Problem with mamba install modules

The install_STRONG.sh scripts makes a mamba call:
mamba env create -f $STRONG_dir/conda_env.yaml &>>$LOG
When the script gets to this step, here's the error message:
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/ffeee55f.json" was modified by another program
bioconda/linux-64 (check zst)                       Checked  0.3s
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/2a957770.json" was modified by another program
bioconda/noarch (check zst)                         Checked  0.1s
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/c484148c.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/0c60671d.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/ebe486dd.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/bcb51836.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/497deca9.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/09cdf8bf.json" was modified by another program
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/47929eba.json" was modified by another program
pkgs/main/linux-64 (check zst)                      Checked  0.2s
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/3e39a7aa.json" was modified by another program
pkgs/main/noarch (check zst)                       Checked  0.0s
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/2ce54b42.json" was modified by another program
pkgs/r/linux-64 (check zst)                         Checked  0.0s
warning  libmamba Cache file "/mnt/strong/tools/apps/miniconda3.10/pkgs/cache/4ea078d6.json" was modified by another program
pkgs/r/noarch (check zst)                           Checked  0.1s
[+] 0.2s
anaconda/linux-64 ━━━━━━━━━━━━━━━╸━━━━━━━━━━   0.0 B /  ??.?MB @  ??.?MB/s  0.2s
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/conda/exception_handler.py", line 16, in __call__
    return func(*args, **kwargs)
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/conda_env/cli/main.py", line 49, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/conda/notices/core.py", line 123, in wrapper
    return func(*args, **kwargs)
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 163, in execute
    result[installer_type] = installer.install(
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/mamba/mamba_env.py", line 55, in mamba_install
    index = load_channels(pool, channel_urls, repos, prepend=False)
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/mamba/utils.py", line 142, in load_channels
    index = get_index(
  File "/mnt/strong/tools/apps/miniconda3.10/lib/python3.10/site-packages/mamba/utils.py", line 123, in get_index
    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (23) Failed writing received data to disk/application [https://conda.anaconda.org/anaconda/noarch/repodata.json.zst]
Failure writing output to destination

$ /mnt/strong/tools/apps/miniconda3.10/bin/mamba create -f /mnt/strong/tools/apps/STRONG/conda_env.yaml
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_ROOT=/mnt/strong/tools/apps/miniconda3.10
CURL_CA_BUNDLE=
LD_PRELOAD=
MANPATH=:
MODULEPATH=/etc/scl/modulefiles:/etc/scl/modulefiles:/usr/share/Modules/modulefil
es:/etc/modulefiles:/usr/share/modulefiles
PATH=/mnt/strong/tools/apps/miniconda3.10/bin:/home/yeej/.local/bin:/home/y
eej/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin
:/usr/sbin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
 active environment : None
   user config file : /home/yeej/.condarc

populated config files : /home/yeej/.condarc
conda version : 23.5.0
conda-build version : not installed
python version : 3.10.12.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.28=0
__linux=4.18.0=0
__unix=0=0
base environment : /mnt/strong/tools/apps/miniconda3.10  (writable)
conda av data dir : /mnt/strong/tools/apps/miniconda3.10/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/anaconda/linux-64
https://conda.anaconda.org/anaconda/noarch
https://conda.anaconda.org/r/linux-64
https://conda.anaconda.org/r/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /mnt/strong/tools/apps/miniconda3.10/pkgs
/home/yeej/.conda/pkgs
envs directories : /mnt/strong/tools/apps/miniconda3.10/envs
/home/yeej/.conda/envs
platform : linux-64
user-agent : conda/23.5.0 requests/2.28.1 CPython/3.10.12 Linux/4.18.0-425.3.1.el8.x86_64 rocky/8.7 glibc/2.28
UID:GID : 41154:59900
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Also tried miniconda3.8 with same error.
I'm using Rocky 8.7.
Any ideas how to resolve?
Thank you

Hello,
Can you try again? I think I saw that before: Mamba downloads packages but flag dl as fails. Once you restart it works. Otherwise, from error message it could be issue with permission to write inside the folder?

Hello,
If "try again" you mean run install_STRONG.sh again, I just tried with the same error message.  I even tried 5 consecutive times.  For me, looks like when mamba is called it fails almost immediately, meaning no packages are installed.
$ conda list
packages in environment at /mnt/strong/tools/apps/miniconda3.10:

Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
biopython                 1.81                     pypi_0    pypi
boltons                   23.0.0          py310h06a4308_0
brotlipy                  0.7.0           py310h7f8727e_1002
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.5.7             hbcca054_0    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h5eee18b_3
charset-normalizer        2.0.4              pyhd3eb1b0_0
conda                     23.5.0          py310hff52083_1    conda-forge
conda-content-trust       0.1.3           py310h06a4308_0
conda-package-handling    2.0.2           py310h06a4308_0
conda-package-streaming   0.7.0           py310h06a4308_0
contourpy                 1.1.0                    pypi_0    pypi
cryptography              39.0.2          py310h34c0648_0    conda-forge
cycler                    0.11.0                   pypi_0    pypi
dill                      0.3.6                    pypi_0    pypi
fmt                       9.1.0                h924138e_0    conda-forge
fonttools                 4.41.0                   pypi_0    pypi
gfapy                     1.2.3                    pypi_0    pypi
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4             py310h06a4308_0
jsonpatch                 1.32               pyhd3eb1b0_0
jsonpointer               2.1                pyhd3eb1b0_0
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.20.1               h81ceb04_0    conda-forge
ld_impl_linux-64          2.38                 h1181459_1
libarchive                3.6.2                h039dbb9_1    conda-forge
libcurl                   8.1.2                h409715c_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h6a678d5_6
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libmamba                  1.4.7                h658169a_0    conda-forge
libmambapy                1.4.7           py310h8aae740_0    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsolv                   0.7.24               hfc55251_1    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.11.4               h0d562d8_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.4.7           py310h51d5547_0    conda-forge
matplotlib                3.7.2                    pypi_0    pypi
multiprocess              0.70.14                  pypi_0    pypi
ncurses                   6.4                  h6a678d5_0
networkx                  3.1                      pypi_0    pypi
numpy                     1.25.1                   pypi_0    pypi
openssl                   3.1.1                hd590300_1    conda-forge
packaging                 23.0            py310h06a4308_0
pandas                    2.0.3                    pypi_0    pypi
pathos                    0.3.0                    pypi_0    pypi
patsy                     0.5.3                    pypi_0    pypi
pillow                    10.0.0                   pypi_0    pypi
pip                       23.0.1          py310h06a4308_0
pluggy                    1.0.0           py310h06a4308_1
pox                       0.3.2                    pypi_0    pypi
ppft                      <IP_ADDRESS>                  pypi_0    pypi
progressbar2              4.3b0                    pypi_0    pypi
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h5eee18b_0
pycparser                 2.21               pyhd3eb1b0_0
pygam                     0.9.0                    pypi_0    pypi
pyopenssl                 23.0.0          py310h06a4308_0
pyparsing                 3.0.9                    pypi_0    pypi
pysocks                   1.7.1           py310h06a4308_0
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python-utils              3.7.0                    pypi_0    pypi
python_abi                3.10                    3_cp310    conda-forge
pytz                      2023.3                   pypi_0    pypi
readline                  8.2                  h5eee18b_0
reproc                    14.2.4               h0b41bf4_0    conda-forge
reproc-cpp                14.2.4               hcb278e6_0    conda-forge
requests                  2.28.1          py310h06a4308_1
ruamel.yaml               0.17.21         py310h5eee18b_0
ruamel.yaml.clib          0.2.6           py310h5eee18b_1
scipy                     1.11.1                   pypi_0    pypi
setuptools                65.6.3          py310h06a4308_0
six                       1.16.0             pyhd3eb1b0_1
sqlite                    3.41.1               h5eee18b_0
statsmodels               0.14.0                   pypi_0    pypi
tk                        8.6.12               h1ccaba5_0
toolz                     0.12.0          py310h06a4308_0
tqdm                      4.65.0          py310h2f386ee_0
typing-extensions         4.7.1                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
urllib3                   1.26.15         py310h06a4308_0
wheel                     0.38.4          py310h06a4308_0
xz                        5.2.10               h5eee18b_1
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.19.0          py310h5eee18b_0
zstd                      1.5.2                hfc55251_7    conda-forge
Thank you

