrow @safe @nogc ;-)
Thanks @ZombineDev

@wilzbach I will make a pass over the module and   add pure nothrow @safe @nogc to the unittests, but I first need this PR merged.

These look more like asserts then enforces to me.

@ZombineDev Please add a warning in the changelog about this change

Alright, will do later today.

Is there a way to see the rendered changelog on @CyberShadow's tester?

Is there a way to see the rendered changelog on @CyberShadow's tester?

No sadly not atm - see #4228 for details,  for now you can only compile the file on its own with e.g. dmd -D changelog.dd.

Ping @9il @DmitryOlshansky, is there anything else for me to do?

Auto-merge toggled on

Thanks, @9il!


Falco 0.38.0 crashes with -pc/-pk and any plugin loaded

Describe the bug
Deploy Falco 0.38.0 with any configuration that has -pc or -pk and enable a plugin, such as k8s_audit
Defaulted container "falco" out of: falco, falcoctl-artifact-follow, falco-driver-loader (init), falcoctl-artifact-install (init)
Tue Jun  4 08:56:33 2024: Using deprecated config key 'rules_file' (singular form). Please use new 'rules_files' config key (plural form).
Tue Jun  4 08:56:33 2024: Falco version: 0.38.0 (x86_64)
Tue Jun  4 08:56:33 2024: Falco initialized with configuration files:
Tue Jun  4 08:56:33 2024:    /etc/falco/falco.yaml
Tue Jun  4 08:56:33 2024: System info: Linux version 5.15.0-72-generic (buildd@lcy02-amd64-035) (gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #79-Ubuntu SMP Wed Apr 19 08:22:18 UTC 2023
Tue Jun  4 08:56:33 2024: Loading plugin 'k8saudit' from file /usr/share/falco/plugins/libk8saudit.so
Tue Jun  4 08:56:33 2024: Loading plugin 'json' from file /usr/share/falco/plugins/libjson.so
Tue Jun  4 08:56:33 2024: Loading rules from file /etc/falco/falco_rules.yaml
Tue Jun  4 08:56:33 2024: Loading rules from file /etc/falco/k8s_audit_rules.yaml
Error: /etc/falco/k8s_audit_rules.yaml: Invalid
1 Errors:
In rules content: (/etc/falco/k8s_audit_rules.yaml:0:0)
    rule 'Disallowed K8s User': (/etc/falco/k8s_audit_rules.yaml:122:2)
    rule output: (/etc/falco/k8s_audit_rules.yaml:125:10)
------
  output: K8s Operation performed by user not in allowed list of users (user=%ka.user.na...
          ^
------
LOAD_ERR_COMPILE_OUTPUT (Error compiling output): invalid formatting token container.id container_image=%container.image.repository container_image_tag=%container.image.tag container_name=%container.name k8s_ns=%k8s.ns.name k8s_pod_name=%k8s.pod.name

If you think about it, this is actually the same concept as https://github.com/falcosecurity/falco/issues/466

Possibly introduced by #3135 ? Which fixed the -p not being applied to output from other sources than syscall, i.e. k8s_audit. Perhaps a distinction can be made which flag is used? Apply -p to all sources and apply -pc/-pk only to syscall source?


Vijay/json smart version change

Changing versions of azure-client-authentication package, azure-client-runtime, azure-arm-client-runtime packages to 1.7.14. This change is only to resolve a security vulnerability present in one of its indirect dependencies. These new versions depend on a newer version of the json-smart package in which the security vulnerability is addressed.
More info #23225

tagging @anuchandy and @ki1729 as fyi


Fixed IndexError when ensembling = True but number of pipelines to search over is 1

Closes #1387

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


Add a batcher to wait for changes

I am very new to Go. I've set up a development environment on my macOS with the VSCode editor & vscode-go plugin.
I am using refresh to (re)run my application and I noticed that the build/run events are triggered twice.
Since this library already has a provision for adding a build delay, I thought it might be useful to implement a 'batcher' that waits for the duration of buildDelay and emits a single event.
In my case, it works best if I set the build delay to 500ms.

Not an admin but this looks good

Sorry for the delay on this one, I must've just missed it. Thanks for the PR.


[CH] New Excel format compatibility: retur null for invalidated 2015-02-29

Describe the bug
When read date field of a csv file, if it contains '2015-02-29', spark returns null, gluten backend clickhouse returns '2015-03-01'
To Reproduce
Expected behavior
return null as vanilla spark does.
Additional context
No

@loneylee

fixed by https://github.com/oap-project/gluten/pull/2044


Updates suggested

The page has following information

AFAIK there is no requirement to have an active subscription. Please update the documentation to reflect the same

Is being owner of application principal give access to add an application?
Please update link to Azure portal if possible.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 74f69861-fd51-b4f0-e31e-fbe7b85c228d
Version Independent ID: 121a0f4b-811a-ed2f-bb9d-e69e4fa22bcd
Content: Quickstart: Add an enterprise application - Azure AD
Content Source: articles/active-directory/manage-apps/add-application-portal.md
Service: active-directory
Sub-service: app-mgmt
GitHub Login: @davidmu1
Microsoft Alias: davidmu

@shekhar-jha
Thanks for your feedback! We will investigate and update as appropriate.

@shekhar-jha
Thanks for your feedback! I've assigned this issue to the author who will investigate and update as appropriate.

@shekhar-jha
Since this issue is a duplicate of https://github.com/MicrosoftDocs/azure-docs/issues/85747, I'll go ahead and close this one out.
Thank you for the feedback, and for your time and patience.


Added sql-server tests for dbt 1.3.0 to 1.8.0

Overview

Update type - breaking / non-breaking

[x] Minor bug fix
[ ] Documentation improvements
[ ] Quality of Life improvements
[ ] New features (non-breaking change)
[ ] New features (breaking change)
[ ] Other (non-breaking change)
[ ] Other (breaking change)
[ ] Release preparation

What does this solve?

Outstanding questions

What databases have you tested with?

