text:
Failed to pull singularity image

Hi, I'm experiencing an error related to singularity images. I run the pipeline as described in https://github.com/nf-core/rnaseq/issues/481
Here's the log:
executor >  pbs (4)
[98/20b915] process > INPUT_CHECK:SAMPLESHEET_CHE... [100%] 1 of 1, cached: 1 ✔
[6d/35856c] process > CAT_FASTQ (tumor_R1)           [100%] 1 of 1, cached: 1 ✔
[ca/abf284] process > FASTQC_UMITOOLS_TRIMGALORE:... [100%] 1 of 1, cached: 1 ✔
[0f/3f31b3] process > FASTQC_UMITOOLS_TRIMGALORE:... [100%] 1 of 1, cached: 1 ✔
[24/9fa24a] process > SORTMERNA (tumor_R1)           [100%] 1 of 1, cached: 1 ✔
[6f/4b3d46] process > ALIGN_STAR:STAR_ALIGN (tumo... [100%] 1 of 1, cached: 1 ✔
[64/800680] process > ALIGN_STAR:BAM_SORT_SAMTOOL... [100%] 1 of 1, cached: 1 ✔
[e4/9c4a76] process > ALIGN_STAR:BAM_SORT_SAMTOOL... [100%] 1 of 1, cached: 1 ✔
[d0/65f8df] process > ALIGN_STAR:BAM_SORT_SAMTOOL... [100%] 1 of 1, cached: 1 ✔
[83/c5e2e3] process > ALIGN_STAR:BAM_SORT_SAMTOOL... [100%] 1 of 1, cached: 1 ✔
[ee/87f4d3] process > ALIGN_STAR:BAM_SORT_SAMTOOL... [100%] 1 of 1, cached: 1 ✔
[-        ] process > MULTIQC_CUSTOM_FAIL_MAPPED     -
[-        ] process > PRESEQ_LCEXTRAP (tumor_R1)     -
[47/fd4a28] process > MARK_DUPLICATES_PICARD:PICA... [100%] 1 of 1, cached: 1 ✔
[-        ] process > MARK_DUPLICATES_PICARD:SAMT... -
[-        ] process > MARK_DUPLICATES_PICARD:BAM_... -
[-        ] process > MARK_DUPLICATES_PICARD:BAM_... -
[-        ] process > MARK_DUPLICATES_PICARD:BAM_... -
[-        ] process > STRINGTIE                      -
[-        ] process > SUBREAD_FEATURECOUNTS (tumo... -
[-        ] process > FEATURECOUNTS_MERGE_COUNTS     -
[-        ] process > DESEQ2_QC_FEATURECOUNTS        -
[-        ] process > SUBREAD_FEATURECOUNTS_BIOTY... -
[-        ] process > MULTIQC_CUSTOM_BIOTYPE         -
[98/bd1c69] process > GET_CHROM_SIZES (genome.fa)    [100%] 1 of 1, cached: 1 ✔
[-        ] process > BEDTOOLS_GENOMECOV             -
[-        ] process > UCSC_BEDRAPHTOBIGWIG           -
[-        ] process > QUALIMAP_RNASEQ                -
[-        ] process > DUPRADAR                       -
[-        ] process > RSEQC:RSEQC_BAMSTAT            -
[-        ] process > RSEQC:RSEQC_INNERDISTANCE      -
[-        ] process > RSEQC:RSEQC_INFEREXPERIMENT    -
[-        ] process > RSEQC:RSEQC_JUNCTIONANNOTATION -
[-        ] process > RSEQC:RSEQC_JUNCTIONSATURATION -
[-        ] process > RSEQC:RSEQC_READDISTRIBUTION   -
[-        ] process > RSEQC:RSEQC_READDUPLICATION    -
[-        ] process > MULTIQC_CUSTOM_STRAND_CHECK    -
[9d/5ed2e5] process > QUANTIFY_SALMON:SALMON_QUAN... [100%] 1 of 1, cached: 1 ✔
[82/3d44d9] process > QUANTIFY_SALMON:SALMON_TX2G... [100%] 1 of 1, cached: 1 ✔
[e6/b6f1aa] process > QUANTIFY_SALMON:SALMON_TXIM... [100%] 1 of 1, cached: 1 ✔
[dd/716235] process > QUANTIFY_SALMON:SALMON_MERG... [100%] 1 of 1, cached: 1 ✔
[a0/ee9f13] process > QUANTIFY_SALMON:SALMON_SE_G... [100%] 1 of 1, cached: 1 ✔
[54/61202a] process > QUANTIFY_SALMON:SALMON_SE_T... [100%] 1 of 1, cached: 1 ✔
[f7/b599e6] process > DESEQ2_QC_SALMON               [100%] 1 of 1, cached: 1 ✔
[-        ] process > GET_SOFTWARE_VERSIONS          -
[-        ] process > MULTIQC                        -
-[nf-core/rnaseq] [PASS] STAR 5% mapped threshold: 55.72% - tumor_R1.
Pulling Singularity image docker://quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1 [cache dbs/singularity_cache/quay.io-biocontainers-rseqc-3.0.1--py37h516909a_1.img]
Pulling Singularity image docker://quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0 [cache dbs/singularity_cache/quay.io-biocontainers-bedtools-2.29.2--hc088bd4_0.img]
Pulling Singularity image docker://quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0 [cache dbs/singularity_cache/quay.io-biocontainers-stringtie-2.1.4--h7e0af3c_0.img]
Pulling Singularity image docker://quay.io/biocontainers/bioconductor-dupradar:1.18.0--r40_1 [cache dbs/singularity_cache/quay.io-biocontainers-bioconductor-dupradar-1.18.0--r40_1.img]
Pulling Singularity image docker://quay.io/biocontainers/qualimap:2.2.2d--1 [cache dbs/singularity_cache/quay.io-biocontainers-qualimap-2.2.2d--1.img]
Error executing process > 'BEDTOOLS_GENOMECOV (tumor_R1)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name quay.io-biocontainers-bedtools-2.29.2--hc088bd4_0.img docker://quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0 > /dev/null
  status : 255
  message:
    INFO:    Converting OCI blobs to SIF format
    FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: unable to create new build: while ensuring correct compression algorithm: while reading test squashfs: open /scratch/27815062.moab/bundle-temp-868906504/squashfs-gzip-comp-test-098449530: no such file or directory

I saw this issue happening almost any run I tried.
Thanks in advance!

Hi @l0ka it may be because your home directory is full. There should be a ~/.singularity directory there that could be filling up. Can you try and delete that and try again? It may be easier to respond to these failures on the #rnaseq channel on the nf-core Slack workspace.

Hi @drpatelh, This worked out for me when I moved into a directory with more storage, Thanks.

Great thanks for letting me know @AhmedMohamed1993! I think that is the solution here so will close 👍

Hi @drpatelh, sorry for the late reply, I was very busy these days.
Anyway, I'm still experiencing this issue sometimes. As you can see from https://github.com/nf-core/rnaseq/issues/481 I set the cacheDir parameter (specifically it's a folder outside my /home directory, in the HPC cluster storage and there are plenty of  PBs available) and all pipeline runs are performed outside /home. Additionally, if I rerun the pipeline using the -resume flag sometimes it works fine and sometimes it fails with the very same error.
In the next days I'm planning to analyze a lot of samples, so I will have more precise details and I'll let you know.
Thank you!

Hi @l0ka . No worries 🙂 So the cacheDir parameter controls where the final images are stored but if you are downloading Docker containers and using -profile singularity then they need to be converted to Singularity images. This creates a bunch of temp files in ~/.singularity that eventually fill up your home directory and start generating errors like you reported above. The easiest solution is to soft-link that directory to somewhere where you have enough space.
It's odd though that you say it's an intermittent issue...in theory you shouldn't be able to download any more images if your home directory is full. Anyway, I definitely think this is a local issue.

The ~/.singularity directory is already symlinked outside /home, I'm sorry I forgot to mention it before. That's also why I found this thing odd. Since you're sure it cannot be a "pipeline-related" issue, the only one thing I can think about is some problems with the storage/folders. I'll check and keep you posted if I run into this issue again.

Hi @drpatelh I finally had time to inspect the results. I run the pipeline on 33 samples. I submit a job (pbs system) for each sample, to have single log files. Out of 33 runs, 18 were ok and 15 failed. Among the 15 failed runs:

1 failed because a fastq is corrupted;
1 failed with this message:
Unknown error accessing project nf-core/rnaseq -- Repository may be corrupted: /home/people/aluloc/.nextflow/assets/nf-core/rnaseq
1 failed because exceeded walltime limit;
1 failed because of PICARD_MARKDUPLICATES:

Error executing process > 'RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (tumor_R1)'

Caused by:
  Process `RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES (tumor_R1)` terminated with an error exit status (1)

Command executed:

  picard \
      -Xmx36g \
      MarkDuplicates \
      ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp \
      INPUT=tumor_R1.sorted.bam \
      OUTPUT=tumor_R1.markdup.sorted.bam \
      METRICS_FILE=tumor_R1.markdup.sorted.MarkDuplicates.metrics.txt