Yes I was thinking you could try again the command line:
/mnt/strong/tools/apps/miniconda3.10/bin/mamba create -f /mnt/strong/tools/apps/STRONG/conda_env.yaml
But then if it fail it fail. You wrote in your first message that you tried different miniconda version and that the target directory is writable.  Or maybe not.
We can test if conda is possible at all, did you try installing some random software with conda/mamba? I would try installing anything in base, first with mamba (should fail) then with conda (hopefully doesn't). Then if conda works you can have it solve the env, which latest time I tried took 24h. But maybe they improved.
Final, tryhard solution is to create a singularity container (I should do that at some point) and run the strong install there.

$ /mnt/strong/tools/apps/miniconda3.10/bin/mamba create -f /mnt/strong/tools/apps/STRONG/conda_env.yaml
usage: mamba create [-h] [--clone ENV] (-n ENVIRONMENT | -p PATH) [-c CHANNEL]
[--use-local] [--override-channels]
[--repodata-fn REPODATA_FNS] [--experimental {jlap,lock}]
[--strict-channel-priority] [--no-channel-priority]
[--no-deps | --only-deps] [--no-pin] [--copy] [-C] [-k]
[--offline] [-d] [--json] [-q] [-v] [-y] [--download-only]
[--show-channel-urls] [--file FILE]
[--no-default-packages]
[--solver {classic} | --experimental-solver {classic}]
[--dev]
[package_spec ...]
mamba create: error: one of the arguments -n/--name -p/--prefix is required
$ which mamba
/mnt/strong/tools/apps/miniconda3.10/bin/mamba
"We can test if conda is possible at all".  OK, I took the mamba piece out of the picture and used conda exclusively by performing "conda install" for the packages specified in conda_env.yaml.
That is,
conda create STRONG
conda activate STRONG
conda install snakemake
conda install metabat2
conda install biopython
...
conda install xorg-libxt
One thing I did not do is specify the version number as specified in conda_env.yaml.  What I noticed conda will stall if I try to specify anything other than the current version available.  Also conda for some reason cannot install bam-readcount so I skipped it (conda install -c bioconda bam-readcount).
After I installed all the packages in the STRONG env, I attempted install_STRONG.sh script:
$ ./install_STRONG.sh
SPAdes install ongoing
SPAdes install succesfully
creating STRONG env
/mnt/strong/tools/apps/miniconda3.10
Installing BayesPaths
Installing DESMAN
no issue found with install
=====> I guess the "no issue found with install" is a good sign so the next step is run your suggest test.
=====> test-config.yaml:
------ Samples ------
samples: ['sample*'] # specify a list samples to use or '*' to use all samples
------ Resources ------
threads : 8 # single task nb threads
------ Assembly parameters ------
#data:  /home/ubuntu/STRONG_Runs/Test  # path to data folder
data:  /mnt/strong/tools/apps/STRONG_Runs/Test  # path to data folder
----- Annotation database -----
#cog_database: /home/ubuntu/rpsblast_cog_db/Cog # COG database
cog_database: /mnt/strong/tools/apps/STRONG_database/rpsblast_cog_db/Cog # COG d
atabase
----- Binner ------
binner: "concoct"
----- Binning parameters ------
concoct:
contig_size: 1000
read_length: 150
assembly:
assembler: spades
k: [77]
mem: 2000
threads: 24
----- BayesPaths parameters ------
bayespaths:
nb_strains: 5
nmf_runs: 1
max_giter: 1
min_orf_number_to_merge_bins: 18
min_orf_number_to_run_a_bin: 10
percent_unitigs_shared: 0.1
----- DESMAN parameters ------
desman:
execution: 1
nb_haplotypes: 10
nb_repeat: 5
min_cov: 1
-----  Evaluation ------
evaluation:
execution: 1
#    genomes: "/home/ubuntu/STRONG_Runs/Test/Eval" # path to reference genom
es
genomes: "/mnt/strong/tools/apps/STRONG_Runs/Test/Eval" # path to reference
genomes
=====> Received this error message:
Job 7: Assembling with metaSPAdes
Reason: Missing output files: assembly/spades/assembly.fasta, assembly/high_res/graph_pack.gfa
=====> Full output:
./bin/STRONG --config ./SnakeNest/test_config.yaml $SRPATH/TestResults --threads 8 --verbose
Step #1 - Assembly / Binning / COG Annotation
Config file config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job                         count    min threads    max threads