[ ] Snowflake
[ ] Google BigQuery
[ ] Databricks
[ ] Spark
[x] SQL Server
[ ] N/A

Connecting to the SQL Server docker container doesn't seem to be that straight forward. I'm looking into different options.
I also accidentally removed the postgres 1.5.0 and 1.6.0 tests. I should have removed the SQL Server tests because those don't exist. That has been done.
Might be better to either leave out the SQL Server tests for now and add them later when I can tests the tests better?
@michelley-an What do you think?

I've removed sql-server from the default test matrix and I've created it's own job.
Tests succeed in my fork.

Going to add comments for syntax (looks like the versions should be "2022"), using this as my guide

Could you review my comments and test the changes locally?

I think I'm unable to see your comments. Which files did you comment?

I think postgres is failing because a the new prerelease for 1.9.0, I'm testing solutions in #446

I think I got it. I set dbt-core~=1.8.0 as dependecy for the 1.8.0 postgres tests. The postgres tests on my end are now succeeding!

I changed the deps to look like this:

I think it should work now.

Anything I can do to help here? I got the postgres tests to work in my repo. See my last comment.

We released a new version yesterday to fix the postgres bug, I'll create a new PR with your changes shortly


Communicate with Ryuk over the Docker connection

Related to #3136

@bsideup Sorry for late response - what's the trick again to try this commit as dependency?

@bsideup Ok, finally got some time to run it. If fails.
20/12/18 22:03:49.411 [testcontainers-ryuk] WARN o.t.u.ResourceReaper: Ryuk connection failure
java.lang.RuntimeException: java.net.SocketException: Socket closed
	at com.github.dockerjava.api.async.ResultCallbackTemplate.throwFirstError(ResultCallbackTemplate.java:158)
	at com.github.dockerjava.api.async.ResultCallbackTemplate.awaitCompletion(ResultCallbackTemplate.java:93)
	at org.testcontainers.utility.ResourceReaper.lambda$null$1(ResourceReaper.java:105)
	at org.testcontainers.utility.ResourceReaper$$Lambda$542/1971736492.run(Unknown Source)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.SocketException: Socket closed
	at java.net.SocketInputStream.socketRead0(Native Method)
	at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
	at java.net.SocketInputStream.read(SocketInputStream.java:170)
	at java.net.SocketInputStream.read(SocketInputStream.java:141)
	at org.testcontainers.shaded.okio.Okio$2.read(Okio.java:140)
	at org.testcontainers.shaded.okio.AsyncTimeout$2.read(AsyncTimeout.java:237)
	at org.testcontainers.shaded.okio.RealBufferedSource.read(RealBufferedSource.java:51)
	at org.testcontainers.shaded.okhttp3.internal.http1.Http1ExchangeCodec$AbstractSource.read(Http1ExchangeCodec.java:389)
	at org.testcontainers.shaded.okhttp3.internal.http1.Http1ExchangeCodec$UnknownLengthSource.read(Http1ExchangeCodec.java:529)
	at org.testcontainers.shaded.okhttp3.internal.connection.Exchange$ResponseBodySource.read(Exchange.java:286)
	at org.testcontainers.shaded.okio.RealBufferedSource$1.read(RealBufferedSource.java:436)
	at org.testcontainers.shaded.com.github.dockerjava.core.FramedInputStreamConsumer.accept(FramedInputStreamConsumer.java:30)
	at org.testcontainers.shaded.com.github.dockerjava.core.FramedInputStreamConsumer.accept(FramedInputStreamConsumer.java:12)
	at org.testcontainers.shaded.com.github.dockerjava.core.DefaultInvocationBuilder.lambda$executeAndStream$1(DefaultInvocationBuilder.java:275)
	at org.testcontainers.shaded.com.github.dockerjava.core.DefaultInvocationBuilder$$Lambda$380/664856708.run(Unknown Source)
	... 1 common frames omitted

on java.lang.RuntimeException: java.lang.IllegalStateException: Timed out waiting for the default Ryuk filters to be registered
I'll try to work on this some more to figure out why the socket was closed. I think it's the DockerClient socket.

Going to rework


Include "Back to top" Icon

Hi,
first of all thanks for this great template, it is much appreciated! One feature I found missing when creating a homepage with minimal-mistakes was a back to the top icon that is always in the right lower corner and can be used to scroll back to the top at any time. I implemented this for my homepage by creating a simple new class in _sidebar.scss with fixed position:
.sidebar__top {
  position: fixed;
  bottom: 1.5em;
  right: 2em;
  z-index: 10;
}

And included it in default.html with an awesome font icon and a link to #site-nav:

I linked to #site-nav so that clicking the icon scrolls all the way to the top of the page and not only to the first header. A working example can be seen here: www.pandapower.org
Is this something that would be interesting to include in the template as an option? I am fairly new to website design in general and the template specifically, so I don't know if and how this would possibly interfere with other features. But I would be willing to try to clean up the solution and put in a pull request if you think this would be a good idea to have in the template.
Cheers
Leon

How you've customized the theme to add this feature looks fine to me.
Not sure if I'm interested in adding the feature though. I'll leave it marked as under consideration and see if there's any interest in it.

+1 to me :)
I've added this nice tweak to my installation as well :)

One thing I am still struggling with: the back-to-the top icon in the current implementation disappears behind the footer:

Setting the z-index to a higher number does not seem to make a difference. @mmistakes: can you give me a hint how I could bring the icon above the footer?

@lthurner Change it's source order. Put it after
 and it'll appear above it.

Thanks a lot, works like a charm! I have updated the description above accordingly.

+1 this will be a nice feature in the theme, and also required since lenghthy posts when viewed on mobile have toc on the top (toc are not sticky on mobile). Users have to scroll all the way to top to acess toc.