  echo $(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > picard.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:17,788
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1244
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:29,767
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1957
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:16,387
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1350
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:7,075
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1264
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:28,429
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1197
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:20,654
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	Large duplicate set. size = 1313
  INFO	2020-11-06 14:12:37	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:18,069
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1294
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:14,687
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1021
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:1,642
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1011
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:14,705
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1404
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:28,791
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1556
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:21,766
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	Large duplicate set. size = 1027
  INFO	2020-11-06 14:12:38	OpticalDuplicateFinder	compared         1,000 ReadEnds to others.  Elapsed time: 00:00:00s.  Time for last 1,000:    0s.  Last read position: 0:14,308
  INFO	2020-11-06 14:12:40	MarkDuplicates	Traversing fragment information and detecting duplicates.
  INFO	2020-11-06 14:12:46	MarkDuplicates	Sorting list of duplicate records.
  INFO	2020-11-06 14:12:49	MarkDuplicates	After generateDuplicateIndexes freeMemory: 18014140976; totalMemory: 27699183616; maxMemory: 38654705664
  INFO	2020-11-06 14:12:49	MarkDuplicates	Marking 54115970 records as duplicates.
  INFO	2020-11-06 14:12:49	MarkDuplicates	Found 150959 optical duplicate clusters.
  INFO	2020-11-06 14:12:49	MarkDuplicates	Reads are assumed to be ordered by: coordinate
  INFO	2020-11-06 14:14:20	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:30s.  Time for last 10,000,000:   90s.  Last read position: 2:216,299,484
  INFO	2020-11-06 14:15:52	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:02s.  Time for last 10,000,000:   92s.  Last read position: 6:32,132,427
  INFO	2020-11-06 14:17:20	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:31s.  Time for last 10,000,000:   88s.  Last read position: 9:9,442,111
  .command.run: line 38: /dev/fd/62: No such file or directory
  INFO	2020-11-06 14:18:49	MarkDuplicates	Written    40,000,000 records.  Elapsed time: 00:05:59s.  Time for last 10,000,000:   88s.  Last read position: 12:94,962,998
  INFO	2020-11-06 14:20:06	MarkDuplicates	Written    50,000,000 records.  Elapsed time: 00:07:16s.  Time for last 10,000,000:   77s.  Last read position: 14:50,053,433
  INFO	2020-11-06 14:21:25	MarkDuplicates	Written    60,000,000 records.  Elapsed time: 00:08:35s.  Time for last 10,000,000:   78s.  Last read position: 14:50,320,475
  INFO	2020-11-06 14:22:47	MarkDuplicates	Written    70,000,000 records.  Elapsed time: 00:09:57s.  Time for last 10,000,000:   81s.  Last read position: 16:84,600,295
  INFO	2020-11-06 14:24:10	MarkDuplicates	Written    80,000,000 records.  Elapsed time: 00:11:20s.  Time for last 10,000,000:   83s.  Last read position: 22:38,879,746
  INFO	2020-11-06 14:24:43	MarkDuplicates	Writing complete. Closing input iterator.
  INFO	2020-11-06 14:24:43	MarkDuplicates	Duplicate Index cleanup.
  INFO	2020-11-06 14:24:43	MarkDuplicates	Getting Memory Stats.
  INFO	2020-11-06 14:24:44	MarkDuplicates	Before output close freeMemory: 132199224; totalMemory: 142606336; maxMemory: 38654705664
  INFO	2020-11-06 14:24:45	MarkDuplicates	Closed outputs. Getting more Memory Stats.
  INFO	2020-11-06 14:24:45	MarkDuplicates	After output close freeMemory: 49317928; totalMemory: 58720256; maxMemory: 38654705664
  [Fri Nov 06 14:24:45 GMT 2020] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 17.59 minutes.
  Runtime.totalMemory()=58720256
  .command.run: line 166: kill: (18008) - No such process
  INFO:    Cleaning up image...

1 failed because of QUALIMAP_RNASEQ:

Error executing process > 'RNASEQ:QUALIMAP_RNASEQ (tumor_R1)'

Caused by:
  Process `RNASEQ:QUALIMAP_RNASEQ (tumor_R1)` terminated with an error exit status (1)

Command executed:

  unset DISPLAY
  mkdir tmp
  export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
  qualimap \
      --java-mem-size=36G \
      rnaseq \
       \
      -bam tumor_R1.markdup.sorted.bam \
      -gtf genes.gtf \
      -p strand-specific-reverse \
      -pe \
      -outdir tumor_R1

  echo $(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*$//' > qualimap.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Convert SIF file to sandbox...
  ERROR  : Failed to create user namespace: user namespace disabled

3 failed because of TRIMGALORE:

Error executing process > 'RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (tumor_R1)'

Caused by:
  Process `RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (tumor_R1)` terminated with an error exit status (1)

Command executed:

  [ ! -f  tumor_R1_1.fastq.gz ] && ln -s tumor_R1_1.merged.fastq.gz tumor_R1_1.fastq.gz
  [ ! -f  tumor_R1_2.fastq.gz ] && ln -s tumor_R1_2.merged.fastq.gz tumor_R1_2.fastq.gz
  trim_galore \
      --fastqc \
      --cores 4 \
      --paired \
      --gzip \
       \
       \
       \
       \
      tumor_R1_1.fastq.gz \
      tumor_R1_2.fastq.gz
  echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//' > trimgalore.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  126	58	0.8	1	18 40
  127	59	0.8	1	19 40
  128	61	0.8	1	21 40
  129	104	0.8	1	21 83
  130	315	0.8	1	110 205
  131	125	0.8	1	34 91
  132	1452	0.8	1	458 994
  133	86	0.8	1	20 66
  134	37	0.8	1	10 27
  135	36	0.8	1	12 24
  136	19	0.8	1	3 16
  137	26	0.8	1	4 22
  138	26	0.8	1	3 23
  139	31	0.8	1	1 30
  140	15	0.8	1	2 13
  141	20	0.8	1	1 19
  142	14	0.8	1	3 11
  143	18	0.8	1	3 15
  144	20	0.8	1	5 15
  145	16	0.8	1	2 14
  146	36	0.8	1	0 36
  147	19	0.8	1	7 12
  148	51	0.8	1	4 47
  149	70	0.8	1	7 63
  150	304	0.8	1	11 293
  151	4321	0.8	1	76 4245

  RUN STATISTICS FOR INPUT FILE: tumor_R1_2.fastq.gz
  =============================================
  50998158 sequences processed in total
  The length threshold of paired-end sequences gets evaluated later on (in the validation step)

  Validate paired-end files tumor_R1_1_trimmed.fq.gz and tumor_R1_2_trimmed.fq.gz
  file_1: tumor_R1_1_trimmed.fq.gz, file_2: tumor_R1_2_trimmed.fq.gz

  pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory

  >>>>> Now validing the length of the 2 paired-end infiles: tumor_R1_1_trimmed.fq.gz and tumor_R1_2_trimmed.fq.gz <<<<<
  pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
  Writing validated paired-end Read 1 reads to tumor_R1_1_val_1.fq.gz
  Writing validated paired-end Read 2 reads to tumor_R1_2_val_2.fq.gz

  Total number of sequences analysed: 0

  Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (N/A%)
  pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
  Died at /usr/local/bin/trim_galore line 2009.
  pigz: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
  .command.run: line 166: kill: (1962) - No such process
  INFO:    Cleaning up image...

7 failed because of TRIMGALORE_FASTQC:

Error executing process > 'RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (tumor_R1)'

Caused by:
  Process `RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (tumor_R1)` terminated with an error exit status (1)

Command executed:

  [ ! -f  tumor_R1_1.fastq.gz ] && ln -s tumor_R1_1.merged.fastq.gz tumor_R1_1.fastq.gz
  [ ! -f  tumor_R1_2.fastq.gz ] && ln -s tumor_R1_2.merged.fastq.gz tumor_R1_2.fastq.gz
  fastqc --quiet --threads 6 tumor_R1_1.fastq.gz tumor_R1_2.fastq.gz
  fastqc --version | sed -e "s/FastQC v//g" > fastqc.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Convert SIF file to sandbox...
  ERROR  : Failed to create user namespace: user namespace disabled

All jobs were launched at the very same time, allocating the same resources (CPUs, RAM, walltime) and using the same config file. Notably, for some of the failed samples I previously obtained successful runs, when I was testing the pipeline (using the very same code, config, options, ecc...).
I'll try to rerun the pipeline, using the -resume option for the failed samples and see what happen.

Update: rerunning the pipeline using the -resume option caused the abortion of the run, exiting with the same error messages as before. Now I completely cleared the ~/.singularity cache folder (it was "only" 611MB and it is symlinked to another location, so definitely no problems of space) and launch the pipeline from the beginning and it seems to be running fine.

Yeah, sorry @l0ka. I tried to wipe my cache and start again and I had all sorts of intermittent issues where the pipeline failed to pull different containers... 😏 I thought the container hosting etc would be much more stable than this but we will just have to deal with this on case-by-case basis. I am going to add some docs to the main README of the pipeline to suggest using NXF_SINGULARITY_CACHEDIR or singularity.cacheDir when running with Singularity. At least this means that you only need to go through the hassle of pulling these containers once and then you can re-use them for future runs. Thank you for all of your feedback!

More docs added in https://github.com/nf-core/rnaseq/pull/490

Ok, cool, now I'm relieved :relieved: At least we know what to do when it fails to pull containers.
Thanks for the support and good luck with the new release!! Can't wait to try it :smirk:

Hi I met this problem but no use when I delete the singularity dir. Could you check it ? Thanks
N E X T F L O W  ~  version 21.10.1
Launching rnaseq/main.nf [elated_ramanujan] - revision: bb0fa33a13

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__  __ /   /  \ |__) |__         }  {   | \| |       \__, \__/ |  \ |___     \-.,--,                                         .,._,'
nf-core/rnaseq v3.4
Core Nextflow options
runName            : elated_ramanujan
containerEngine    : singularity
container          : nfcore-rnaseq.simg
launchDir          : /scratch-cbe/users/shuangyang.wu/H1/rnaseq
workDir            : /scratch-cbe/users/shuangyang.wu/H1/rnaseq/work
projectDir         : /scratch-cbe/users/shuangyang.wu/H1/rnaseq/rnaseq
userName           : shuangyang.wu
profile            : singularity
configFiles        : /scratch-cbe/users/shuangyang.wu/H1/rnaseq/rnaseq/nextflow.config
Input/output options
input              : sample.csv
Reference genome options
genome             : TAIR10
fasta              : s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa
gtf                : s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf
gene_bed           : s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed
star_index         : s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/
Alignment options
skip_markduplicates: true
!! Only displaying parameters that differ from the pipeline defaults !!
If you use nf-core/rnaseq for your analysis please cite:

The pipeline
https://doi.org/10.5281/zenodo.1400710

The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

Software dependencies
https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES               [  0%] 0 of 1
executor >  local (1)
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
executor >  local (1)
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
[9a/ec55f5] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa)   [  0%] 0 of 1
[-        ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP                              -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ                              -
executor >  local (1)
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
[9a/ec55f5] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa)   [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP                              -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ                              -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT                  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION               -
executor >  local (1)
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRAN... -
[9a/ec55f5] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa)   [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SA... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP                              -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE                                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHT... -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ                              -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT                  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION                 -
[-        ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION                  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS                  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC                                      -
Pulling Singularity image https://depot.galaxyproject.org/singularity/python:3.8.3 [cache /scratch-cbe/users/shuangyang.wu/H1/rnaseq/work/singularity/depot.galaxyproject.org-singularity-python-3.8.3.img]
Execution cancelled -- Finishing pending tasks before exit
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /scratch-cbe/users/shuangyang.wu/H1/rnaseq/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa)'
Caused by:
Process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa) terminated with an error exit status (255)
Command executed:
samtools
faidx
genome.fa
cut -f 1,2 genome.fa.fai > genome.fa.sizes
cat <<-END_VERSIONS > versions.yml
GET_CHROM_SIZES:
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS
Command exit status:
255
Command output:
(empty)
Command error:
INFO:    Converting SIF file to temporary sandbox...
FATAL:   while extracting /scratch-cbe/users/shuangyang.wu/H1/rnaseq/work/singularity/depot.galaxyproject.org-singularity-samtools-1.10--h9402c20_2.img: root filesystem extraction failed: extract command failed: ERROR  : Failed to create user namespace: user namespace disabled
: exit status 1
Work dir:
/scratch-cbe/users/shuangyang.wu/H1/rnaseq/work/9a/ec55f5af0ff3ff2e8e2cc1803bf51e
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
Unexpected error [AbortedException]
-- Check script 'rnaseq/./workflows/rnaseq.nf' at line: 603 or see '.nextflow.log' file for more details

repo: nf-core/rnaseq


text:
Make publishDir mode configurable.