all                             1              1              1
bed_orfs                        1              1              1
bedtools_split_cov              8              1              1
bowtie_align                    8              8              8
bowtie_index                    1              8              8
cat_split_annotation            1              1              1
compute_avg_cov                 1              1              1
concoct                         1              8              8
copy_fasta                      1              1              1
coverage                        1              1              1
create_bin_folders              1              1              1
cut_contigs                     1              1              1
extract_SCG_sequences           1              1              1
get_SCG_tables                  1              1              1
initial_quantity_of_bins        1              1              1
merge_contigs                   1              8              8
parse_cogs_annotation           1              1              1
prodigal                        1              1              1
reads_yaml                      1              1              1
refine                          1              8              8
rpsblast                      100              1              1
samtools_sort                   8              8              8
simplify                        1              8              8
spades                          1              8              8
split_fasta                     1              1              1
unitig_profiles                 1              8              8
total                         146              1              8
Resources before job selection: {'_cores': 8, '_nodes':<PHONE_NUMBER>854775807}
Ready jobs (2)
Select jobs to execute...
Welcome to the CBC MILP Solver
Version: 2.10.10
Build Date: Apr 19 2023
command line - cbc /tmp/f18348a88825414bb730a38b3b0a5d33-pulp.mps max timeMode elapsed branch printingOptions all solution /tmp/f18348a88825414bb730a38b3b0a5d33-pulp.sol (default strategy 1)
At line 2 NAME          MODEL
At line 3 ROWS
At line 7 COLUMNS
At line 18 RHS
At line 21 BOUNDS
At line 24 ENDATA
Problem MODEL has 2 rows, 2 columns and 4 elements
Coin0008I MODEL read with 0 errors
Option for timeMode changed from cpu to elapsed
Continuous objective value is 16 - 0.00 seconds
Cgl0004I processed model has 1 rows, 2 columns (2 integer (2 of which binary)) and 2 elements
Cutoff increment increased from 1e-05 to 1.9999
Cbc0038I Initial state - 0 integers unsatisfied sum - 0
Cbc0038I Solution found of 16
Cbc0038I Before mini branch and bound, 2 integers at bound fixed and 0 continuous
Cbc0038I Mini branch and bound did not improve solution (0.00 seconds)
Cbc0038I After 0.00 seconds - Feasibility pump exiting with objective of 16 - took 0.00 seconds
Cbc0012I Integer solution of 16 found by feasibility pump after 0 iterations and 0 nodes (0.00 seconds)
Cbc0001I Search completed - best objective 16, took 0 iterations and 0 nodes (0.00 seconds)
Cbc0035I Maximum depth 0, 0 variables fixed on reduced cost
Cuts at root node changed objective from 16 to 16
Probing was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Gomory was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Knapsack was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Clique was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
MixedIntegerRounding2 was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
FlowCover was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
TwoMirCuts was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
ZeroHalf was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Result - Optimal solution found
Objective value:                16.00000000
Enumerated nodes:               0
Total iterations:               0
Time (CPU seconds):             0.00
Time (Wallclock seconds):       0.00
Option for printingOptions changed from normal to all
Total time (CPU seconds):       0.00   (Wallclock seconds):       0.00
Selected jobs (1)
Resources after job selection: {'_cores': 0, '_nodes':<PHONE_NUMBER>854775806}
[Sun Jul 16 14:09:14 2023]
Job 7: Assembling with metaSPAdes
Reason: Missing output files: assembly/spades/assembly.fasta, assembly/high_res/graph_pack.gfa
    /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
    cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
    cp assembly/spades//K77/saves/00_before_simplification/graph_pack* $(dirname assembly/high_res/graph_pack.gfa)

Full Traceback (most recent call last):
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/executors/init.py", line 2561, in run_wrapper
run(
File "/mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake", line 50, in __rule_spades
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/shell.py", line 294, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;
/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
cp assembly/spades//K77/saves/00_before_simplification/graph_pack* $(dirname assembly/high_res/graph_pack.gfa)' returned non-zero exit status 1.
[Sun Jul 16 14:09:14 2023]
Error in rule spades:
jobid: 7
input: /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz, /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz
output: assembly/spades/assembly.fasta, assembly/high_res/graph_pack.gfa
log: assembly/spades.log (check log file(s) for error details)
shell:
    /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
    cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
    cp assembly/spades//K77/saves/00_before_simplification/graph_pack* $(dirname assembly/high_res/graph_pack.gfa)

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Full Traceback (most recent call last):
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/executors/init.py", line 2561, in run_wrapper
run(
File "/mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake", line 50, in __rule_spades
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/shell.py", line 294, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;
/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
cp assembly/spades//K77/saves/00_before_simplification/graph_pack* $(dirname assembly/high_res/graph_pack.gfa)' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/executors/init.py", line 656, in _callback
raise ex
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/executors/init.py", line 642, in cached_or_run
run_func(args)
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/site-packages/snakemake/executors/init.py", line 2597, in run_wrapper
raise RuleException(
snakemake.exceptions.RuleException: CalledProcessError in file /mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake, line 22:
Command 'set -euo pipefail;
/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
cp assembly/spades//K77/saves/00_before_simplification/graph_pack $(dirname assembly/high_res/graph_pack.gfa)' returned non-zero exit status 1.
File "/mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake", line 22, in __rule_spades
RuleException:
CalledProcessError in file /mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake, line 22:
Command 'set -euo pipefail;
/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py --meta --only-assembler --save-gp -t 8 -k 77 -m 2000 -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz -1 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz -2 /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz -o assembly/spades/ &> assembly/spades.log
cp assembly/spades//contigs.fasta assembly/spades/assembly.fasta
cp assembly/spades//K77/saves/00_before_simplification/graph_pack* $(dirname assembly/high_res/graph_pack.gfa)' returned non-zero exit status 1.
File "/mnt/strong/tools/apps/STRONG/SnakeNest/Assembly.snake", line 22, in __rule_spades
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Resources before job selection: {'_cores': 8, '_nodes':<PHONE_NUMBER>854775807}
Ready jobs (1)
Select jobs to execute...
Using greedy selector because only single job has to be scheduled.
Selected jobs (1)
Resources after job selection: {'_cores': 7, '_nodes':<PHONE_NUMBER>854775806}
[Sun Jul 16 14:09:14 2023]
rule reads_yaml:
output: samples.yaml
jobid: 33
reason: Missing output files: samples.yaml
resources: tmpdir=/tmp
Config file config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Sun Jul 16 14:09:15 2023]
Finished job 33.
1 of 146 steps (1%) done
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-07-16T140914.151182.snakemake.log
unlocking
removing lock
removing lock
removed all locks
Traceback (most recent call last):
File "/mnt/strong/tools/apps/STRONG/./bin/STRONG", line 94, in
call_snake(["--snakefile", "SnakeNest/SCogSubGraph.snake"])
File "/mnt/strong/tools/apps/STRONG/./bin/STRONG", line 83, in call_snake
subprocess.check_call(base_params + extra_params, stdout=sys.stdout, stderr=sys.stderr)
File "/mnt/strong/tools/apps/miniconda3.10/envs/STRONG/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['snakemake', '--directory', '/mnt/strong/tools/apps/STRONG_Runs/TestResults', '--cores', '8', '--config', 'LOCAL_DIR=/mnt/strong/tools/apps/STRONG', '--configfile=/mnt/strong/tools/apps/STRONG_Runs/TestResults/config.yaml', '--latency-wait', '120', '-k', '-p', '-r', '--verbose', '--snakefile', 'SnakeNest/SCogSubGraph.snake']' returned non-zero exit status 1.

Hi,
Happy you managed to install most things. I don't remember but I think bam-readcount is needed mostly for Desman.
If you don't mind, the log would be better as a joined file, it's a bit hard to read here.
Anyway, there is an issue with spades. Can you join the log file which is at: assembly/spades.log. The install script checks that one of the utils has been compiled, this should be sufficient check but maybe there is still an issue?