Already stale? I like this feature and enhanced it in my implementaitons as well. :)

Nice feature! Does this also work when using the remote theme? So far, I couldn't get it to work.
I've added the default.html under _layouts and added a _sidebar.scss under _sass/minimal-mistakes. In the _sidebar.scss, I only have the following code:
.sidebar__top {
  position: fixed;
  bottom: 1.5em;
  right: 2em;
  z-index: 10;
}

Any idea what the problem could be? Do I also need to copy and paste the remaining code in _sidebar.scss? Or do I need to copy and override any other files (eg, in _sass)? Not sure, how to debug this.

In fact, the "to top button" is there! But it's just at the very bottom of the website. So to go to the top, I'd have to scroll to the very bottom first? Not very convenient.
How could I adjust the button to float and stay at the top left corner while scrolling? So not at a fixed position on the website, but instead fixed at the top left corner of the screen?

@lthurner Did you have the same problem that the button was at the top left corner of the page (absolute) and not in the corner of the window the user sees? In your linked website, it looks good. Any ideas what the problem could be in my case with the remote theme?

@stefanbschneider sorry just saw this now - I never had the problem that you describe. I can have a look at it, but I am in no means a CSS expert, so not sure if I can help. Can you link me to your code though? I wasn't able to find your github pages repo quickly

@lthurner Sorry, it's a private repo. But it uses the remote theme. I only added the default.html in a _layouts folder. It looks like this:
<!DOCTYPE html>

    {% include head.html %}
    {% include head/custom.html %}

    {% include_cached skip-links.html %}
    {% include_cached browser-upgrade.html %}
    {% include_cached masthead.html %}

      {{ content }}

    {% if site.search == true %}

        {% include_cached search/search_form.html %}

    {% endif %}

        {% include footer/custom.html %}
        {% include_cached footer.html %}

    {% include scripts.html %}

Does this help? What other info would you need? If necessary, I can try to reproduce the problem on a smaller example page.
Thanks for the help!

Defining the position in cm might not be a good idea, have your tried em or px instead? Otherwise it looks correct to me.
Have your checked if your _sass folder looks similar to mine: https://github.com/e2nIEE/pandapower-homepage/tree/master/_sass. I think it was necessary to include the minimal-mistakes.scss file as well, although I don't remember exactly why...

Thanks a lot! Adding the minimal-mistakes.scss file into my _sass folder solved the problem! cm worked fine, but I do prefer em now - thanks for the tip. :)

I've just found this well-maintained library, https://github.com/vfeskov/vanilla-back-to-top
You just need to include its script, don't have to include any CSS:


Release should be runnable

I know this is a personal project, but that the release is not runnable upfront is really annoying. It would be very nice to have a correct settings.json and just a tiddlywiki shipped with each release s.t. a simple node .\server.js fires up a working copy.
That included to also have editions/empty (currently editions.zip is shipped and this means tiddlywiki.js --init fails because no edition empty is available) available for anyone who wants to follow the installation guide.

This is a good suggestion, I'll keep it in mind.


[Caloris2] [Better data sources] Use the new configuration system for the Slack bot

@lasryaric what's the status here?
Moving to caloris 2 but maybe should be closed?

Working on it now.

Assigning to you and moving to In progress

This was done here. Closing


Fix NewRelic monitoring

Updated 8/8

[x] Get error logging working

Updated 7/19 -- next steps per https://github.com/DoSomething/ds-mdata-responder/issues/518#issuecomment-233766089

[x] Remove the New Relic add-on
[x] Remove the custom NR code (require('newrelic');)
[x] Verify we have no more NR-related log activity
[x] Re-introduce the newer NR package in code

Original description
I'm not sure when it stopped, but it seems like we're no longer getting any reporting to our NewRelic account from this app.
Initially thought that it may be because require('newrelic') isn't the first line in server.js like the NewRelic docs ask for it to be. But that change was done in late 2014 and I'm pretty sure we didn't just go through the entirety of 2015 without getting any NewRelic reporting.

The logs on production are flooded with New Relic related messages, making it really hard to spot any other errors.

2016-07-18T15:09:19.214273+00:00 app[web.1]: {"v":0,"level":10,"name":"newrelic","hostname":"9e24e984-e7c8-4f7b-8cc5-f72b27e63081","pid":14,"time":"2016-07-18T15:09:19.213Z","msg":"Not creating segment "timers.setTimeout" because no transaction was active","component":"tracer"}
2016-07-18T15:09:29.528610+00:00 app[web.2]: {"v":0,"level":10,"name":"newrelic","hostname":"eb8c319a-467a-4c85-b398-8c01785579b4","pid":14,"time":"2016-07-18T15:09:29.528Z","msg":"Not tracing MongoDB unknown._executeQueryCommand(); no New Relic transaction.","component":"mongodb"}
2016-07-18T15:09:29.528973+00:00 app[web.2]: {"v":0,"level":10,"name":"newrelic","hostname":"eb8c319a-467a-4c85-b398-8c01785579b4","pid":14,"time":"2016-07-18T15:09:29.528Z","msg":"Not tracing MongoDB unknown._executeQueryCommand(); no New Relic transaction.","component":"mongodb"}

cc @blisteringherb

Similar errors reported in this thread. New Relic suggests:

the original forum poster's application did not handle web requests. If an application does not handle web requests (e.g. it only takes care of some background process) you may need to use custom instrumentation for data to appear in New Relic.

It looks as though we have two New Relic integrations in the production Heroku app.
There’s the integration in code, which loads the library and reads the env vars set in Heroku, and then there’s the generic add-on.
The integration in code would be the one generating error messages, and the one that should be reporting into our main New Relic account.
The other one is happily reporting to the auto-created New Relic account we were looking at.

There's this message in the New Relic dashboard:

There are both old and new time metrics for this time window. The response time is accurate, but if you use asynchronous code the stacked bars may not be. To fix this, upgrade all of your agents to versions that support the new time metrics.

Per that link -- our app should be running NewRelic 1.25 or higher, our package.json currently is set to 1.11.5.