Just a suggestion, feel free to discard...
In our lab, we prefer to use link over copy because our file system supports it and copying is a waste of time and space.
PR checklist

[x] PR is to dev rather than master
[x] This comment contains a description of changes (with reason)
[ ] Ensure the test suite passes (nextflow run . -profile test,docker).
[ ] Make sure your code lints (nf-core lint .).
[x] Documentation in docs is updated
[x] CHANGELOG.md is updated

Learn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md

I guess that one has to be merged in first, then all the linting errors should be gone hopefully 🤞
https://github.com/nf-core/rnaseq/pull/382

Merge #394 first!

source: gharchive/pull-request

authors: apeltzer grst

license: MIT

license_type: permissive

license_source: github-api


text:
Upcoming event banner doesn't show the next event

... but some event further in the future (maybe the most recently added one?). Showing the next occurring event might make more sense and would also help to not miss the recurring online meetings.

Fixed! Will be live soon!

source: gharchive/issue

authors: Freymaurer StellaEggels


text:
add issue templates

added templates for bugs, missing topics, missing tutorials and for pull requests

#2


text:
running with nohup causes unpacking error

This is the error:

File "/usr/local/lib/python2.7/dist-packages/pytube/cli.py", line 98, in get_terminal_size
rows, columns = os.popen('stty size', 'r').read().split()
ValueError: need more than 0 values to unpack

apparently "stty size" when ran under nohup returns

stty: standard input: Inappropriate ioctl for device

and not the with and the height of the terminal, which is what stty expects

When you do a nohup, the process is no longer attached to the terminal. As such, it is not able to get the height and width of the terminal.

repo: nficano/pytube

license: Unlicense


text:
480p is not detected

Clearly, the video in browser has 480p and its quality is good enough. Pytube does not detect this resolution at all.
yt = YouTube('https://www.youtube.com/watch?v=OFDT-BRU6Zo')
yt.streams.all()
[<Stream: itag="43" mime_type="video/webm" res="360p" fps="30fps" vcodec="vp8.0" acodec="vorbis">, <Stream: itag="18" mime_type="video/mp4" res="360p" fps="30fps" vcodec="avc1.42001E" acodec="mp4a.40.2">, <Stream: itag="36" mime_type="video/3gpp" res="240p" fps="30fps" vcodec="mp4v.20.3" acodec="mp4a.40.2">, <Stream: itag="17" mime_type="video/3gpp" res="144p" fps="30fps" vcodec="mp4v.20.3" acodec="mp4a.40.2">]

Hm...
My parsing result for this videoID is:
<Stream: itag="17" mime_type="video/3gpp" res="144p" fps="30fps" vcodec="mp4v.20.3" acodec="mp4a.40.2">
{
"itag":17,
"url":"https:...",
"mimeType":"video/3gpp; codecs=\"mp4v.20.3, mp4a.40.2\"",
"bitrate":51374,
"width":176,
"height":144,
"lastModified":"1474228861952205",
"contentLength":"7946376",
"quality":"small",
"qualityLabel":"144p",
"projectionType":"RECTANGULAR",
"averageBitrate":51373,
"audioQuality":"AUDIO_QUALITY_LOW",
"approxDurationMs":"1237437",
"audioSampleRate":"22050"
},
<Stream: itag="18" mime_type="video/mp4" res="360p" fps="30fps" vcodec="avc1.42001E" acodec="mp4a.40.2">
{
"itag":18,
"url":"https:...",
"mimeType":"video/mp4; codecs=\"avc1.42001E, mp4a.40.2\"",
"bitrate":308270,
"width":480,
"height":360,
"lastModified":"1474228871878290",
"contentLength":"47679150",
"quality":"medium",
"qualityLabel":"360p",
"projectionType":"RECTANGULAR",
"averageBitrate":308255,
"audioQuality":"AUDIO_QUALITY_LOW",
"approxDurationMs":"1237391",
"audioSampleRate":"44100"
},
<Stream: itag="36" mime_type="video/3gpp" res="240p" fps="30fps" vcodec="mp4v.20.3" acodec="mp4a.40.2">
{
"itag":36,
"url":"https:...",
"mimeType":"video/3gpp; codecs=\"mp4v.20.3, mp4a.40.2\"",
"bitrate":174350,
"width":320,
"height":240,
"lastModified":"1474228886702265",
"contentLength":"26966139",
"quality":"small",
"qualityLabel":"240p",
"projectionType":"RECTANGULAR",
"averageBitrate":174335,
"audioQuality":"AUDIO_QUALITY_LOW",
"approxDurationMs":"1237437",
"audioSampleRate":"22050"
},
<Stream: itag="43" mime_type="video/webm" res="360p" fps="30fps" vcodec="vp8.0" acodec="vorbis">
{
"itag":43,
"url":"https:...",
"mimeType":"video/webm; codecs=\"vp8.0, vorbis\"",
"bitrate":2147483647,
"width":640,
"height":360,
"lastModified":"1474326126568872",
"contentLength":"33388685",
"quality":"medium",
"qualityLabel":"360p",
"projectionType":"RECTANGULAR",
"audioQuality":"AUDIO_QUALITY_MEDIUM"
}
I parse the original html page and I got the exact same result.
P.S. But, Third-party programs, such as IDM, find 8 download links. Including with quality 480p


text:
Azure: Implement forced VM shutdown

AzureHostingManager.StopClusterAsync() currently ignores the stopMode parameter and always shuts the cluster down gracefully.
It looks like Azure added the capability for non-graceful shutdown int 2019 but this isn't available the Fluent API.  We'll probably need to upgrade to the latest API to pick this up.

DONE

repo: nforgeio/neonKUBE


text:
Kubernetes setup

[x] Linux configuration

[x] NTP sources
[x] Verify APT package cache is working
[x] Kernel settings
[x] Improve entropy generation

[x] Download/cache client-side Kubernetes binaries
[x] Node setup
[x] Create cluster
[x] Ensure that Kubernetes folders will end up on mounted Azure/AWS drives.
It looks like this is already handled by the symbolic Docker folder links to /mnt-data.
[x] Node labels: kubectl label nodes <node-name> <label-key>=<label-value> ...
[x] Configure Helm

[x] Helm executable on Windows?

[x] Configure network
[x] Configure Istio/ingress
[x] Login commands

[x] login context
[x] login ls
[x] login import file
[x] login export file
[x] login status
[x] logout

[x] Connection commands:

[x] neon ssh
[x] neon scp
[x] Uncomment strong password code

[x] Dashboard command

[x] local proxy

[ ] Components

[x] network CNI: reason:NetworkPluginNotReady
[x] Optionally allow pods on masters:
kubectl taint nodes --all node-role.kubernetes.io/master-
[x] Dashboard

[x] HA load balancer
[x] Do we need an entropy generator?
https://wiki.archlinux.org/index.php/Rng-tools
https://wiki.archlinux.org/index.php/Haveged

Loose ends:

[x] Auto start isn't working
[x] Can we rename the "Start the app" check box to neonKUBE Desktop from the exe name?
[x] Create the NEONKUBE_PROGRAM_FOLDER environment variable and set this to the program files path.  Be sure to delete this for uninstall.
[x] Uninstall needs to terminate the desktop app if it's running so everything can be removed.
[x] Desktop should ensure that only a single instance of itself is running.

I moved a few lower priority items to #424 and am going to close this.


text:
[CodeGen] List<List> generates unexpected ` character

Here's an example of some generated code for a nested List:
this.Coordinates = property.Value.ToObject<global::System.Collections.Generic.List<List`1>>(RoundtripDataHelper.Serializer);

Merged this into #538

authors: jefflill marcusbooyah


text:
SshProxy sudo init not working on XenServer/XCP-ng

I recently refactored how disabling sudo password prompts work for SshProxy<T>.  I tested this VMs provisioned via our Ubuntu 20.04.x templates on both Hyper-V and XenServer/XCP-ng (an exisiting instance).
XenServer/XCP-ng provisioning operations are now failing on a brand-new XCP-ng installation:
*** STATUS: connecting...
*** WAITFORBOOT: CONNECT TO [10.0.0.5:22]
*** STATUS: prepare: user folders
START: sudo bash -c 'if [ -f "/etc/sshproxy-init" ] ; then exit 0; else exit 1; fi'
STDERR
    sudo: sorry, you must have a tty to run sudo
END [ERROR=1]
*** STATUS: prepare: sudo
*** STATUS: connected
*** Downloading: /etc/os-release
START: sudo bash -c 'cp /etc/os-release /home/root/.neonkube/download/os-release-e31e0dcc-7b28-4267-9f61-a33793831cd0'
STDERR
    sudo: sorry, you must have a tty to run sudo
END [ERROR=1]
*** ERROR: *** ERROR Downloading: [SshProxyException]: [exitcode=1]: sudo: sorry, you must have a tty to run sudo