Hello, part 1 of 3.  install.log from the STRONG directory (3678 lines).
install.log

Hello, part 2 of 3.  /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades.log
$ cat /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades.log
Command line: /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py     --meta   --only-assembler        --save-gp       -t      8       -k      77     -m       2000    -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz        -o      /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades
System information:
SPAdes version: 3.14.0
Python version: 3.10.12
OS: Linux-4.18.0-425.3.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Traceback (most recent call last):
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py", line 639, in
main(sys.argv)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py", line 579, in main
print_params(log, log_filename, command_line, args, cfg)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py", line 322, in print_params
print_used_values(cfg, log)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py", line 112, in print_used_values
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename))
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/init.py", line 72, in load
return loader.get_single_data()
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/constructor.py", line 37, in get_single_data
return self.construct_document(node)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/constructor.py", line 46, in construct_document
for dummy in generator:
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/constructor.py", line 398, in construct_yaml_map
value = self.construct_mapping(node)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/constructor.py", line 204, in construct_mapping
return super().construct_mapping(node, deep=deep)
File "/mnt/strong/tools/apps/STRONG/SPAdes/assembler/share/spades/pyyaml3/constructor.py", line 126, in construct_mapping
if not isinstance(key, collections.Hashable):
AttributeError: module 'collections' has no attribute 'Hashable'

Hello, part 3 of 3.  /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades/spades.log
$ cat /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades/spades.log
Command line: /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py     --meta   --only-assembler        --save-gp       -t      8       -k      77     -m       2000    -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R1.fq.gz        -1      /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R1.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample1/sample1_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample2/sample2_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample3/sample3_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample4/sample4_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample5/sample5_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample6/sample6_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample7/sample7_R2.fq.gz        -2      /mnt/strong/tools/apps/STRONG_Runs/Test/sample8/sample8_R2.fq.gz        -o      /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades
System information:
SPAdes version: 3.14.0
Python version: 3.10.12
OS: Linux-4.18.0-425.3.1.el8.x86_64-x86_64-with-glibc2.28
Output dir: /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:

Hi
I googled that error message, it seems to be an issue with spades version. Can you update it to 3.15.4 using:
https://cab.spbu.ru/files/release3.15.4/manual.html#sec2

Hello, thank you for all the help so far.   I downloaded the precompiled Linux version and still the same error message when I run the test job:
[Tue Jul 18 09:24:12 2023]
Job 7: Assembling with metaSPAdes
Reason: Missing output files: assembly/high_res/graph_pack.gfa, assembly/spades/assembly.fasta
Here are my steps,
$ cd /mnt/strong/tools/apps/STRONG
$ mv SPAdes SPAdes-original
$ wget --no-check-certificate http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz
$ tar -xzf SPAdes-3.15.4-Linux.tar.gz
$ ln -s SPAdes-3.15.4-Linux SPAdes
$ ls SPAdes/bin/
cds-mapping-stats     rnaviralspades.py            spades_init.py
cds-subgraphs         spades-bwa                   spades-ionhammer
coronaspades.py       spades-convert-bin-to-fasta  spades-kmercount
mag-improve           spades-core                  spades-kmer-estimating
metaplasmidspades.py  spades-corrector-core        spades.py
metaspades.py         spades-gbuilder              spades-read-filter
metaviralspades.py    spades-gmapper               spades-truseq-scfcorrection
plasmidspades.py      spades-gsimplifier           spaligner
rnaspades.py          spades-hammer                truspades.py
check_on_dependencies.py and new SPAdes:
------------------------------------------------------------------------------
Following issues where found :
SPAdes is not compiled
------------------------------------------------------------------------------
check_on_dependencies.py and original SPAdes:
no issue found with install

Hi,
Hum, that in itself is not an error message but just information on what task is being run (assembly with spade, since output have not been generated previously). When I run it on terminal, i see these message in green color which is quite different to the red color of when it did fail. If it fail due to any sort of error, you would have it in red? Also, for spade assembly you the logs would be more informative, the one at: assembly/spades.log.

Hello, I think you want see the test run output in color?  Please have a look at this pdf link.
SPAdes-test01.pdf
Here's the output of spades.log:
$ cat /mnt/strong/tools/apps/STRONG_Runs/TestResults/assembly/spades.log
/usr/bin/bash: line 1: /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py: No such file or directory
I'm running the precompiled Linux binary of SPAdes downloaded from the site you suggested.  The precompiled version does not contain the assembler directory.
Thank you

Hello,
Thanks for the pdf, that's neat. How did you even do that?
Anyway, I'm sorry but I'm going to be limited in how I can help you. Unless I'm wrong, you have an issue of installation where you did install that new version of spades but not exactly where STRONG is expecting it. Strong is expecting it in the STRONG repos. You need to either reinstall spades in the correct folder or just do a symlink and replace /mnt/strong/tools/apps/STRONG/SPAdes/assembler/bin/spades.py by the new install you have, which, if you followed the instructions to the letter should be at: /bin/spades.py
Best,
Seb

Hello,
I used putty to copy and paste the text into Word which retained the color.
For the past two weeks, on and off I've been trying to install STRONG natively using the instructions on this github page (Plan A).   When this didn't work I initiated this thread (Plan B).   I tried Plan A again today and the mamba portion of install_STRONG.sh worked and it returned "no issue found with install".  I even executed your suggested test job which ran for about 40 minutes and all I saw was white, blue, yellow and green text.  So I think it all worked.  Something with the mamba backend must be the culprit as my environment didn't change and I was consistent on how I perform the installation.  So at least for now I'm good and have a good working version of STRONG.
Sorry, this may have been a false alarm.
Thanks for your time on helping me troubleshoot.

Happy it worked in the end :)


[test] Verify that TypeDecoder handles same-type constraints properly

Follow-up for #25984 recommended by Slava. (RemoteAST is next but that might actually have problems…or I might be holding it wrong.)

@swift-ci Please test

@swift-ci Please smoke test

@swift-ci Please smoke test Linux

@slavapestov Ping. I think there's no downside to taking these tests, even if we have to leave the Remote* ones for later?


automate adding skipped redirects to no-skip list

the 'copy last skipped url' is problematic in that it often doesn't write the url to the clipboard, or must be clicked multiple before it does
whether this feature works or not isn't really my point however - i would like to propose a change that i think would eliminate this problem and make adding urls to the no-skip list easier
instead of having to copy and edit the last skipped url, then open the preferences and add it to the list, i would suggest changing the 'copy last skipped url' menu item to something like 'whitelist last skipped url' - upon clicking that, a pop-up is displayed with the url in an edit control so the user can edit it if need be, after which an 'enter' key press, or a 'save' button press would add the url to the list

I have no interest or time to work on this.


test_tcnn_instant_ngp_field() Segmentation Fault

test_tcnn_instant_ngp_field() has a segfault. This test is only run locally since the github actions don't have tcnn. Interestingly the segfault does not occur if you run the test using the debugger.

No longer an issue.


Possible compatibility problem with node 4.0?  Can't build on Raspberry Pi - Debian Jessie

node -v ==> v4.0.0
node-gyp -v ==> v3.0.2
uname -a ==> Linux rpi0 4.1.6+ #810 PREEMPT Tue Aug 18 15:19:58 BST 2015 armv6l GNU/Linux
Many C++ compile errors.  I'll be happy to generate a clean npm debug log if someone can tell me how to attach it.
root@rpi0: /home/jnavratil/pmon$ npm -g install i2c
|