My suggestion is

Remove the New Relic add-on
Remove the custom NR code (require('newrelic');)
Verify we have no more NR-related log activity
Re-introduce the newer NR package in code

Thanks @mshmsh5000, I'll give it a shot. I did just try updating package.json to 1.28.3 and restarting but still get the error.
2:11:19 PM web.1 |  {"v":0,"level":10,"name":"newrelic","hostname":"Aarons-MacBook-Pro-2.local","pid":1029,"time":"2016-07-19T21:11:19.284Z","msg":"Not creating segment \"timers.setTimeout\" because no transaction was active","component":"tracer"}

Will try from scratch per the steps in your suggestion.

Deployed 1.0.1 to production, which has stopped all of the New Relic noise in the logs.
@mshmsh5000  - It also looks like our Heroku add-on New Relic activity has stopped too, although I haven't disabled the Heroku add-on through the UI, so that's a little unexpected (I think?). The transactions stop right around the time of deploy:

@mshmsh5000 Confirming our next step should be to disable the add-on within the Heroku UI (step 1) to complete step 3?

Well now! Does that mean that the Heroku add-on doesn't work without the Heroku lib loaded in the app code?

@mshmsh5000 Do you mean it won't work without the New Relic (not Heroku) lib loaded?
I've done a little reading that would have been a little more useful to look at yesterday -- the answer sure looks likes YES, we need to add the newrelic package -- see step 7. I'll work on adding back in locally to try pinpoint where the noise is coming from..

This add-on seems to be logging activity but not errors.
Our implementation is using the Wayne add-on for $0.00/month. I'm seeing some 401's from Mobile Commons that are nowhere to be found in the New Relic add-on's interface in the "Errors" page. When I navigate to "Error analytics" it urges to upgrade.
Refs #562
cc @blisteringherb

I've changed our production key to post to our main New Relic account to an app named Gambit instead of ds-mdata-responder-heroku, and I've turned off reporting locally and on staging by setting config variable NEW_RELIC_ENABLED=false.
Will give a day or two to 👀 but we should be in a good place to disable the Heroku New Relic add-on completely.
cc @blisteringherb @sheyd

I'm seeing some 403's in our New Relic around the time of yesterday's deployment adding checks for x-gambit-api-key, so I think it's safe to close out the last remaining todo for this.

When I've tested with 404 errors, they didn't appear - but that's by default (per New Relic support in our Heroku ticket).
For application errors, we can add our own custom events if we want them to appear in new Relic... further progress can be tracked in #562
Related reading:

https://discuss.newrelic.com/t/process-crashing-errors-are-not-being-reported/27765
https://discuss.newrelic.com/t/how-to-get-notified-about-error-events/31312/4
http://stackoverflow.com/questions/26964009/detecting-process-crashes-with-new-relic-in-nodejs


Switch to image entity

Home Assistant 2023.7 introduces a new image entity. This seems more applicable since it does not require a continuous stream. A qr code is exactly one of the examples. There are already some platforms that use it: https://rc.home-assistant.io/blog/2023/06/28/release-20237/#image-entities

Thanks for the hint. I am going to look into it.


Fix crash in Hystrix logging when uninitialized

Description
From time to time, I'm seeing Hystrix test failures in cibuild, caused by a NullReferenceException. For example, this one:
Starting test execution, please wait...
A total of 1 test files matched the specified pattern.
The active test run was aborted. Reason: Test host process crashed : Unhandled exception. System.NullReferenceException: Object reference not set to an instance of an object.
   at Steeltoe.CircuitBreaker.Hystrix.Test.TestObserverBase`1.OnNextCore(T value) in /home/vsts/work/1/s/src/CircuitBreaker/test/Hystrix.Test/TestObserverBase.cs:line 63
   at System.Reactive.SafeObserver`1.WrappingSafeObserver.OnNext(TSource value) in /_/Rx.NET/Source/src/System.Reactive/Internal/SafeObserver.cs:line 40
   at System.Reactive.Subjects.Subject`1.OnNext(T value) in /_/Rx.NET/Source/src/System.Reactive/Subjects/Subject.cs:line 145
   at System.Reactive.AutoDetachObserver`1.OnNextCore(T value) in /_/Rx.NET/Source/src/System.Reactive/Internal/AutoDetachObserver.cs:line 71
   at System.Reactive.SafeObserver`1.WrappingSafeObserver.OnNext(TSource value) in /_/Rx.NET/Source/src/System.Reactive/Internal/SafeObserver.cs:line 40
   at System.Reactive.Linq.ObservableImpl.SelectMany`2.ObservableSelector._.InnerObserver.OnNext(TResult value) in /_/Rx.NET/Source/src/System.Reactive/Linq/Observable/SelectMany.cs:line 952
   at System.Reactive.Linq.ObservableImpl.Aggregate`2._.OnCompleted() in /_/Rx.NET/Source/src/System.Reactive/Linq/Observable/Aggregate.cs:line 138
   at System.Reactive.Sink`1.ForwardOnCompleted() in /_/Rx.NET/Source/src/System.Reactive/Internal/Sink.cs:line 55
   at System.Reactive.Subjects.Subject`1.OnCompleted() in /_/Rx.NET/Source/src/System.Reactive/Subjects/Subject.cs:line 78
   at System.Reactive.Linq.ObservableImpl.Window`1.TimeHopping._.Tick() in /_/Rx.NET/Source/src/System.Reactive/Linq/Observable/Window.cs:line 330
   at System.Reactive.Concurrency.Scheduler.<>c__67`1.<SchedulePeriodic>b__67_0(ValueTuple`2 t) in /_/Rx.NET/Source/src/System.Reactive/Concurrency/Scheduler.Services.Emulation.cs:line 79
   at System.Reactive.Concurrency.NewThreadScheduler.Periodic`1.Run() in /_/Rx.NET/Source/src/System.Reactive/Concurrency/NewThreadScheduler.cs:line 169
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state)

The affected line is:
_output.WriteLine("ReqLog" + "@ " + Time.CurrentTimeMillis + " : " + HystrixRequestLog.CurrentRequestLog.GetExecutedCommandsAsString());

Apparently, HystrixRequestLog.CurrentRequestLog returns null when !HystrixRequestContext.IsCurrentThreadInitialized. There are a lot of usages in the codebase. So instead of updating them all to account for null using the ?. operator, it now returns an immutable empty instance to avoid the crash.
Quality checklist

[x] Your code complies with our Coding Style.
[ ] You've updated unit and/or integration tests for your change, where applicable.
[ ] You've updated documentation for your change, where applicable.
If your change affects other repositories, such as Documentation, Samples and/or MainSite, add linked PRs here.
[ ] There's an open issue for the PR that you are making. If you'd like to propose a new feature or change, please open an issue to discuss the change or find an existing issue.
[ ] You've added required license files and/or file headers (explaining where the code came from with proper attribution), where code is copied from StackOverflow, a blog, or OSS.