*** STACK:    at Neon.Kube.SshProxy`1.Download(String source, Stream output) in C:\src\neonKUBE\Lib\Neon.Kube\Proxies\SshProxy.cs:line 1538
START: sudo bash -c 'if [ -f "/home/root/.neonkube/download/os-release-e31e0dcc-7b28-4267-9f61-a33793831cd0" ] ; then rm "/home/root/.neonkube/download/os-release-e31e0dcc-7b28-4267-9f61-a33793831cd0" ; fi'
STDERR
    sudo: sorry, you must have a tty to run sudo
END [ERROR=1]
*** STATUS: [x] DONE
*** STATUS: check: virtual machines
START: xe vm-list params=all
END [OK]
*** STATUS: [x] DONE
*** STATUS: check: template
START: xe template-list params=all
END [OK]
*** STATUS: download: vm template (slow)
START: xe sr-list params=all
END [OK]
START: xe vm-import url=http://s3-us-west-2.amazonaws.com/neonforge/kube/xenserver-ubuntu-20.04.latest.xva sr-uuid=80273954-87d9-5ac4-8610-11953ce1f5b8
END [OK]
START: xe template-list params=all
END [OK]
START: xe template-param-set uuid=8aa4cc12-b9cf-5d9a-4285-ebdfb5488086 name-label=neon-ubuntu-20.04.latest
END [OK]
START: xe template-list params=all
END [OK]
*** STATUS: [x] DONE
START: xe host-list
END [OK]
START: xe host-param-list uuid=84f17839-6c52-4a90-8131-be3eadaf9778
END [OK]
*** STATUS: [jeff-master-0]: create: virtual machine
START: xe template-list params=all
END [OK]
START: xe sr-list params=all
END [OK]
START: xe vdi-list
END [OK]
START: xe vm-install template=neon-ubuntu-20.04.latest new-name-label=jeff-master-0 sr-uuid=80273954-87d9-5ac4-8610-11953ce1f5b8
END [OK]
START: xe vm-param-set uuid=3a8e1412-6285-1342-e940-06dd3454d84a VCPUs-at-startup=4 VCPUs-max=4
END [OK]
START: xe pool-list
END [OK]
START: xe pool-param-list uuid=f9a8ecae-bd48-d4a6-5656-955da2903e38
END [OK]
START: xe pool-param-set uuid=f9a8ecae-bd48-d4a6-5656-955da2903e38 other-config:auto_poweron=true
END [OK]
START: xe vm-param-set uuid=3a8e1412-6285-1342-e940-06dd3454d84a other-config:auto_poweron=true
END [OK]
START: xe vm-memory-limits-set uuid=3a8e1412-6285-1342-e940-06dd3454d84a dynamic-max=2147483648 dynamic-min=2147483648 static-max=2147483648 static-min=2147483648
END [OK]
START: xe vm-disk-list uuid=3a8e1412-6285-1342-e940-06dd3454d84a
END [OK]
START: xe vdi-resize uuid=5af9d730-2dee-43d8-83e1-61aec2456efd disk-size=10737418240
END [OK]
START: xe vm-list params=all
END [OK]
START: sudo bash -c 'mkdir /var/opt/neon-temp-sr'
STDERR
    sudo: sorry, you must have a tty to run sudo
END [ERROR=1]
START: sudo bash -c 'mkdir /var/opt/neon-temp-sr/68a1157b-b1af-43ad-a523-08c0cf08a045'
STDERR
    sudo: sorry, you must have a tty to run sudo
END [ERROR=1]
*** STATUS: ERROR[1]
*** ERROR: [RemoteCommandException]: [exitcode=1]: sudo bash -c 'export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/lib/neonkube/bin:/lib/neonkube/setup && mkdir /var/opt/neon-temp-sr/68a1157b-b1af-43ad-a523-08c0cf08a045'

*** ERROR: [RemoteCommandException]: [exitcode=1]: sudo bash -c 'export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/lib/neonkube/bin:/lib/neonkube/setup && mkdir /var/opt/neon-temp-sr/68a1157b-b1af-43ad-a523-08c0cf08a045'

*** STACK:    at Neon.Kube.SshProxy`1.RunCommand(String command, RunOptions runOptions, Object[] args) in C:\src\neonKUBE\Lib\Neon.Kube\Proxies\SshProxy.cs:line 2672
   at Neon.Kube.SshProxy`1.SudoCommand(String command, RunOptions runOptions, Object[] args) in C:\src\neonKUBE\Lib\Neon.Kube\Proxies\SshProxy.cs:line 2828
   at Neon.XenServer.XenClient.CreateTempIso(String isoPath, String srName) in C:\src\neonKUBE\Lib\Neon.XenServer\XenClient.cs:line 365
   at Neon.Kube.XenServerHostingManager.ProvisionVirtualMachines(SshProxy`1 xenSshProxy) in C:\src\neonKUBE\Lib\Neon.Kube.XenServer\XenServerHostingManager.cs:line 401
   at Neon.Kube.XenServerHostingManager.<Provision>b__14_2(SshProxy`1 node, TimeSpan stepDelay) in C:\src\neonKUBE\Lib\Neon.Kube.XenServer\XenServerHostingManager.cs:line 234
   at Neon.Kube.SetupController`1.<>c__DisplayClass39_0.<PerformStep>b__2(SshProxy`1 node) in C:\src\neonKUBE\Lib\Neon.Kube\Setup\SetupController.cs:line 532

Note these errors: sudo: sorry, you must have a tty to run sudo
Note that XenServer/XCP-ng are running on Centos, not Ubuntu.  The existing server had already been configured to disable sudo password prompts (from previous connections) whereas the brand new server needs to be configured.  I must need to do something different for Centos.

Here's a link discussing this:
https://www.shell-tips.com/linux/sudo-sorry-you-must-have-a-tty-to-run-sudo/
It looks like Centos/RHEL shipped with a /etc/sudoers file that requires a TTY which people complained about back in 2014 as non-standard and not really helpful:
https://bugzilla.redhat.com/show_bug.cgi?id=1020147#c9
This was fixed back in 2014, but who knows whether XenServer/XCP-ng ever picked up the new version.

I recently removed the SshProxt<T> code that used SSH.NET ShellStream to tweak these values:
// We need to make sure requiretty is turned off and that sudo can execute commands without a password.
// The sleeps are required when using the ShellStream, otherwise the commands won't work.

using (var sh = sshClient.CreateShellStream("terminal", 80, 40, 80, 40, 1024))
{
    sh.WriteLine("grep -qxF 'Defaults !requiretty' /etc/sudoers.d/notty || echo 'Defaults !requiretty' >> /etc/sudoers.d/notty");
    Thread.Sleep(500);
    sh.WriteLine("grep -qxF '%sudo    ALL=NOPASSWD: ALL' /etc/sudoers.d/nopasswd || echo '%sudo    ALL=NOPASSWD: ALL' >> /etc/sudoers.d/nopasswd");
    Thread.Sleep(500);
}

...so we've been missing with security all along.
This code is no longer required for Ubuntu servers and it wouldn't quite work for XenServer/XCP-ng because CentOS doesn't ship with the /etc/sudoers.d/notty and /etc/sudoers.d/nopasswd files.  Rather than hardcoding a solution that works just for this scenario, I'm going to add an optional action parameter to SshProxy<T>.Connect() and WaitForBoot() that will be called immediately after the SSH connection is established such that the caller can take the appropriate actions.

I ended up just handling this in SshProxt<T> code rather than exposing a custom action to keep things simple.

FIXED for v2.2.0


text:
Not handle error event

/cc @nfroidure
In this line https://github.com/nfroidure/SVGPathData/blob/master/src/SVGPathData.js#L114
Error:
SyntaxError: Unexpected character "N" at index 2.
    at SVGPathDataParser._transform (/path/to/node_modules/svg-pathdata/src/SVGPathDataParser.js:461:28)
    at SVGPathDataParser.Transform._read (/path/to/node_modules/svg-pathdata/node_modules/readable-stream/lib/_stream_transform.js:159:10)
    at SVGPathDataParser.Transform._write (/path/to/node_modules/svg-pathdata/node_modules/readable-stream/lib/_stream_transform.js:147:83)
    at doWrite (/path/to/node_modules/svg-pathdata/node_modules/readable-stream/lib/_stream_writable.js:313:64)
    at writeOrBuffer (/path/to/node_modules/svg-pathdata/node_modules/readable-stream/lib/_stream_writable.js:302:5)
    at SVGPathDataParser.Writable.write (/path/to/node_modules/svg-pathdata/node_modules/readable-stream/lib/_stream_writable.js:241:11)
    at Function.SVGPathData.parse (/path/to/node_modules/svg-pathdata/src/SVGPathData.js:124:10)
    at new SVGPathData (/path/to/node_modules/svg-pathdata/src/SVGPathData.js:4:31)
    at /path/to/node_modules/svgicons2svgfont/src/index.js:341:20
    at Array.forEach (native)
    at SVGIcons2SVGFontStream._svgIcons2SVGFontStreamFlush [as _flush] (/path/to/node_modules/svgicons2svgfont/src/index.js:313:12)
    at SVGIcons2SVGFontStream.<anonymous> (/path/to/node_modules/readable-stream/lib/_stream_transform.js:115:49)
    at SVGIcons2SVGFontStream.g (events.js:291:16)
    at emitNone (events.js:86:13)
    at SVGIcons2SVGFontStream.emit (events.js:185:7)
    at prefinish (/path/to/node_modules/readable-stream/lib/_stream_writable.js:475:12)
    at finishMaybe (/path/to/node_modules/readable-stream/lib/_stream_writable.js:483:7)
    at afterWrite (/path/to/node_modules/readable-stream/lib/_stream_writable.js:367:3)
    at onwrite (/path/to/node_modules/readable-stream/lib/_stream_writable.js:358:9)
    at WritableState.onwrite (/path/to/node_modules/readable-stream/lib/_stream_writable.js:122:5)
    at afterTransform (/path/to/node_modules/readable-stream/lib/_stream_transform.js:81:3)
    at TransformState.afterTransform (/path/to/node_modules/readable-stream/lib/_stream_transform.js:58:12)
    at SAXStream.svgicons2svgfontSaxEnbCb (/path/to/node_modules/svgicons2svgfont/src/index.js:259:7)
    at emitNone (events.js:86:13)
    at SAXStream.emit (events.js:185:7)
    at SAXParser.SAXStream._parser.onend (/path/to/node_modules/sax/lib/sax.js:190:10)
    at emit (/path/to/node_modules/sax/lib/sax.js:640:35)
    at end (/path/to/node_modules/sax/lib/sax.js:683:5)
    at SAXParser.end (/path/to/node_modules/sax/lib/sax.js:154:24)
    at SAXStream.end (/path/to/node_modules/sax/lib/sax.js:248:18)

I am use https://github.com/nfroidure/svgicons2svgfont package in my package https://github.com/itgalaxy/webfont. If i run watch and use normalize: true and have one bad svg icon (empty file), other icons is good, i got this error.

This exception is probably raised by the fact you are providing a SVG file with invalid path data (probably a string begginning by N). I think you should avoid sending empty SVG files to this module.
That said, i would need more feedback in order to support you in solving this issue. A sample project reproducing the behavior with a minimal set of icons would be the best.

@nfroidure thanks for answer, if I find the time to'll create an example

Closing since no move for a long time.

authors: evilebottnawi nfroidure

repo: nfroidure/SVGPathData

license: mit

license_source: bigquery


text:
Use correct pitch-bend range

In MIDI, the pitch-bend range is 2 per default, but can be modified via specific RPN messages, usually followed by specific "Data Entry" messages: http://midi.teragonaudio.com/tech/midispec/rpn.htm
Please take those MIDI messages into account, so that the pitch bend is correct.
Examples where MIDIFile.js does not take those MIDI messages into account correctly are discussed at https://github.com/surikov/webaudiofont/issues/93
Thank you!

Thanks for notifying us! Unfortunately I have no idea  how  to implement it, so I hope someone else will.

As far as I understand, this is achieved by three to four consecutive MIDI control messages. In hexadecimal, they look like this:
B06500
B06400
B00602
B02604
The "0" after the "B" is the MIDI channel (for example zeroth channel that plays a guitar) for which the pitch-bend range is being set.
The "02" in the end of the third message is the number of semitones by which the pitch can bend.
The "04" in the end of the fourth message is the number of cents to be added to the semitones.
The last message is optional, i.e. if there is no message of the form /B.26../ (like "B02604" in the example) then the number of cents is zero.
Here is an example MIDI file where this happens around the 65th MIDI message in the file.