<EMAIL_ADDRESS>install /usr/local/lib/node_modules/i2c
node-gyp rebuild

make: Entering directory '/usr/local/lib/node_modules/i2c/build'
CXX(target) Release/obj.target/i2c/src/i2c.o
../src/i2c.cc: In function 'void ReadBlock(const v8::FunctionCallbackInfov8::Value&)':
../src/i2c.cc:162:47: error: no matching function for call to 'New(int32_t&)'
Local buffer = node::Buffer::New(len);
^
../src/i2c.cc:162:47: note: candidates are:
In file included from ../src/i2c.cc:2:0:
/root/.node-gyp/4.0.0/include/node/node_buffer.h:28:40: note: v8::MaybeLocalv8::Object node::Buffer::New(v8::Isolate*, size_t)
NODE_EXTERN v8::MaybeLocalv8::Object New(v8::Isolate* isolate, size_t length);
^
/root/.node-gyp/4.0.0/include/node/node_buffer.h:28:40: note:   candidate expects 2 arguments, 1 provided
/root/.node-gyp/4.0.0/include/node/node_buffer.h:31:40: note: v8::MaybeLocalv8::Object node::Buffer::New(v8::Isolate*, v8::Localv8::String, node::encoding)
NODE_EXTERN v8::MaybeLocalv8::Object New(v8::Isolate* isolate,
^
/root/.node-gyp/4.0.0/include/node/node_buffer.h:31:40: note:   candidate expects 3 arguments, 1 provided
/root/.node-gyp/4.0.0/include/node/node_buffer.h:36:40: note: v8::MaybeLocalv8::Object node::Buffer::New(v8::Isolate*, char*, size_t, node::Buffer::FreeCallback, void*)
NODE_EXTERN v8::MaybeLocalv8::Object New(v8::Isolate* isolate,
^
/root/.node-gyp/4.0.0/include/node/node_buffer.h:36:40: note:   candidate expects 5 arguments, 1 provided
/root/.node-gyp/4.0.0/include/node/node_buffer.h:43:40: note: v8::MaybeLocalv8::Object node::Buffer::New(v8::Isolate*, char*, size_t)
NODE_EXTERN v8::MaybeLocalv8::Object New(v8::Isolate* isolate,
^
/root/.node-gyp/4.0.0/include/node/node_buffer.h:43:40: note:   candidate expects 3 arguments, 1 provided
i2c.target.mk:86: recipe for target 'Release/obj.target/i2c/src/i2c.o' failed
make: *** [Release/obj.target/i2c/src/i2c.o] Error 1
make: Leaving directory '/usr/local/lib/node_modules/i2c/build'
gyp ERR! build error
gyp ERR! stack Error: make failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/local/lib/node_modules/npm/node_modules/node-gyp/lib/build.js:270:23)
gyp ERR! stack     at emitTwo (events.js:87:13)
gyp ERR! stack     at ChildProcess.emit (events.js:172:7)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:200:12)
gyp ERR! System Linux 4.1.6+
gyp ERR! command "/usr/local/bin/node" "/usr/local/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /usr/local/lib/node_modules/i2c
gyp ERR! node -v v4.0.0
gyp ERR! node-gyp -v v3.0.1
gyp ERR! not ok
npm ERR! Linux 4.1.6+
npm ERR! argv "/usr/local/bin/node" "/usr/local/bin/npm" "-g" "install" "i2c"
npm ERR! node v4.0.0
npm ERR! npm  v2.14.2
npm ERR! code ELIFECYCLE
npm ERR<EMAIL_ADDRESS>install: node-gyp rebuild
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the<EMAIL_ADDRESS>install script 'node-gyp rebuild'.
npm ERR! This is most likely a problem with the i2c package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR!     node-gyp rebuild
npm ERR! You can get their info via:
npm ERR!     npm owner ls i2c
npm ERR! There is likely additional logging output above.
npm ERR! Please include the following file with any support request:
npm ERR!     /home/jnavratil/pmon/npm-debug.log

+1

Same issue here ...

+1

I have the same issue of it not compiling on a BeagleBone with Debian and Node v<IP_ADDRESS> .

Exactly the same issue here.
(as a dependency of cylon-raspi)

node 4.0 requires a major re-write of native v8 modules. I likely won't be able to get to this for sometime. If someone wants to tackle it and send me a pull request, i'll merge it, and submit a release.

Kelly,
Thanks for the heads up.  In theory I could do this (I've been a C programmer for years, I'm not a C++ maven), but my complete unfamiliarity with the code base makes my success unlikely.
I'm just building a Raspian system and am not married to Node 4.0.  Do you have a clue to which node version is compatible with i2c?  If not, I'll report back with my results as I try to find one.

In the mean time, I'm using i2c-bus with node v4

The Node version that was compatible with i2c is Node 0.10     Stable Version

That is incorrect, it should work for v0.12.7 and everything before. So everything prior to the 4.0 release.

Oh thanks :D did you how to fix this problem?
I2c is no working and I need to install cylon-raspy.

For now just use nvm to install node 0.12.7 and you should be able to use cylon-raspi with i2c.

This pull request is working: https://github.com/kelly/node-i2c/pull/70/commits
You can implement it immediately using the following snippet in your packages.json.
"i2c": "https://github.com/polaris/node-i2c"

+1 need this :)

Anvanza, I don't suppose there is a way you can show me how to do this, or point me in the direction of some generic instructions. Am still quite new to this!
TIA

Anvanza, never mind, I didn't take your comment literally enough. Works great for lots of my sensors, Thanks for the heads-up!

If your application has a module which has node-i2c as a subpackage, rather than modify the module, just install the workaround version globally.
npm install -g https://github.com/jnovack/node-i2c/archive/master.zip
When you npm install your application, the module will see you already have it and use the local "fixed" copy.

jnovack,
I reviewed yours and anvanza's files and it seems yours is trying to be a more universal solutions.  So I tried it, and received....
npm install -g https://github.com/jnovack/node-i2c/archive/master.zip
npm ERR! not a package /tmp/npm-19977-c99c1b5a/github.com/jnovack/node-i2c/archive/master.zip
npm ERR! Linux 4.1.13+
npm ERR! argv "/usr/local/bin/node" "/usr/local/bin/npm" "install" "-g" "https://github.com/jnovack/node-i2c/archive/master.zip"
npm ERR! node v4.2.4
npm ERR! npm  v2.14.12
npm ERR! path /tmp/npm-19977-c99c1b5a/unpack-9d46181a9b21/package.json
npm ERR! code ENOENT
npm ERR! errno -2
npm ERR! syscall open
npm ERR! enoent ENOENT: no such file or directory, open '/tmp/npm-19977-c99c1b5a/unpack-9d46181a9b21/package.json'
npm ERR! enoent This is most likely not a problem with npm itself
npm ERR! enoent and is related to npm not being able to find a file.
npm ERR! enoent
Any thoughts?
You see the versions of node and npm.  This is being installed on a Raspberry Pi running an updated Jessie.

jnovack,
Flying completely by the seat of my pants, and as root (shivver!), I...
wget "https://github.com/jnovack/node-i2c/archive/master.zip"
unzip master.zip
cd node-i2c-master/
npm -g install .
Things seemed to work.  I've not done any testing yet.  Thoughts?

New instructions:
git clone https://github.com/jnovack/node-i2c/
cd node-i2c/
npm install -g .

You can see the changes I've made here. All I've done is isolate node version v4 code as a quick and dirty work-around and set the version to be 0.2.1-alpha.1.  This ensures that any update of the REAL package will overwrite my package.

+1 on this being a problem for my projects

+1

+1

I need to install i2c which is used as a submodule of cylon-raspi. I encountered the same issue, I am using node.js 4.X stable.
I know that the Node version that was compatible with i2c is Node 0.12.x Stable version as mentioned above, however I want  to use the latest stable node.js to run my MEAN stack web application, from where I can hook up my raspberry and do some automation thing from my web page.
The node.js 4.X support will be highly appreciated, thank you for the great work.