/azp run Steeltoe.All


依赖brolog导致puppet在nodejs 16下无法工作

import { getLoggable } from 'brolog';
^^^^^^^^^^^
SyntaxError: Named export 'getLoggable' not found. The requested module 'brolog' is a CommonJS module, which may not support all module.exports as named exports.
CommonJS modules can always be imported via the default export, for example using:
import pkg from 'brolog';
const { getLoggable } = pkg;
at ModuleJob._instantiate (node:internal/modules/esm/module_job:124:21)
at async ModuleJob.run (node:internal/modules/esm/module_job:181:5)
at async Promise.all (index 0)
at async ESMLoader.import (node:internal/modules/esm/loader:281:24)
at async loadESM (node:internal/process/esm_loader:88:5)
at async handleMainPromise (node:internal/modules/run_main:65:12)

Please try the latest version of https://github.com/wechaty/getting-started and it should be ok.
If you still experiencing this problem, please provide reproducible steps.

已经是最新版本
eslizn@cabrio getting-started$ git log
commit 3db2365d6e6763e03388c9d0d9249b92cfabe758 (HEAD -> main, origin/main, origin/HEAD)
Author: Huan (<E6><9D><8E><E5><8D><93><E6><A1><93><EMAIL_ADDRESS>Date:   Sat Oct 30 19:25:42 2021 +0800

    1.0.1

eslizn@cabrio getting-started$ yarn --force
yarn install v1.22.17
[1/5] 🔍  Validating package.json...
[2/5] 🔍  Resolving packages...
[3/5] 🚚  Fetching packages...
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
warning<EMAIL_ADDRESS>The engine "wechaty" appears to be invalid.
[4/5] 🔗  Linking dependencies...
warning "wechaty ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning "wechaty ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning " ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning " ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning "wechaty-puppet-wechat ><EMAIL_ADDRESS>has unmet peer dependency "brolog@>=1".
warning " ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning " ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>warning "@chatie/eslint-config > @typescript-eslint/eslint-plugin ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>|| >= 3.2.0-dev || >= 3.3.0-dev || >= 3.4.0-dev || >= 3.5.0-dev || >= 3.6.0-dev || >= 3.6.0-beta || >= 3.7.0-dev || >= 3.7.0-beta".
warning " ><EMAIL_ADDRESS>has unmet peer dependency<EMAIL_ADDRESS>[5/5] 🔨  Rebuilding all packages...
success Saved lockfile.
✨  Done in 7.95s.
eslizn@cabrio getting-started$ npm run start:js

><EMAIL_ADDRESS>start:js
> node examples/ding-dong-bot.js

file:///Users/eslizn/go/src/github.com/wechaty/getting-started/node_modules/state-switch/dist/esm/src/state-switch.js:12
import { getLoggable } from 'brolog';
         ^^^^^^^^^^^
SyntaxError: Named export 'getLoggable' not found. The requested module 'brolog' is a CommonJS module, which may not support all module.exports as named exports.
CommonJS modules can always be imported via the default export, for example using:

import pkg from 'brolog';
const { getLoggable } = pkg;

    at ModuleJob._instantiate (node:internal/modules/esm/module_job:124:21)
    at async ModuleJob.run (node:internal/modules/esm/module_job:181:5)
    at async Promise.all (index 0)
    at async ESMLoader.import (node:internal/modules/esm/loader:281:24)
    at async loadESM (node:internal/process/esm_loader:88:5)
    at async handleMainPromise (node:internal/modules/run_main:65:12)

Node.js v17.0.1

Yes, that's the latest version.
Have you tried to reinstall all the NPM modules so that the dependencies is the latest too?
rm -fr node_modules package-lock.json
npm install

经测试npm安装的正常，而通过yarn安装的会报这个错误

Wechaty community is always using npm, please use NPm version v7 or above.
Thank you very much for your information!


Better interaction with other Microsoft products

I would like to see a more in dept interaction with other (Microsoft) applications.
like now it’s possible to open Microsoft Teams when searching the application, but I would also like the possibility to type for example ‘Teams: John Doe’ which then will not only open Teams but also directly focus on the chat with the given person so I can immediately start typing a new message to him.
same for Microsoft ToDo. Type thing like ‘todo: my new task’ which will add it to ‘my day’. That way it’s already registered and in view
I don’t have any preference on syntax, as long as it’s possible:D I’m open for discussion!

Tracked in #4233


[Ungraded Exercise #2] Level 4 - Issue with too many beeps

Hi, I'm currently getting this as an output:

When the correct output for the code should be:

The current implementation of my code uses Supplier to keep track of the traces and of the value, and all the changes to the traces are made in the context of the Supplier<>. How do I get rid of the multiple unwanted beeps? Is it because of issues with lazy evaluation?