Here's my fix of this issue in a "fork" of MIDIFile.js:
Commit: https://github.com/surikov/webaudiofont/compare/master...page200:webaudiofont:master
Pull request: https://github.com/surikov/webaudiofont/pull/95/commits/64ffca58d26d9ca78e433eed562d9268ed7bee9e
I haven't checked whether such a fix belongs into https://github.com/nfroidure/midifile or https://github.com/nfroidure/midievents. Anyway, probably these two repos should be updated to the aforementioned "fork" because that "fork" has things like slides (pitch bend) and parseSong(), which https://github.com/nfroidure/midifile doesn't seem to have yet.

@page200 this repository is meant to be used per other libraries and is just providing a midi file reader. Best practices is not to copy/paste the code but use the library and provide pull requests to the repository in order to allow all users to benefit from the changes for their various needs (see dependent packages)..
Feel free to report those changes via a pull request if you think it will be interesting for other users.

authors: mk-pmb nfroidure page200

repo: nfroidure/midifile


text:
Error webpack-dev-server

Hello, I cloned the repository and follow the installation Arians, but when running npm run server, have the following error:
0 info it worked if it ends with ok
1 verbose cli [ 'C:\Program Files\nodejs\node.exe',
1 verbose cli 'C:\Program Files\nodejs\node_modules\npm\bin\npm-cli.js',
1 verbose cli 'run',
1 verbose cli 'server' ]
2 info using npm@2.9.1
3 info using node@v0.12.3
4 verbose node symlink C:\Program Files\nodejs\node.exe
5 verbose run-script [ 'preserver', 'server', 'postserver' ]
6 info preserver angular2-rxjs-chat@1.0.0
7 info server angular2-rxjs-chat@1.0.0
8 verbose unsafe-perm in lifecycle true
9 info angular2-rxjs-chat@1.0.0 Failed to exec server script
10 verbose stack Error: angular2-rxjs-chat@1.0.0 server: webpack-dev-server
10 verbose stack Exit status 1
10 verbose stack at EventEmitter. (C:\Program Files\nodejs\node_modules\npm\lib\utils\lifecycle.js:213:16)
10 verbose stack at EventEmitter.emit (events.js:110:17)
10 verbose stack at ChildProcess. (C:\Program Files\nodejs\node_modules\npm\lib\utils\spawn.js:24:14)
10 verbose stack at ChildProcess.emit (events.js:110:17)
10 verbose stack at maybeClose (child_process.js:1015:16)
10 verbose stack at Process.ChildProcess._handle.onexit (child_process.js:1087:5)
11 verbose pkgid angular2-rxjs-chat@1.0.0
12 verbose cwd C:\xampp\htdocs\Laravel\AngularChat\angular2-rxjs-chat
13 error Windows_NT 6.1.7601
14 error argv "C:\Program Files\nodejs\node.exe" "C:\Program Files\nodejs\node_modules\npm\bin\npm-cli.js" "run" "server"
15 error node v0.12.3
16 error npm v2.9.1
17 error code ELIFECYCLE
18 error angular2-rxjs-chat@1.0.0 server: webpack-dev-server
18 error Exit status 1
19 error Failed at the angular2-rxjs-chat@1.0.0 server script 'webpack-dev-server'.
19 error This is most likely a problem with the angular2-rxjs-chat package,
19 error not with npm itself.
19 error Tell the author that this fails on your system:
19 error webpack-dev-server
19 error You can get their info via:
19 error npm owner ls angular2-rxjs-chat
19 error There is likely additional logging output above.
20 verbose exit [ 1, true ]

old issue but if anyone has the same upgrade node as per #6

authors: edsonalvesan ndcunningham


text:
Timeline dawn / dusk indications use astronomical twilight

The SunCalc code can support civil, nautical and astronomical twilight, and this should probably be a configuration option.

I will take a look at this.

authors: bradh kwilson-bits

repo: ngageoint/opensphere


text:
В README.md спорные рекомендации

Здравствуйте.

Make sure you have cgi.fix_pathinfo set to "1" or commented out in php.ini

Спорный совет согласно этой статье http://habrahabr.ru/post/100961/ лучше выставить в 0.
Единственный минус, который это даст - $_SERVER['PHP_SELF'] не заполняется, по этому если он используется :( (например в dle насколько я помню видел такое), то стоит добавить в начало стартового скрипта:
$_SERVER['PHP_SELF'] = $_SERVER['SCRIPT_NAME'] . $_SERVER['PATH_INFO'];
Вот это мне кажется и стоит добавить в примечание.
UPD: Кстати в доке по yii2 http://www.yiiframework.com/doc-2.0/guide-installation.html говорят еще и это:

When using this configuration, you should set cgi.fix_pathinfo=0 in the php.ini file in order to avoid many unnecessary system stat() calls.

README.md обновлен

authors: Claud Umkus

repo: nginx-boilerplate/nginx-boilerplate


text:
Integrate unit-docs with Netlify

Right now the Unit docs are manually built and deployed; we have an account with Netlify we can use to automate this, and get nice things like PR previews.

[x] Hook up Netlify to this repo
[ ] Ensure deploy previews are enabled and working
[ ] Flip DNS for unit.nginx.org to point to our Netlify-hosted docs

cc: @jcahilltorre

A couple extra tasks:

[ ] Decide what to do with sitemap.xml (Google no longer accepts sitemap pings)
[ ] Edit Makefile to copy over security.txt before deployment

Decide what to do with sitemap.xml (Google no longer accepts sitemap pings)

I'd suggest we continue generating and publishing a valid sitemap.xml. Sitemaps are still supported, it's just that the unauthenticated pings have gone away.

Ensure deploy previews are enabled and working

For future reference, we had to flip a setting in the Netlify console to allow deploy previews from untrusted users:

I think we're pretty much ready to go with the DNS change over.

authors: callahad danielledeleo

repo: nginx/unit-docs


text:
[bug] can't setTitle() from .component

I'm submitting a ...  (check one with "x")
[x] bug report => check the README and search github for a similar issue or PR before submitting
[ ] support request => check the README and search github for a similar issue or PR before submitting
[ ] feature request

Current behavior

Only setTag() works on a component. setTitle() doesn't set any title, even if true is added as a second parameter. It simply ignores, and fallbacks to the default title set in app.module.
Expected/desired behavior

Being able to set the title from a component.
Minimal reproduction of the problem with instructions

Angular app is composed of a bootstrapping app.module, which is then divided in pages.module (composed of multiple blocks, ie: about-page), and blocks.module (composed of  multiple HTML elements, ie: slideshow-block).
Followed the README.md.
Please tell us about your environment:

Angular version: 2.4.7

Browser: [all]

Language: [TypeScript 2.1.6]

Node (for AoT issues): node --version =  7.4.0

Just realised there was the same issue on vinaygopinath/ng2-meta issue #7. The trick is to use setTimeout as it follows:
setTimeout(() => {
  this.metaService.setTitle('test');
});

However, I don't fully understand what's happening. Is the setTitle() waiting for a request to end?
Should this behaviour be changed?
Sorry for any confusion.

Hi @zM4J8ksETHCq, it's OK to open issues. Actually it's a great contribution to development of this utility.
However, this issue seems to be duplicate of #22, and I'm closing it. You can track current status on #22.

Can you make a release with this issue solved?

Hi @rannaot, I'd like to make it just now.
However, there're a lot of files needs to be reverted while ngx-translate integration is being completed. Within a few days I'll make the release.

https://github.com/nglibs/meta/releases/tag/v0.2.0-rc.4

repo: nglibs/meta


text:
Can NGL delete atoms selected or change atoms position

Can i use NGL to modify molecules in 3d view? and how?
for example, to delete some atoms

No, you cannot do that currently. You can think of NGL as a visualizer but there is currently no infrastructure for edition.

authors: ashipiling ppillot

repo: nglviewer/ngl


text:
Development time packages are potentially marked as production packages

I'm submitting a...

[ ] Regression (a behavior that used to work and stopped working in a new release)
[ ] Bug report
[ ] Performance issue
[ ] Feature request
[ ] Documentation issue or request
[x] Support request
[ ] Other... Please describe:

Current behavior
We are performing a license collection in our project, which crawls through all of our production (e.g. "dependencies") packages and their subdependencies. Couple of collected libraries originate from transloco packages, which only seem to be relevant during development time.
parse-json
yarn why v1.22.5
[1/4] Why do we have the module "parse-json"...?
[2/4] Initialising dependency graph...
[3/4] Finding dependency...
[4/4] Calculating file sizes...
=> Found "parse-json@5.0.0"
info Reasons this module exists
   - "@ngneat#transloco#@ngneat#transloco-utils#cosmiconfig" depends on it
   - Hoisted from "@ngneat#transloco#@ngneat#transloco-utils#cosmiconfig#parse-json"

has-flag
yarn why v1.22.5
[1/4] Why do we have the module "has-flag"...?
[2/4] Initialising dependency graph...
[3/4] Finding dependency...
[4/4] Calculating file sizes...
=> Found "has-flag@3.0.0"
info Reasons this module exists
   - "@ngneat#transloco#ora#chalk#supports-color" depends on it
   - Hoisted from "@ngneat#transloco#ora#chalk#supports-color#has-flag"

Expected behavior
Some Transloco packages should be marked as devDependencies as they are not used during browser runtime.

cosmiconfig package is used to load package.json files
ora package showcases a fancy loading spinner in terminal

Or are these packages added under "dependencies", for publishing reason?
Environment
Installed transloco packages

"@ngneat/transloco-locale@1.3.0"

"@ngneat/transloco-utils@1.1.1"

"@ngneat/transloco@2.17.3"

Node version: v12.9.1

yarn v1.22.5

Could you please be more specific and tell us which packages you think should be devDependencies?

@antpyykk I have checked about the packages you mentioned, those packages used as dependencies for Transloco's schematics and needed for publishing the package.

authors: antpyykk itayod

repo: ngneat/transloco


text:
Why no data?

I followed the config posted in issue: Why so complicated? #562 and was able to get client to handshake. That's as far as I've ever gotten with wireguard-ui. Other than the client being able to ping itself, nothing on the wireguard vpn responds to pings or anything else.
I've also followed 3 or 4 different guides using docker to setup wireguard + wireguard-ui with the same results. The client handshakes but no data, ever.
Why no data?
Please help!

Is this a duplicate of #553?

authors: billwestrup trbtm

repo: ngoduykhanh/wireguard-ui


text:
Egde option

add grafical interface of the edge option of the radar plot methods.

I am working on this one now. I just need a file to test and then I'll create a PR for inspection.