@kawashimaken This thread has been running for months, you'd be better off forking the cylon-raspi repo and altering it to use a different i2c library. I remember being pointed in the direction of one when I came here with the same issue. I'll look up the name for you.

@alexellis Thank you for your info and your advice! I will definitely check out your repo! I hope I can make a smooth swap to i2c-bus.


Basic support for paravirtualized images

This is by no means complete, but I wanted to see if anyone else is interested using the older paravirtualized instance types?
spot pricing for the c4.large instances is going crazy:

These huge price spikes cause instance terminations regardless of lifecycled which look like this in a job:
$ docker-compose -f .buildkite/docker-compose.yml -p buildkite135479143c984704a4046342d74118a4 kill
ERROR: Couldn't connect to Docker daemon at http+docker://localunixsocket - is it running?

If it's at a non-standard location, specify the URL with the DOCKER_HOST environment variable.
$ docker-compose -f .buildkite/docker-compose.yml -p buildkite135479143c984704a4046342d74118a4 rm --force --all -v
ERROR: Couldn't connect to Docker daemon at http+docker://localunixsocket - is it running?

If it's at a non-standard location, specify the URL with the DOCKER_HOST environment variable.
$ docker-compose -f .buildkite/docker-compose.yml -p buildkite135479143c984704a4046342d74118a4 down
ERROR: Couldn't connect to Docker daemon at http+docker://localunixsocket - is it running?

If it's at a non-standard location, specify the URL with the DOCKER_HOST environment variable.

Older instance types seem to have much more capacity, and lower more stable prices:

These are the bare minimum changes required to use the PV instances like m1.large, if there is interest perhaps the mappings should support these instance types automatically?

Interesting…

@Vektah I haven't actually added support for spot pricing notifications to lifecycled yet btw.

https://github.com/lox/lifecycled/issues/3

So, is the aim just to do this for the packer builder @Vektah? Or agent instances?

@Vektah I haven't actually added support for spot pricing notifications to lifecycled yet btw.

I doubt we would be able to delay them even if we were listening to them? Once your spot price has been exceeded I imagine AWS forcefully kill that instance pretty quickly.

So, is the aim just to do this for the packer builder @Vektah? Or agent instances?

I dont think the packer builder needs to change as long as whatever instance its built on support both PV and HVM.
Ideally there would be pre built paravirtualized AMIs pushed up setting an instance type that is PV only would use one of a PV image. I think HVM is preferred where ever its available.

So for spot instances, we're going add some kind of signal support to say "I'm shutting down, so cancel this job but feel free to retry" and a pipeline step can say retryable or something similar, and it'll just reschedule it to run again.
As for PV support, it'd be great to add support for this with some kind of mapping. Assuming it's not massive overhead?

Well, it's certainly nicer to get the 2 minutes extra lead time that termination notifications provide. Would allow for a graceful shutdown in most cases.

My vote would be 👎 for adding support for PV instance types. I think they are a dying breed and not worth the complexity it would introduce to the stack .


Placeholder Output Fix

If you do /papi bparse username %essentials_kit_is_available_kitname% it shows &aON or &cOFF, not yes nor no.

@Neeonn by default the placeholders output yes and no. They output other stuff for you because you have changed the output in plugins/PlaceholderAPI/config.yml.
I'll close this PR now. I don't know who is responsible for this but please lmk if I shouldn't next time.


Convert airforces

Air forces are converted, but air fields are not yet converted.

Now they are.


Feature Request: Enhanced File Management and Workspace Features

Feature Request: Enhanced File Management and Workspace Features
Description
I commonly make notes and concept diagrams in Excalidraw , using it as a PWA . Though accessing and viewing files from the default file system of my machine becomes tedious and time consuming. I am aware of Excalidraw+  but it is not built to work with the local storage.
I think that a better navigation and file access management can be implemented to work with the current PWA , without relying on any other database.

Broad Outline for Proposed Features

Folder Selection:

Allow users to select a specific folder on their local file system as a workspace using the File System Access API.

File Listing:

Display all files and subfolders within the selected folder in a sidebar for quick access and organization.

Load Saved Folder:

On startup, check Local Storage for a previously selected folder and prompt the user to either use that folder or select a new one.

Change Folder Option:

Provide functionality for users to change the selected folder, updating the Current Workspace with the new selection.

Multiple tab interface:

Implementation of multiple tabs for viewing different files from the local storage, if such is possible.

User-Friendly Interface:

Create an intuitive user interface that integrates these file management features seamlessly with the existing drawing functionalities of Excalidraw.

Benefits

Improved Organization: Users can keep their projects organized within specific folders, making it easier to manage multiple drawings.
Enhanced User Experience: Quick access to recently used files and folders improves overall usability.
Increased Efficiency: Dynamically accessing files without needing to upload or manage them on a server streamlines the workflow for users.

I acknowledge that I know less than little of the application architecture and overall storage system . Therefore, please let me know if the features I’ve mentioned are feasible to implement.  Thank you for your consideration!

I don't think we will ever be implementing custom directory UI. You shall be presented with an OS-level directory when you are saving or opening a scene.
For tabs, closing as a duplicate of https://github.com/excalidraw/excalidraw/issues/1543.

Is it technically possible to do so ? If yes then I will try to implement it on my own in the future. Thankyou for your response.

Is it technically possible to do so ?
If yes then I will try to implement it on my own in the future. Thankyou
for your response.
On Sun, Nov 3, 2024 at 7:13 PM Marcel Mraz @.***> wrote:

I don't think we will ever be implementing custom directory UI. You shall
be presented with an OS-level directory when you are saving or opening a
scene.
For tabs, closing as a duplicate of #1543
https://github.com/excalidraw/excalidraw/issues/1543.
—
Reply to this email directly, view it on GitHub
https://github.com/excalidraw/excalidraw/issues/8746#issuecomment-2453432850,
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NewPullRequest: newIssue: Error 3988: Conversion from collation utf8mb4_0900_ai_ci into utf8_general_ci impossible for parameter

Description
Renovate can creates a branch but not create a PR. It leads to a conversion error in the db. Gitea is migrate. I assume unicode can't be handled. See the question emoticon in "Screenshots".
Gitea Version
1.18.3
Can you reproduce the bug on the Gitea demo site?
No
Log Gist
No response
Screenshots
   ---

    ❓ Got questions? Check out Renovate's [Docs](https://docs.renovatebot.com/), particularly the Getting Started section.
    If you need any further assistance then you can also [request help here](https://github.com/renovatebot/renovate/discussions).