Currently, level 5 already works.

tracer being a Supplier is not sufficient since it requires multiple get calls whenever you want to modify it. try making it a Function<Consumer<String>, String>, that way the Consumer is involved in generating the trace, and can consume the trace as it's generated. the value returned by applying tracer should be similar to that of value, so that the process of updating tracer in map and flatMap can utilise this value.

tracer being a Supplier is not sufficient since it requires multiple get calls whenever you want to modify it. try making it a Function<Consumer<String>, String>, that way the Consumer is involved in generating the trace, and can consume the trace as it's generated. the value returned by applying tracer should be similar to that of value, so that the process of updating tracer in map and flatMap can utilise this value.

hi may I know what Consumer you use when you try to construct the Str using of() ? Cuz you need an input to construct a new Str right?

the Consumer is the input of the Function. you just need to define the Function, not the Consumer

finals is over you can close this issue


OSGi-fying Entire Stack

Added functionality to make use of OPC-UA Stack library in dynamic
module environment (OSGi)

I want to explore the route that netty takes for OSGI compatibility (see here), which is to use the maven-bundle-plugin's generate-manifest goal, and to leave the packaging and dependencies as they are.

@amitjoy can you avoid embedding the jool dependency? Its jar can be osgified separately in the maven build of your osgi project. Or you could submit a PR to the jool repo. It would also simplify the Committer Questionnaire approval if you plan to use Opcua with an Eclipse project.

@cdealti I have already committed one PR to OSGi-fy jool library. For the time-being, I had to embed the dependency and as soon as the jool library gets available in Maven Repo as OSGi Bundle, I would remove the dependency to be embedded in the classpath.
@kevinherron The netty libraries that OPC-UA stack is using are already OSGi-fied and I have already tested the application in my end.

Closing; this will be implemented as part of the 'osgi' branch.


License

Would you please add license to the library? I am considering using it for a commercial project and without the license I am not able to do so. Thanks

MIT License added. Sorry for the 1 year delay, lol


Problem with library installation for PlatformIO

Hello. I'm trying to install this library for PlatformIO ESP-IDF project. Sorry if my problem is not exactly related to this library, but I don't know what to do now. I did a clean reinstall of VSCode, PlatformIO and started a new ESP-IDF project to ensure there are no legacy code conflicts.

Installation by PlatformIO Library Register gives me this error:

Error: Could not find the package with 'someweisguy/esp_dmx @ ^3.0.0-beta' requirements for your system 'windows_amd64'

Deleting "lib_deps =<EMAIL_ADDRESS>from platformio.ini allows me to build the project, but I get several errors in dmx_hal.h:

too few arguments to function 'uart_ll_set_baudrate'
too few arguments to function 'uart_ll_get_baudrate'
control reaches end of non-void function [-Werror=return-type]
too few arguments to function 'uart_ll_set_baudrate'
'uart_dev_t' has no member named 'uart_conf0_reg_t'
'uart_dev_t' has no member named 'uart_conf0_reg_t'
control reaches end of non-void function [-Werror=return-type]
'uart_dev_t' has no member named 'uart_status_reg_t'
control reaches end of non-void function [-Werror=return-type]

And one in esp_dmx.h:

implicit declaration of function 'esp_timer_get_time' [-Werror=implicit-function-declaration]

Cloning "esp_dmx-release-v3.0" folder into /components folder of my project causes #include "esp_dmx.h" error.

Cloning  "esp_dmx-release-v3.0" folder into /lib folder causes last five dmx_hal.h errors from 1. but no other errors.

Are there any other ways to install a library to PlatformIO ESP-IDF project?

Thanks for the feedback!
I'm not sure what is causing this, but I have some guesses. Which ESP32 are you using? The base ESP32? Or something like the ESP32-S3? And what version of ESP-IDF are you using?

I believe I have found the primary issue. The v3.0.0-beta tagged version of this library did not support ESP-IDF v5, which PlatformIO now uses!
I have added ESP-IDF v5 support as of January, so it should be a pretty straightforward fix - just need to publish a new tagged version. However, I am now seeing that PlatformIO inexplicably does not include certain files from ESP-IDF v5. So PlatformIO says it uses ESP-IDF v5, but it's not actually v5. So I am going to add some fixes for this issue and I'll publish a new tagged version ASAP!
If you could still verify that you're using ESP-IDF v5 on PlatformIO and which ESP32 hardware you're using, that would be excellent!

Yes, I'm using ESP32-S3. And the latest ESP-IDF version, I guess it is v5.0 according to changelog, I don't know how to check it in VSCode.
I had some of the features missing after clean VSCode reinstall too. It seems that reinstalling and just updating is not the same.
Thanks for reply and upcoming fix!

This appears to be fixed! I published v3.0.1-beta with the new changes.
BUT: I was a dummy and published the PlatformIO package before testing for ESP32-S3. So for right now, you will have to clone this repo into your lib folder on PIO. I am waiting for the package to become unpublish on PIO. Once it is, I will republish it with the fixes for ESP32-S3, and close this issue.
Let me know if you have any issues!

hello, I am trying to use the Library in an arduino Projekt in Platformio.
Project configuration:

[env:FirstFlash]
platform = espressif32
board = esp32doit-devkit-v1
framework = arduino
monitor_speed = 115200
upload_speed = 115200
board_build.filesystem = littlefs

Is the Library Arduino compatible?
I installed the new version in the lib folder as described but I get a boatload of compiling errors similar to these ones:

lib/esp_dmx/src/rdm_types.h:238:3: error: conflicting types for 'rdm_disc_unique_branch_t'
} rdm_disc_unique_branch_t;
^~~~~~~~~~~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/esp_rdm.h:8,
from lib/esp_dmx/src/esp_dmx.h:15,
from lib/esp_dmx/src/private/rdm_encode/functions.h:7,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:238:3: note: previous declaration of 'rdm_disc_unique_branch_t' was here
} rdm_disc_unique_branch_t;
^~~~~~~~~~~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/private/rdm_encode/functions.h:9,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:245:16: error: redefinition of 'struct rdm_disc_mute_t'
typedef struct rdm_disc_mute_t {
^~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/esp_rdm.h:8,
from lib/esp_dmx/src/esp_dmx.h:15,
from lib/esp_dmx/src/private/rdm_encode/functions.h:7,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:245:16: note: originally defined here
typedef struct rdm_disc_mute_t {
^~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/private/rdm_encode/functions.h:9,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:251:3: error: conflicting types for 'rdm_disc_mute_t'
} rdm_disc_mute_t;
^~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/esp_rdm.h:8,
from lib/esp_dmx/src/esp_dmx.h:15,
from lib/esp_dmx/src/private/rdm_encode/functions.h:7,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:251:3: note: previous declaration of 'rdm_disc_mute_t' was here
} rdm_disc_mute_t;
^~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/private/rdm_encode/functions.h:9,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:256:16: error: redefinition of 'struct rdm_device_info_t'
typedef struct rdm_device_info_t {
^~~~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/esp_rdm.h:8,
from lib/esp_dmx/src/esp_dmx.h:15,
from lib/esp_dmx/src/private/rdm_encode/functions.h:7,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:256:16: note: originally defined here
typedef struct rdm_device_info_t {
^~~~~~~~~~~~~~~~~
*** [.pio/build/FirstFlash/lib7f7/esp_dmx/esp_dmx.c.o] Error 1
*** [.pio/build/FirstFlash/lib7f7/esp_dmx/esp_rdm.c.o] Error 1
In file included from lib/esp_dmx/src/private/rdm_encode/functions.h:9,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:269:3: error: conflicting types for 'rdm_device_info_t'
} rdm_device_info_t;
^~~~~~~~~~~~~~~~~
In file included from lib/esp_dmx/src/esp_rdm.h:8,
from lib/esp_dmx/src/esp_dmx.h:15,
from lib/esp_dmx/src/private/rdm_encode/functions.h:7,
from lib/esp_dmx/src/private/rdm_encode/functions.c:1:
lib/esp_dmx/src/rdm_types.h:269:3: note: previous declaration of 'rdm_device_info_t' was here
} rdm_device_info_t

in main.cpp i only imported the header esp_dmx.h do I need to do something with it in the code?
I am not shure if my Problems belong in this issiue or if I should open a new one, please Advise.
similar error messages apear while using Version 3.0.0-beta downloaded over PlatformIO

Thank you! The code builds perfectly without any errors now. Unfortunately, I can't test it on a esp32-s3 board right now, because there is some problem with uploading after VSCode reinstall, but it is not library related, so I have no more questions, thanks again.

Hi Bombenscheck,
It appears to work on Arduino for me. You should be able to use v3.0.1-beta by cloning it from git into your lib folder. Let me know if that works for you.
It appears PlatformIO has unpublished the mistake I made but I am still having issues publishing fixes. I am hoping this issue will be resolved soon.

OK, I Removed all Files from my lib Folder and imported it again. Now it works... I have no Idea what went wrong the first time around.
Thanks @someweisguy  for your answer.

This should be resolved, so I am going to close this issue.
It turns out that when you ask PlatformIO to unpublish your release, they don't let you republish the release later with the same version number. So I had to publish v3.0.2-beta. You should now be able to add this library as a dependency using the PIO dependency manager.
Let me know if you run into any more issues and I will reopen this ticket!


Modifications to enable O(log N) cost add_axis_index

I have converted the representation of axis indexes to go from list to the SortedSet representation. This changes the time complexity of updates from O(N^2) to O(log N).  This makes it possible to perform significantly larger acquisition sequences than is currently possible.

@carlkesselman Looks great overall, thanks for figuring this out!
It looks like this is not working right now because in requirements.txt you list sortedcontainter not sortedcontainers. Can you push a fix (Its not letting me edit directly)?

Opps… sorry about that.  Fixed.
Carl
On Jun 14, 2023, at 7:04 AM, Henry Pinkard @.***> wrote:
@carlkesselmanhttps://urldefense.us/v2/url?u=https-3A__github.com_carlkesselman&d=DwMCaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=sGCma2ufaUVT-N141kRIZQ&m=PUq68IVPuwLetUqdeIaIKTzIk0Ti35VggOsRA-SRqKBxGqB4uoH2Dmriz39NsSbR&s=j07tzKfL-o74Dyowet4_3wtv_D6mjKW3cXMlU9mYD0Q&e= Looks great overall, thanks for figuring this out!
It looks like this is not working right now because in requirements.txt you list sortedcontainter not sortedcontainers. Can you push a fix (Its not letting me edit directly)?
—
Reply to this email directly, view it on GitHubhttps://urldefense.us/v2/url?u=https-3A__github.com_micro-2Dmanager_NDTiffStorage_pull_120-23issuecomment-2D1591277678&d=DwMCaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=sGCma2ufaUVT-N141kRIZQ&m=PUq68IVPuwLetUqdeIaIKTzIk0Ti35VggOsRA-SRqKBxGqB4uoH2Dmriz39NsSbR&s=CMUdGNS8YvuPEyhJlPqyuf5CEp3ksM-IAEVJsj427Oc&e=, or unsubscribehttps://urldefense.us/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AA3OGXWCJFDMR4P74SU6Z2DXLHAH3ANCNFSM6AAAAAAZFQ6WJQ&d=DwMCaQ&c=qzHnJIRvjI6L-clJH8JwLQvf_Iq43fzikf6aoxZgMb8&r=sGCma2ufaUVT-N141kRIZQ&m=PUq68IVPuwLetUqdeIaIKTzIk0Ti35VggOsRA-SRqKBxGqB4uoH2Dmriz39NsSbR&s=FAPrh56Me4dVE51Hko3uexAJFB7sG-chShNkuAtX4v8&e=.
You are receiving this because you were mentioned.Message ID: @.***>


[FLINK-18629] Add type to ConnectedStreams#keyBy

What is the purpose of the change
Adding a generic type to the method makes it possible to pass the type
from a lambda function. Otherwise a wildcard type '?' is derived as
Object and thus TypeExtractor extract a GenericTypeInfo for the
key.
Brief change log

Changed method ConnctedStream#keyBy to accept KeySelector of the same generic type in both scala and java API
Replaced an internal KeySelectorWithType class in scala API with explicitly passing the keyType to the underlying java API.