Will you take a look at PR#154?
I didn't add the code to the plot_grid. I think it should work the same, though. Correct?

yes, it could work just the same in plot_grid, this is however not much of a problem in the grid as it don't have the closing of azimuth problem.
I actually don't fully understand what it is the underling pyart error that create that problem, but if edge=False solves the problem, I'm fine with it.

I believe it has to do with the interpolation that pyart performs to extract the edge from the gate center information. If there is wonky data then the interpolation gets a weird value. Is this correct @jjhelmus ?

for reference the original source of this issue: https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/artview-users/7gSpxa6_POM/MkRQGPwaBAAJ

I believe it has to do with the interpolation that pyart performs to extract the edge from the gate center information. If there is wonky data then the interpolation gets a weird value.

The range, azimuth and elevation data stored in Py-ART's Radar class refers to the center of the range bin. If this is always set correctly is another question but typically even if the gates locations are specified differently it makes little perceivable difference.  Therefore for each gate we need to calculate the locations of the "edges" of  quadrilateral which will be have a center at the gate location.
For the range dimension this is relatively straight forward. For gates not at the endpoints, the edge is halfway between the gates. At the ends we extrapolate by adding or adding or subtracting half the distance from the previous/next gate.
The azimuth/elevation dimension are a bit more difficult, as we need to take into account the possible periodic nature of the dimension and some physical limitation (elevation should be between 0 and 180 degrees) but the idea is similar, find the mid-point between rays and extrapolate at the edges.  This work good if the sampling of the azimuth or elevation is fairly uniform but if you have a big break or a wonky ray it can mess things up.  I'm guessing that is what is going in the linked example.

Thanks for the explanation @jjhelmus.

Issue closed in PR #154

authors: gamaanderson jjhelmus nguy

repo: nguy/artview


text:
Is it somehow possible to eliminate ?

Is your feature request related to a problem? Please describe.
I would like to use CSS Grid to style my forms. Therefore it is needed to eliminate this (<formly-field>) structural element, due to the internal working (direct children mechanics like CSS Flexbox) of CSS Grids. So, I need a structure like that:
<formly-form class="css-grid" [form]="form" [fields]="fields" [model]="model">
  <ng-container *ngFor="let e of fields">

  </ng-container>
</formly-form>

To apply a CSS Grid on <formly-field> make not really sense, because each row is an "own" CSS Grid. What do your think?

I think you could just set form-field to
formly-field {
   display: contents;
}

That's something I was thinking about and now I have the solution which is ready and it'll be introduced in V6 alpha version.
Could you please help me find a better name for the opt-it :pray::
FormlyModule.forRoot({
+ extras: {
+   eliminateFormlyField: true,
+ },
}),

I think it depends how you accomplish this.
What are the implications of this change anyway?
Just for the record, is it true that the author's example would undermine the basic functionality of Formly?

The new behavior will act like <router-outlet></router-outlet>, the content will be rendered right after the formly-field component and not inside.
Also I'm working on a way to define an inline type which allows override all formly types (including the core ones):
For example to define input type:
    <form-form [form]="form" [fields]="fields" [model]="model">
      <ng-template formlyTemplate="input" let-field>
		<input [formControl]="field.formControl" />
      </ng-template>
    </form-form>

and fields which concern this issue it would be something like:
    <form-form [form]="form" [fields]="fields" [model]="model">
      <ng-template formlyTemplate let-field>
        <ng-container *ngFor="let f of field.fieldGroup">

...

...

        </ng-container>
      </ng-template>
    </form-form>

Or:
    <form-form [form]="form" [fields]="fields" [model]="model">
      <ng-template formlyTemplate let-field>
        <formly-field *ngFor="let f of field.fieldGroup" [field]="f"></formly-field>
      </ng-template>
    </form-form>

This will solve many issues including this one:

https://github.com/ngx-formly/ngx-formly/issues/2707
https://github.com/ngx-formly/ngx-formly/issues/2077
https://github.com/ngx-formly/ngx-formly/issues/2086

hope you like it!

For naming, I would choose something along the lines of render formly field element: false because I think that way could/should be the new standard.

What about
externallyRenderFields: false
That way we define rendering fields as baseline internal to the firmly
field and this allows to externally render them.
On Sun, Mar 7, 2021, 12:38 PM Manuel Meister notifications@github.com
wrote:

For naming, I would choose something along the lines of render formly
field element: false because I think that way could/should be the new
standard.
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You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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.

I think you could just set form-field to
formly-field {
   display: contents;
}

That's right. But the support is still very  "experimental" and buggy. See: https://caniuse.com/css-display-contents.
I would also tend to name it renderFormlyFieldElement: false, but set it internally to true on default (so that the old behavior is the default).

I think the proposal is great and makes Formly much more flexible:

It allows detaching the form from the layout, so we don't need to declare wrapper components.
It allows using input types without having to register them on the Formly module (I understand that it would work with any Form ControlValueAccessor, right?). This way we'd be able to use lazy-loaded components.
-It keeps the default functionality.

Thanks!

@aitboudad great to see this feature being added! Just what I was looking for too!
I agree with the others that renderFormlyFieldElement: false would be a good way to configure this.

When the release will be published ?

Late Today/ or Tomorrow I'll push an initial work, but be aware it's an alpha version and your feedback is a must 😄.
👍 for renderFormlyFieldElement

Could it be applied also the the  tag (Which I really want to omit with the formly-field 😞) ?

You can now give it a try by using 6.0.0-next.1

@ahmedderkaoui

formly-field: use renderFormlyFieldElement

FormlyModule.forRoot({
  extras: { renderFormlyFieldElement: false },
})

formly-group: either override the default formly-group type or use the inline type (better approach):

<form-form [form]="form" [fields]="fields" [model]="model">
  <ng-template formlyTemplate let-field>
    <formly-field *ngFor="let f of field.fieldGroup" [field]="f"></formly-field>
  </ng-template>
</form-form>

for those who're willing to upgrade from v5 check the UPGRADE-6.0.md

Hi @aitboudad ,
Nice, it works fine, thank you very much.
In my case, adding extras: { renderFormlyFieldElement: false } doesn't make any difference, both ways (with custom formlyTemplate and without) worked well.
I like it this way because:

The experience is smoother; the form behaves as always and if you pass a formlyTemplate then the formly-form uses it without the need of configuring the global behavior (renderFormlyFieldElement).
It allows using both flavors everywhere. The renderFormlyFieldElement in the forRoot seems to indicate that all the forms in the app will behave the configured way (renderFormlyFieldElement or not), which would be limiting.

I start working on the docs.
Cheers!

Here is a solution that worked well for me (no need here to set something inside Formly, only CSS trick):
in your styles.css, add :
formly-group {
    display: contents;
}

formly-field {
    display: contents;
}

and for each FieldType and FieldWrapper you have in your project, and which it seems not to be shown correctly with CSS, do the same as above with its Component Selector.
Example :
..
@Component({
 selector: 'buttonType',
 template: `
 // TEMPLATE
 `,
})
..

add:
buttonType {
    display: contents;
}

Another interesting feature not related to this issue but I would like to know your thoughts if you've any :smiley:, please let me know https://github.com/ngx-formly/ngx-formly/issues/2853

authors: ahmedderkaoui aitboudad aleixsuau beeman kenisteward loxy manuelmeister

repo: ngx-formly/ngx-formly


text:
Error: Request failed, status 404

When I switch to the gpt4 model, the following error appears in the generated answer, but when I switch to gpt3.5, the correct result is output, why?
Error: Request failed, status 404

app.js:1 new t
app://obsidian.md/app.js:1:717762

app.js:1 Jw
app://obsidian.md/app.js:1:717954

app.js:1
app://obsidian.md/app.js:1:718631

app.js:1
app://obsidian.md/app.js:1:235836

app.js:1 Object.next
app://obsidian.md/app.js:1:235941

app.js:1 a
app://obsidian.md/app.js:1:234680

Same issue for me. I have access to GPT-4, and I've also tried gpt-3.5-turbo, same error.
Error: Request failed, status 404
    at new t (app.js:1:717762)
    at Jw (app.js:1:717954)
    at app.js:1:718631
    at app.js:1:235836
    at Object.next (app.js:1:235941)
    at a (app.js:1:234680)

Edit: Was able to update the plugin to latest and the problem seems to have resolved itself. Thanks!

How do you get whitelisted?

I would like to suggest that you check the most recent version of the plugin, which is v0.3.1, as it features improved error messages that are more expressive. This update could enhance the overall performance and user experience of the plugin, and may provide helpful insights in the event of any issues that arise.

authors: dep kgust nhaouari piaoxi1517

repo: nhaouari/obsidian-textgenerator-plugin


text:
fixed typos related to YAML

I noticed a few occurrences of YMAL instead of YAML. I refactored the code and messages according to that.
This is my first pull request, hope I'm doing everything correctly ;)

Thank you for submitting your first pull request! Your contribution is appreciated.
Regarding the refactoring of "YMAL" to "YAML", it is great to see that you have taken the initiative to improve the code and messages. Consistency in spelling and terminology is important for clarity and readability, so your changes will definitely be helpful.
I will review your code changes and provide feedback if necessary. Keep up the good work!

authors: nhaouari uberrice


text:
Support post/put/delete in LR Client

@andrus , please review

A few thoughts:

Trying to think how we can explicitly hide unsupported options for a given request type. E.g. DELETE does not support all the GET request options (include/exclude/etc). On the other hand POST and PUT support those.
This may be a new task, but PUT/POST would benefit from a type-safe builder for its payload instead of taking a String.

After offline discussion accepted as is, as we don't have better options at the moment. Perhaps we'll have better ideas later.

authors: andrus atomashpolskiy

repo: nhl/link-rest


text:
Plugin wrongly assumes that images are stored in collection directory

I'm using the include like this:
{% assign path = file_name | prepend: "assets/cms" %}
{% cloudinary {{ path }} alt={{ alt_text }}" %}

For a file_name example.jpg in a post of the collection _my_collection I get the error:
[Cloudinary] Couldn't find this image to check its width: [ directory with my project]/_my_collection/posts/assets/cms/example.jpg.

Apparently it's assumed that the images are stored in collection's directory. I'm using Forestry, so all images for all collections are stored in assets/cms. The prepend: "assets/cms" part isn't causing this by the way.
Is there a way to include paths relative to the root of the project?