    ---

This PR has been generated by Renovate Bot.
0 0 false true 0  0<PHONE_NUMBER><PHONE_NUMBER> 0 false] - 769.507µs
2023/02/11 10:45:59 .../api/v1/repo/pull.go:420:CreatePullRequest() [I] [63e763d7] [SQL] ROLLBACK [] - 2.040923ms
2023/02/11 10:45:59 .../api/v1/repo/pull.go:425:CreatePullRequest() [E] [63e763d7] NewPullRequest: newIssue: Error 3988: Conversion from collation utf8mb4_0900_ai_ci into utf8_general_ci impossible for parameter
2023/02/11 10:45:59 [63e763d7] router: completed POST /api/v1/repos/SpaceUp/SWS/pulls for <IP_ADDRESS>:0, 500 Internal Server Error in 282.1ms @ repo/pull.go:251(repo.CreatePullRequest)
2023/02/11 10:45:59 models/auth/token.go:160:GetAccessTokenBySHA() [I] [63e763d7-32] [SQL] SELECT id, uid, name, token_hash, token_salt, token_last_eight, created_unix, updated_unix FROM access_token WHERE (token_last_eight = ?) [c37d6d3b] - 824.249µs
Git Version
2.30.2
Operating System
Debian
How are you running Gitea?
It's self-hosted and scheduled by supervisor.
Database
MySQL

Please check all your database tables has the same collation.

Shouldn't migrate fix it? What should be the right one for all tables?

Use gitea convert

Worked, thanks!


Cannot read property 'remove' of undefined

onUnmount component error:
Cannot read property 'remove' of undefined
in Control.js#L99

Thanks for noticing! I really should start thinking how to add tests to the library, it becomes a little bit difficult to add new features without regression 😓
I'll try to fix this ASAP!

Should be fixed in 2.1.2. Could you check, please?

@gribnoysup thank you. Well job.


Remove Preview flag for User, Login, Role dialogs

The User, Login and Role dialogs should be moved from behind the Preview Features flag for the July release since they have gone through validation to be included in the default stable feature set.

Closing as this was discussed and is "by design" to hold off on removing the preview flag.


Unify the form of nouns in packages names

This project uses different forms of noun. e.g., controllers and utils are plural, but service is singular. I suggest renaming them all into singular form, because Golang standard library uses singular noun as its package names (e.g.: encoding/... instead of encodings/...).
You can find more discussions at:

https://github.com/golang-standards/project-layout/issues/7
https://dmitri.shuralyov.com/idiomatic-go/entries/5#comment-2

Also, I suggest following the naming guidelines here and here. Meaning that generic packages such as utils should be broken up. However I understand it's a hard work to re-organize the code, especially that this project is migrated from an existing Java backend. How do you think?

Indeed I agree that the current project structure needs some modifications. We tried to maintain the project structure as stated in https://github.com/golang-standards/project-layout.
Unifying the usage to a singular form would be more feasible for a cleaner project layout. We'll refactor it once got time :D
Thanks a lot for the issue!

Fixed in #38


Attributes not showing - even after publish

I'm trying to copy attributes from the marketing list entity to a new custom entity .  The process seems to complete, and then I choose to "Publish All" customizations in the default solution and I'm still unable to see the fields in the target.
If I try the process again thinking it didn't work, I get the message the fields I am trying to move are already created in the destination.
Is there some specific way to make the new fields appear in the default soltion? I'm just using the "publish all customizations".
I am on crm 9.1 on premise.

Hi @mc625569,
Is this issue still valid since you reported it?
Sometimes Dynamics seems to experience slowness in updating the metadata in the UI, but I have very seldom encountered this in online organizations. Might be more common in on premise systems.
Kind regards,
Florian

Hi Florian,
They did appear when I returned to the system the next day.  I initially waited about 30 minutes after creation and didn't see the new fields. So sometime between when I logged off for the night and the next morning they appeared.  I will use the tool a little more and see if I can get more precise timing.  Publishing the entity did not seem to fix the issue/


Add a static badge for Frogbot

[x] All tests passed. If this feature is not already covered by the tests, I added new tests.
[x] This pull request is on the dev branch.
[x] I used gofmt for formatting the code before submitting the pull request.

Added a new svg badge to the images directory of the frogbot repository.
Added the badge to the README of Frogbot.
Added a new section to the documentation, describing how the badge can be added to the README file of a repository.

we can also add the icon to the badge , and change the color to green :)
what do you think ?

Looks great @EyalDelarea!
If you don't have comments and can approve this PR, I'll go ahead and merge it.


Trying To Avoid Hitters vs Pitchers In Same Lineup

So my understanding is when using the restrict positions for opposing teams method it should not have hitters and the opposing team pitcher in the same lineups.
optimizer.restrict_positions_for_opposing_team(['P'], ['1B', '2B', '3B', 'C', 'SS', 'OF'])
I noticed this works sometimes and sometimes it doesn't.  You can test it how I did by taking the salaries for a 2 game slate, run the optimizer, see which pitcher it likes.  Then find an opposing team hitter and edit his projection to something high like 100, then run it again.  The optimizer will pick the same pitchers but add that hitter as well.

I had the same problem. My solution was to change from 'P' to 'SP' because that it is formatted in the CSV.  It should work after that.

I had the same problem. My solution was to change from 'P' to 'SP' because that it is formatted in the CSV. It should work after that.

I appreciate the help, unfortunately it still doesn't work. Thanks anyways.

Can you post a picture of you csv and code? This issue was resolved with the last release. @ravashjalil


Describe your issue and include the command you're running, flutter_desktop version, browser version
flutter doctor -v
Flutter windows desktop application is closed immediately after starting.
Please find the flutter doctor -v
flutter doctor -v
[√] Flutter (Channel dev, 2.3.0-16.0.pre, on Microsoft Windows [Version 10.0.18363.1734], locale en-US)
• Flutter version 2.3.0-16.0.pre at C:\Users\sxn13\AppData\Local\Flutter\flutter_windows_2.3.0-16.0.pre-dev\flutter
• Upstream repository https://github.com/flutter/flutter.git
• Framework revision fa5883b78e (5 months ago), 2021-05-21 13:04:03 -0700
• Engine revision 2f067fc4c5
• Dart version 2.14.0 (build 2.14.0-136.0.dev)
• Pub download mirror https://pub.dartlang.org/
[√] Android toolchain - develop for Android devices (Android SDK version 31.0.0)
• Android SDK at C:\Users\sxn13\AppData\Local\Android\sdk
• Platform android-31, build-tools 31.0.0
• Java binary at: C:\Program Files\Android\Android Studio\jre\bin\java
• Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b01)
• All Android licenses accepted.
[√] Chrome - develop for the web
• Chrome at C:\Program Files (x86)\Google\Chrome\Application\chrome.exe
[√] Visual Studio - develop for Windows (Visual Studio Community 2019 16.10.0)
• Visual Studio at C:\Program Files (x86)\Microsoft Visual Studio\2019\Community
• Visual Studio Community 2019 version 16.10.31321.278
• Windows 10 SDK version 10.0.19041.0
[√] Android Studio (version 4.1.0)
• Android Studio at C:\Program Files\Android\Android Studio
• Flutter plugin can be installed from:
https://plugins.jetbrains.com/plugin/9212-flutter
• Dart plugin can be installed from:
https://plugins.jetbrains.com/plugin/6351-dart
• Java version OpenJDK Runtime Environment (build 1.8.0_242-release-1644-b01)
[√] VS Code (version 1.61.1)
• VS Code at C:\Users\sxn13\AppData\Local\Programs\Microsoft VS Code
• Flutter extension version 3.27.0
[√] Connected device (4 available)
• Windows (desktop)       • windows • windows-x64     • Microsoft Windows [Version 10.0.18363.1734]
• Windows (UWP) (desktop) • winuwp  • windows-uwp-x64 •
• Chrome (web)            • chrome  • web-javascript  • Google Chrome 94.0.4606.81
• Edge (web)              • edge    • web-javascript  • Microsoft Edge 94.0.992.50
• No issues found!