Verifying this change
Added test:

DataStreamTest#testKeyedConnectedStreamsType

Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (yes / no)
The public API, i.e., is any changed class annotated with @Public(Evolving): (yes / no)
The serializers: (yes / no / don't know) -> can change serializer for keys in StateBackends
The runtime per-record code paths (performance sensitive): (yes / no / don't know)
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn/Mesos, ZooKeeper: (yes / no / don't know)
The S3 file system connector: (yes / no / don't know)

Documentation

Does this pull request introduce a new feature? (yes / no)
If yes, how is the feature documented? (not applicable / docs / JavaDocs / not documented)

Even with the required japicmp exclusion I think this is still a good change. 👌


JWT Verification by the public key in client certificate

Title: How Envoy support the JWT (for signature) verification via the client public key in the cert.
Description:

I am trying to set up the Envoy to do the JWT verification. The JWT presents a JWS. From my understanding, a signature should be verified by the server via the public key of the client who sent the request. A normal process would be:

the client use its private key to sign the JWS header and payload
the client send the request with the JWT
the server somehow get the certificate of the client and extract the public key
the server use the public key to verify the signature.

But the documentations about the JWT is very limited. There is no any example about how to make the yaml config to allow the Envoy to extract the client public key and use it. It seems that the Envoy can only get the key from JWKS service or use a inline string. Using a inline string is very confusing to me. How can the Envoy use just one pre-defined JWK to verify a client's signature? The Envoy shouldn't know what certificate the client will present.
So, my question will be:

whether and how Envoy support the mutrual TLS which allow the client to present the certificate.
how to verify the client certificate in Envoy. without a CA, how Envoy define a trusted key store or certificate store to verify the certificate of the client
how to setup Envoy to extract the client certificate as the public key to verify the JWS in the JWT
if I have to use the remote JWKS, how to link a remote JWK with the client who is sending the request for verification

@bnlcnd I would recommend you to read auth0 and JWT related documents first.  I believe many of your questions can be answered by them.  For the questions on how to use JWT filter, it has some examples, they will help.


Cleanup distillation

Miscellaneous cleanups/refactors of surface::distillation:

Replace the mutually recursive check and synth functions with a single term function. Now all logic is contained in one single function, and is IMO easier to understand.
Boolean patterns were erroneously distilled to name patterns instead of boolean patterns in the surface syntax
Avoid allocating an intermediate Vec when distilling a function application to a binop

Nice cleanups!


Enable fuzzing of rav1d

Dav1d has fuzzing workflows configured. We should adopt these to enable detection of any remaining memory safety bugs (e.g. in the assembly routines). It looks like dav1d can fuzz with the following sanitizers enabled: asan, msan, ubsan.

A good first step would be to run the existing tests with address sanitizer enabled. Commands for the C version:
 meson build --buildtype debugoptimized -Dtestdata_tests=true -Dlogging=false -Db_sanitize=address
cd build
export ASAN_OPTIONS=detect_leaks=0 # TODO: figure out why this is required
meson test -v --setup=sanitizer --test-args "--cpumask 0"
meson test -v --setup=sanitizer --test-args "--cpumask 0xff"


Knit.GetController within a Controller - Promise.Error

Hello,
I have made multiple controllers, and I have required them all within my ClientRuntime.client.lua script, but I seem to have some problems with this.
I have one module called MenuController.lua, and another called CameraController.lua, and within my MenuController, I am showing the MainMenu GUI, and within the CameraController, I have a CameraController:Move() function that moves the camera to a position inputted as an argument within the function.
I have used Knit.GetController("CameraController") within my MenuController.lua script, and I am calling the CameraController:Move() function to move the camera to a different position, but sometimes when loading the game, I get a Promise error, and sometimes I don't get a Promise error. The error says that I "attempted to index nil with 'CameraController:Move()'.
MenuController.lua
local knit = require(game:GetService("ReplicatedStorage"):WaitForChild("Knit"))

local MenuController = knit.CreateController {
    Name = "MenuController"
}

local roact = require(game:GetService("ReplicatedStorage"):WaitForChild("Roact"))

local replicatedStorage = game:GetService("ReplicatedStorage")
local players = game:GetService("Players")

local player = players.LocalPlayer
local playerGui = player:WaitForChild("PlayerGui")
local cameraPoints = workspace:WaitForChild("CameraPoints")
local menuCameraPoint = cameraPoints.MenuCameraPoint

local cameraController = knit.GetController("CameraController")

function MenuController:Create()
    local menu = roact.createElement("ScreenGui", {
        Name = "Menu",
        IgnoreGuiInset = true,
        ResetOnSpawn = false
    }, {
        Label = roact.createElement("TextLabel", {
            Name = "Label",
            Text = "Label"
        })
    })

    roact.mount(menu, playerGui, "MainMenu")
end

function MenuController:KnitStart()
    cameraController:Move(menuCameraPoint.CFrame)
    self:Create()
end

return MenuController

CameraController.lua
local knit = require(game:GetService("ReplicatedStorage"):WaitForChild("Knit"))

local CameraController = knit.CreateController {
    Name = "CameraController"
}

local camera = workspace.CurrentCamera

function CameraController:Move(position : CFrame)
    if position then
        repeat
            camera.CameraType = Enum.CameraType.Scriptable
        until camera.CameraType == Enum.CameraType.Scriptable

        camera.CFrame = position
    end
end

return CameraController

Does anyone have any idea why this may be happening, or if I am actually able to call Knit.GetController() within another controller?

This is definitely on you. You're calling it before it exists.

This is definitely on you. You're calling it before it exists. The only safe place to call it is in functions and KnitStart (not KnitInit).

This worked, thank you so much for your response and your help! :)


Add SPDX 2.2.1 support (SBOM) [Work in progress]

See https://spdx.github.io/spdx-spec/ for more details.

/azp run

This is an incredible amount of code for just updating to SPDX 2.2.1; what's actually going on here?