It looks like one can circumvent this issue by using absolute URLs for the source.

repo: nhoizey/jekyll-cloudinary


text:
🛑 Auth is down

In 64fa092, Auth ($AUTH_URL) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Auth is back up in 9cc5821 after 13 minutes.

repo: nhs-work/test-upptime


text:
Prepare for March 2021 Content Style Council meeting

What
Invite people, prepare the agenda and slides for the meeting.
Done when

[ ]  Arrange room - not needed
[x]  Agree meeting date - Sara, Olivia, Karin
[x]  Arrange Teams meeting and send out invite - Lucy
[x]  Firm up agenda with Olivia and Anna
[x] Get issues ready with colleagues
[ ]  Make sure that GitHub is up to date
[ ]  Share agenda and info about topics up for discussion - by email, on NHS.UK and NHS digital service manual Slack
[ ]  Prepare slides with Olivia
[ ] Olivia to chair the meeting - with Sara

Potential issues for this meeting:

Components and headings

Potential issues for this meeting:

Components and headings

Draft agenda
Discussed with @OliviaThornton, @annasutton2, @sarahallen57 and @teodorastraianu1
Welcome and introduction - Olivia
Updates from January meeting - Sara

hyphens and spaces - or dashes - published some more guidance and examples but there are some outstanding issues on GitHub issue
readability tool and link to SMOG calculator - removed from style guide
reading age - Sara to feedback about plans for user research
jab or vaccine - on agenda for this meeting
PDFs - updated guidance published but it's now going to Accessibility Working Group for info – also we may need to clarify our guidance on open document formats (ODFs)

Other updates - Sara

Accessibility testing some content scenarios : components and headings, inset text, hint text
Reviewing care card guidance, do and don't list and review dates - to be republished as patterns

Call out to contribute research findings - Olivia
Issues for discussion and approval - Olivia

covid jab/vaccine - Gerard, Laura or Jean (Sara to let them know)
alt tag change - Anna, Teodora and Sarah
skin symptoms guidance - Anna, Teodora and Sarah - may be just an update or maybe some content for discussion - we'll probably consult further/hold over approval till April meeting - but let's see what people think about where it should go in the style guide
long descriptions - Anna, Teodora and Sarah - probably only an update at this stage
GP systems suppliers - Olivia
 or  for bold - Sara
phlegm, mucus, sputum - Olivia - maybe discussion but not approval

AOB, thank you and close meeting - Olivia

Draft slides: https://hscic365.sharepoint.com/:p:/r/sites/servicemanual/_layouts/15/Doc.aspx?sourcedoc={010E760D-8558-4574-B7AE-CD01FFD199FF}&file=Style Council meeting - March 2021.pptx&action=edit&mobileredirect=true

Waiting for Anna and Olivia to add their slides. I'll pick this up next Monday.

I'll add slides for the long descriptions update on Wednesday.

All done. Close this ticket.

repo: nhsuk/nhsuk-service-manual


text:
SDK Generator should depend on the latest SDK Service

Tech Debt
In the latest 3.1.0.5 release, the generator package 3.1.0.5 is currently depending on service version 3.1.0.1. It should be updated to 3.1.0.5, as some dependencies for the client generator have been included in the 3.1.0.5 service that were not available in the 3.1.0.1 service.
cc: @dixonjoel
AB#2906677

Validated with the latest 3.1.0.6 release, and the issue has been fixed.

repo: ni/measurement-plugin-labview


text:
Possibly flaky test: "should commit mention into the editor on Enter"

🧹 Tech Debt
Saw this test fail on an unrelated PR.

https://github.com/ni/nimble/actions/runs/7576426399/job/20635217943

Created AzDO work item assigned to LIMS: https://ni.visualstudio.com/DevCentral/_workitems/edit/2632606

Intermittent test disabled in https://github.com/ni/nimble/pull/1770
As per nimble intermittent test policy: https://github.com/ni/nimble/blob/adde25d1cad4b59868590e81684a622bbd38b23e/CONTRIBUTING.md#handling-intermittent-test-failures
AzDo issue filed to address disabled test: https://ni.visualstudio.com/DevCentral/_workitems/edit/2632606

authors: m-akinc rajsite

repo: ni/nimble


text:
Rename icon column to mapping column

Pull Request
🤨 Rationale
The icon column now supports various types of mappings (icon, spinner, and text), so we've decided that it should be renamed to the mapping column rather than the icon column.
👩💻 Implementation

Rename the icon column, along with its cell view, group header view, and page object, to be called "mapping" rather than "icon"
Update Angular and Blazor to be aligned with the new name
Lots of updates to support the rename
No functional changes other than renaming components, classes, files, etc.

🧪 Testing

Sanity checked that the storybook docs, Angular example app, and Blazor example app all render as expected
All existing tests still pass

✅ Checklist

[ ] I have updated the project documentation to reflect my changes or determined no changes are needed.

@atmgrifter00, will you buddy this PR for me?


text:
Volslicer asset is too Thin

Hedwig UI:
https://goat.niaid.nih.gov:7333/sessions/U2Vzc2lvbjoyNTE1/samples
Sample name: SARsCov2_B
Pipeline run:
http://44.192.88.156:8080/default/flow-run/25ce4b87-b686-4f1b-a371-15554a41fb58
File Path:
\ai-fas12\RMLEMHedwigDev\Assets\RTB\darrellh\filipgranitn2-2022-1117-BRT_Testing\Cryo-TEM-Tomo-2022-1117-Nov_BRT_testing\SARsCov2_B\SARsCoV2_1
Review by Bryan on 11/17/2022
VolSlicer volume  looks too thin, doesn't look like even binned down that it's the thickness that you supplied (800)

Tested after the fix:
Rerun SARsCov2_B
Pipeline run: http://44.192.88.156:8080/default/flow-run/4b73a453-4e50-44d2-8887-3e71c4b10900
Both runs successfully completed, and the assets VolSlicer and Reconstructed Movie were correct.
Hedwig UI:
https://goat.niaid.nih.gov:7333/sessions/U2Vzc2lvbjoyNTE1/samples
https://goat.niaid.nih.gov:7333/volslicer/UmVjb3JkOjE3NDE5Mg==
https://goat.niaid.nih.gov:7333/recmovie/UmVjb3JkOjE3NDE5Mg==
https://goat.niaid.nih.gov:7333/tiltmovie/UmVjb3JkOjE3NDE5Mg==
See Hansen , Bryan, Feedback:
The reconstructed movie is correct now. VolSlicer looks correct now too
The issue is fixed

fixed in https://github.com/niaid/image_portal_workflows/tree/fix_recon_movie

authors: NetaFG philipmac


text:
set up NIAID internal prefect server as API end point

and tell Seva the IP has changed.

wont do - will run in Spaces.


text:
Improve docker builds and docs

Improve docker builds and add docs how to build docker images.

So bekomme ich damit doch cors Probleme, wenn ich zwei unterschiedliche Server laufen lasse, oder? Noch ein nginx als reverse proxy davor?

Die Anzahl der Server sollte für das Thema CORS-Header irrelevant sein. Insbesondere wenn das ganze eh hinter einem Reverse-Proxy versteckt wird.
Aber ich muss zugeben das Compose-File irritiert mich gerade: unter https://github.com/nick81nrw/PVTools/issues/22#issuecomment-1858861683 hast du geantwortet:

Der relative Pfad müsste passen. Allerdings ist es eigentlich auch quatsch static Files über node zu verteilen. Vielleicht auf nginx umbauen?
Deshalb habe ich den Verweis auf ../../pvtools/dist eigentlich aus dem Backend rausgeworfen. Genau das wird hier aber scheinbar mit der Einbindung des Volumes gemacht.

Meine Erwartung wäre jetzt folgendes Setup gewesen:

Das Frontend ist statisch kompiliert (NODE_ENV=production APP_URL=pvtools.sektorsonne.de:443 GOOGLE_ANALYTICS_ID=xxx npm run generate)
pvtools.sektorsonne.de ist ein Nginx mit Zertifikat der
a. das Frontend statisch ausliefert (Verzeichnis pvtools/dist als Document-Root des Virtual Hosts)
b. die Requests zu /apiRelay auf den Docker-Container für das Backend durchroutet
Das backend läuft dann als Container mit den Umgebungsvariablen NODE_ENV=production APP_URL=pvtools.sektorsonne.de:443

Der "Haupt"-nginx-proxy macht nur auf andere Container weiterleiten und macht letsencrypt. Die App steht komplett für sich und müsste den static und die api ausliefern. Bis jetzt macht das beides der backend-node-server. Für den Haupt-nginx gibt es einfach nur einen upstream für die Domain.
Aktuell baue ich das frontend mit "npm run build", der neue static wird vom node ausgeliefert.
Meiner Einschätzung nach, könnte man einen nginx in der App vor API und static schalten und nach außen einen Port exposen.

Meiner Einschätzung nach, könnte man einen nginx in der App vor API und static schalten und nach außen einen Port exposen.

Das erscheint mir ein bisschen zu viel Infrastruktur. Ich würde den Static-Content entweder gleich in den vorhandenen Reverse-Proxy integrieren oder Anhand der URL den Request im Reverse-Proxy entweder auf das API-Backend oder einen Nginx für den statischen Content verteilen (In meinem PR ist das bauen des Frontends als Multi-Stage-Build angelegt damit am Ende ein Nginx den Inhalt ausliefern kann)
Variante 1: Reverse-Proxy liefert das Frontend mit aus
+---------------+                +-----------+
| Reverse Proxy |                |           |
|               +-- /apiRelay/ --+ Backend   |
| Virtual Host: |                |           |
|    root: dist |                | Port 8082 |
+---------------+                +-----------+

Pseudocode für Nginx-Konfiguration:
location / {
    root /path/to/pvtools/dist;
}

location /apiRelay/ {
    proxy_pass http://127.0.0.1:8082/apiRelay/;
}

Variante 2: Verteilung der Requests für Frontend (Port 8080) und Backend (8082)
                                  +-----------+
                                  |           |
                                  | Frontend  |
                   +----- / ------+           |
+---------------+  |              | Port 8080 |
|               +--+              +-----------+
| Reverse Proxy |
|               +--+              +-----------+
+---------------+  |              |           |
                   +- /apiRelay/ -+ Backend   |
                                  |           |
                                  | Port 8082 |
                                  +-----------+

Pseudocode für Nginx-Konfiguration:
location / {
    proxy_pass http://127.0.0.1:8080/;
}

location /apiRelay/ {
    proxy_pass http://127.0.0.1:8082/apiRelay/;
}


text:
🛑 Authinator is down

In 5b71ae0, Authinator (https://www.authinator.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Authinator is back up in 2106288.

repo: nickadam/status


text:
Error while starting rails server after adding htmltoword gem

I'm added to Gemfile gem 'htmltoword', '0.2.0' into a new rails 4.2.1 app. But than i starts a rails server an error appear.
/home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/htmltoword-0.2.0/lib/htmltoword/action_controller.rb:41:in `': uninitialized constant ActionController::Responder (NameError)
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/htmltoword-0.2.0/lib/htmltoword.rb:26:in `require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/htmltoword-0.2.0/lib/htmltoword.rb:26:in `'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:76:in `require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:76:in `block (2 levels) in require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:72:in `each'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:72:in `block in require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:61:in `each'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler/runtime.rb:61:in `require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/bundler-1.9.5/lib/bundler.rb:134:in `require'
        from /vagrant/HtmlWordConverter/config/application.rb:7:in `'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands/commands_tasks.rb:78:in `require'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands/commands_tasks.rb:78:in `block in server'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands/commands_tasks.rb:75:in `tap'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands/commands_tasks.rb:75:in `server'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands/commands_tasks.rb:39:in `run_command!'
        from /home/vagrant/.rbenv/versions/2.2.2/lib/ruby/gems/2.2.0/gems/railties-4.2.1/lib/rails/commands.rb:17:in `'
        from bin/rails:4:in `require'
        from bin/rails:4:in `'

After removing gem rails server starts normally. What problem in? What versions of Ruby/Rails supported? I tried ruby versions 2.0, 2.1.5, 2.2.2 and Rails 4.2.1. Same problem persist.

Hi Igor, could you try this one:
https://github.com/karnov/htmltoword
We have cleaned it up quite a bit

authors: IgorOsa MadsBuus

repo: nickfrandsen/htmltoword


text:
HealthKit and CloudKit

Support for closures in status/request functions added (Needed for CloudKit async requests).
Added CloudKit (#58)
Added HealthKit (#17)

Do not merge until these are closed:

[x] Add notes to readme about CloudKit's notification https://github.com/nickoneill/PermissionScope/issues/58#issuecomment-133592741
[x] Add notes to readme about HK: Enable HealthKit in the target's Capabilities
[x] Add notes to readme about CK: Enable CloudKit in the target's Capabilities
[ ] https://github.com/nickoneill/PermissionScope/issues/17#issuecomment-134838190

What to do when the user asks for x types to share and y types to read ? Return .Authorized if all of them were ? What about  SharingDenied and NotDetermined  ? Link to the code

Changes commited and swift2 branch merged.
@nickoneill I'll leave the PR merge to you in case you want to change something else.

The cloudkit stuff is still pretty wonky, I'm looking at it now.

Yeah, there are some cases which I wasn't sure how to handle...Hence the TODOs

repo: nickoneill/PermissionScope


text:
Use cases

Use Case 1 - record level validation:
Say I have 2 fields. "Amount" and "Calculation Type". Amount is always a float, however when calculation type is "Percent", Amount must be bounded from 0 to 100.
Use Case 2 - table level validation:
Say I have multiple records and after grouping certain fields, no duplication can be present.
Use case 3 - Multiple coercion functions:
I need to convert a value to string, and perform a couple of other functions before validation. Any tips here?
Appreciate your help! This is probably one of the coolest python projects I've seen in a while.

+1

http://docs.python-cerberus.org/en/latest/customize.html
i don't understand the scenario
#102

@manugarri, can you please elaborate?

@funkyfuture
For (2):
Say I had a column with 1000 rows and I want to say that all 1000 values in this column are in a table of 25000 rows, how would I do that in cerberus?
Or
How would I determine 1 or more columns in aggregate are unique?

Cerberus is only meant to validate one row against a set of rules. Not really designed for such an use case (which seems more suited for a relational database)

ok thx

authors: funkyfuture manugarri nicolaiarocci richiverse

repo: nicolaiarocci/cerberus

license: isc


text:
Why is the input in the terminal buggy?

The input in the terminal does not work properly. It shows incorrectly, but if I expand the terminal a little, the error will visually disappear, but the input continues to give this effect. When deleting, the terminal also behaves strangely.
Introduced the "dig mysql"

expanded the terminal

removed 2 characters from the end

removed all characters

The input in the terminal does not work properly. It shows incorrectly, but if I expand the terminal a little, the error will visually disappear, but the input continues to give this effect. When deleting, the terminal also behaves strangely.
Introduced the "dig mysql"

Did you find a fix? This happens in my system too...

@SinGlEBW I'm gonna look into it. Probabaly will switch the profile as I did have some buggy behaviour in the past as well. stay tuned.

Noting that this also happens on my system with VS Code:
Version: 1.54.3 (system setup)
Commit: 2b9aebd5354a3629c3aba0a5f5df49f43d6689f8
Date: 2021-03-15T10:55:45.459Z
Electron: 11.3.0
Chrome: 87.0.4280.141
Node.js: 12.18.3
V8: 8.7.220.31-electron.0
OS: Windows_NT x64 10.0.18362

@AaronViviano @SinGlEBW I pushed a new version and switched to zsh with cleaner term profile. let me know if you're seeing same issue.

@nicolaka I am not seeing the same issue any more. Though the rendering of the terminal in VS code is still odd.

I'm also seeing a yellow alpha numeric string of 12 characters before command prompt line. Not sure what they are there for. Looks like a shortened git hash. While I highly doubt this is the case, I'm not including it in the picture in case this is some sort of security related key.

@AaronViviano the hash is just the container name that turns into the hostname. The new zsh profile uses the hostname in the prompt that's all.

@nicolaka Good to know! Thank you.

authors: AaronViviano Dishock SinGlEBW nicolaka

repo: nicolaka/netshoot


text:
Slow prediction

The generation of mask is too slow. is there any ways to speed it up?

IIRC, the interpolation was really slow. The current code is a pure-python port of the algorithm in the paper that I used to compare my results. You could try switching to a standard upsampling routine in scilab or pillow.

authors: Zumbalamambo nicolov


text:
Querying strategy for @NiemanLabFuego tweets?

Hiya. I've been having some fun setting up OpenFuego [instances] (http://saracarothers.com/openfuego/politicsfuego/), and have a question about the Twitter account [@NiemanLabFuego] (https://twitter.com/niemanlabfuego)
I've always really found that account useful, so want to set one up in conjunction with my Fuego pages.
My question is: How often do you query to get the right mix of tweets? How many does it request?
I have a cron job set up that, every half hour, looks for the 1 most popular link over the past 6 hours, and if it's new, tweets that out. (Scoring, metadata set to true). It's ok, but seems like it's not quite right ...
Would love to know how the official account queries! Thanks for any info.

Hi Sara! @phelps coded that up, so I'm not 100% sure, but I believe it's triggered whenever a link is in the top 3 of the past 24 hours. (I feel quite confident about the top 3 part, not as much about the 24 hours part.)

Thanks for the info! I tried that over the past few days, seems like it's on the right track. I'm still getting a lot of links over a 24-hour period that break into the top three (so that means more tweets than the Nieman Lab version, which seems to dull the importance of each one, if that makes sense.). Makes me think it's symptom of the universe I'm following, so am going to try tweaking that.

authors: jbenton scarothers

repo: niemanlab/openfuego


text:
Failing tests for process.env types

Just wanted to make a PR showing that the types do not persist in the process.env. There is some documentation in the README that seems to indicate this should work.

ty

authors: jcblw niftylettuce

repo: niftylettuce/dotenv-parse-variables


text:
Error when installing express-cdn

I recieve the following error when attempting to install express-cdn:
npm ERR! Darwin 15.4.0
npm ERR! argv "/usr/local/bin/node" "/usr/local/bin/npm" "install" "express-cdn"
npm ERR! node v6.2.0
npm ERR! npm  v3.8.9
npm ERR! code ELIFECYCLE
npm ERR! optipng-bin@0.3.11 postinstall: node index.js
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the optipng-bin@0.3.11 postinstall script 'node index.js'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the optipng-bin package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node index.js
npm ERR! You can get information on how to open an issue for this project with:
npm ERR!     npm bugs optipng-bin
npm ERR! Or if that isn't available, you can get their info via:
npm ERR!     npm owner ls optipng-bin
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /Users/Jade/Documents/nodetest/nexus-node-api/npm-debug.log

when I update optipng and jpegtran, cdn work again
see #105

fixed in 0.2.9

authors: gagalago zilions

repo: niftylettuce/express-cdn


text:
Add news and edit top for FY2022 renewal deadline

今年度(2022年度)　年度末アカウント継続申請の受付期限延長のお知らせを受け、以下3点、修正いたしました。
1．新たにお知らせのページを作成し、追加
2．トップページにお知らせを追加
3．年度末アカウント継続申請のページにも、期限延長についてのお知らせを簡単に追記
どうぞよろしくお願いいたします。

対処方法を追記するため、一度、プルリクエストを取り下げます。

対処方法を追記いたしました。
お手数をお掛けし申し訳ございませんが、よろしくお願いいたします。


text:
added submenu/links

uses justin's component, so it should work once justin's code gets merged.

Converting source _notebooks/CSP/big-ideas/big-idea-3-part-1-fundamentals/Period5/nolan-y-jacob/2024-09-25-json.ipynb to destination posts/CSP/big-ideas/big-idea-3-part-1-fundamentals/Period5/nolan-y-jacob/2024-09-25-json_IPYNB_2.md
Error parsing YAML front matter: while parsing a block mapping
in "", line 10, column 5:
table1: "/csp/big-idea/p5/3-2-1"
^
expected , but found ''
in "", line 14, column 14:
table3: "/csp/big-idea/p5/3-2-3"


text:
文件夹分类选项关闭后仍然会创建分类文件夹

[✔] 我已经阅读过 FAQ.
[✔] 我查找了现有的问题列表 issues.

环境

系统: [Windows 10 专业工作站版 21H1 19043.985]
速享版本: [2.1.7]

描述这个问题
文件夹分类选项关闭后仍然会创建分类文件夹
在删除了自动创建的文件夹，关闭软件重新打开后会自动创建分类文件夹
无论是英文路径还是中文路径都会出现这个问题
部分日志
[10:24:43] [D/GetX] Instance "SettingController" has been created
[10:24:43] [D/GetX] Instance "SettingController" has been initialized
[10:24:43] [D/GetX] Instance "DeviceController" has been created
[10:24:43] [D/GetX] Instance "DeviceController" has been initialized
[10:24:43] [D/GetX] Instance "ChatController" has been created
[10:24:43] [D/GetX] Instance "ChatController" has been initialized
[10:24:43] [D/GetX] Instance "GetMaterialController" has been created
[10:24:43] [D/GetX] Instance "GetMaterialController" has been initialized
[10:24:43] [V/GlobalInstance] initGlobal
[10:24:43] [D/GetX] GOING TO ROUTE /speedshare/
[10:24:43] [D/GetX] Instance "FileController" has been created
[10:24:43] [D/GetX] Instance "FileController" has been initialized
[10:24:43] [D/GetX] Instance "DownloadController" has been created
[10:24:43] [D/GetX] Instance "DownloadController" has been initialized
截图
GIF

试一下这个版本 https://transfer.sh/vvaEET/SpeedShare_Windows.zip

试一下这个版本 https://transfer.sh/vvaEET/SpeedShare_Windows.zip

这个版本解决了问题