Without additional information, we are unfortunately not sure how to resolve this issue.
We are therefore reluctantly going to close this bug for now.
Please don't hesitate to comment on the bug if you have any more information for us; we will reopen it right away!
Thanks for your contribution.
Could everyone who still has this problem please file a new issue with the exact description of what happens, logs, and the output of flutter doctor -v.
All system setups can be slightly different, so it's always better to open new issues and reference related issues.


Get Partner/Sister colleges

A lot of colleges are interested to do something like KWoC for their institute. There is no necessity for piling up the burden. Hence, KOSS can partner up with colleges and can come up with one single event.
@pranitbauva1997 @DefCon-007
A feedback from student endterm report:
KOSS is doing a great contribution itself to the Open Source community by conducting programmes
such as KWOC which stand to introduce more people in the open source software development.! Being
 outside of IIT-KGP I feel the reach of this programme should be broaden by contacting the college
administration to take necessary steps to notify and allow students to take part in the programme. Also
using some social media platforms to publicise the programme as it would help more students to join the
open source development.

I will working on this part.

I have a few contacts who will be glad to help.


[Scheduling Sample] Appointment details page

Description
Adds the Appointment detail page (/Appointment/:id), including patient profile, appointment details, list of encounters, and upcoming and past appointments for the same Patient.
Page tabs
https://github.com/user-attachments/assets/5ed14aad-1105-4fcb-9c44-0f18f9849bca
Complete, cancel and reschedule actions
https://github.com/user-attachments/assets/776a0179-cdf6-4b1a-affc-153acafc0458
Create encounter action
https://github.com/user-attachments/assets/52d4eca8-dfc1-40ff-92aa-b43d62f60f4a
Closes #4930 and #4931

Updated the UX, now clicking to create an encounter won't open a modal and it will use Appointment data to do it in the background.


Importing clarity sass variables breaks build

[x] bug
[ ] feature request
[ ] enhancement

Expected behavior
Per issue #1956 , clarity's sass variables should be able to be imported and used by importing the following files:
// clr-variables.scss

@import<EMAIL_ADDRESS>@import<EMAIL_ADDRESS>@import<EMAIL_ADDRESS>@import<EMAIL_ADDRESS>
// example.scss

@import "clr-variables.scss";

p {
  color: $clr-red
}

Actual behavior
The Angular project fails to build with the following error message:
ERROR in ./src/app/app.component.scss
Module build failed:
$clr-popover-box-shadow-color: rgba(clr-getColor(dark), 0.25);
                              ^
      Argument `$color` of `rgba($color, $alpha)` must be a color
      in @clr/ui/src/utils/_variables.global.scss (line 83, column 32)

Reproduction of behavior
https://github.com/rjmccluskey/clarity-sass-import-two
Environment details

Angular version: 6.0.3

Clarity version: 0.12.2

OS and version: macOS 10.13.5

Browser: all

Other
@hippee-lee I'm tagging you here since you were the one responding on the last related issue.

@gnomeontherun Unfortunately that did not fix the problem, please see issue #1956 for more information. I updated the linked repo with your suggested fix if you want to try it out.

Dug into this further, and you just aren't including all of the files needed. This can get a little hairy, so really you just need to have your clr-variables.scss file contain the following to get all the variables setup.
@import<EMAIL_ADDRESS>

Thanks for looking into this further. As mentioned in issue #1956, importing dependencies.clarity unfortunately causes other problems. @hippee-lee was working with me on the last issue and might be able to weigh in on this. My simple example repo is fixed by your solution but a larger project I am working on gets different errors.
I understand that it gets complicated to import all the necessary files. The best solution might be to separate out the sass variables so they are independent but I know that this is not easy to do as mentioned by @hippe-lee before.

We aren't in a position to reorganize at the moment, so you'll need to look at the order of files inside of the dependencies.clarity.scss file and try to eliminate ones that you don't need from your build.

Ok thanks I'll give it a try. I'm busy with other work at the moment but when I get back to this I'll update the issue if I'm able to get it working

So at least for me the fix was to import the contents of _dependencies except for @import 'bootstrap/scss/normalize';

@gnomeontherun My team decided to no longer use the clarity sass variables in our code since doing this is not fully supported by clarity. We are instead using a global file with our own variables that have hard coded values aligned with clarity's color/layout styles. Luckily we had already created this global file with our own prefixed variables, but before they pointed to clarity variables, so the refactor was easy enough.
If there are any major style changes in the clarity library we will just update this file instead.
Since the demand to directly reference clarity sass variables seems low, I'd understand if you wanted to close this issue.

Thanks for the update, and we do hope to resolve this in the future when we refactor our SCSS. Unfortunately that is not a short term priority so this is a good solution and I will close it for now.

Thanks for the update, and we do hope to resolve this in the future when we refactor our SCSS. Unfortunately that is not a short term priority so this is a good solution and I will close it for now.

It's a problem I suffer from and even though this issue won't be solved any time soon, it should be kept open in my opinion. I was able to find it only because it was open.

I always suggest looking at open and closed issues, because solutions can be found there. GitHub doesn't always make it clear to view the closed issues in my opinion. Keeping issues open is harder for us to maintain when this is not really indicative of what we plan to do (rebuilding the sass, perhaps with CSS variables instead).
The issue here is not importing the right files in the right order. This isn't a supported case for the time being, and the solution is to either review our current sass imports to see what you need to have, or create a separate variables file for your specific items. Follow our theme instructions on our documentation for the way to do custom themes, which we do support.

Any solution to this for 2.0.0?

In 2.0, there is no longer a clrGetColor() function. So this specific issue should not be a problem. Overall, many of the dependencies have been cleaned up. Best advice is to give it a shot and open a github issue if you feel like you hit a snag.

@mathisscott I gave it a second shot at upgrading to 2.0.0 ... unfortunately things that were possible with 1.x styles are no longer possible in 2.0.0. See #3444
I really appreciate you working on improving the SCSS but at least from my point of view the refactor has greatly regressed flexibility. I think using the maps was a powerful tool letting Clarity users define custom stuff on top of the framework.

Thanks for your feedback, @Rush. I've commented on the issue you opened (#3444) to avoid necro'ing this one.


Update minimum Rustc version (MSVR) to 1.46.0

Rustc was release on 27th of August 2020: https://github.com/rust-lang/rust/blob/master/RELEASES.md#version-1460-2020-08-27, the main benefit was additional support for const functions and #[track_caller] attribute.
This is also required for socket2, which currently requires 1.42.

Tokio's minimum supported Rust version is currently 1.45, and the precedent is that it requires a breaking change to update.

Tokio's minimum supported Rust version is currently 1.45, and the precedent is that it requires a breaking change to update.

It is mentioned in the release blog post: https://tokio.rs/blog/2020-12-tokio-1-0
Would be good to add it to the readme too.

It is mentioned in the release blog post: https://tokio.rs/blog/2020-12-tokio-1-0
Would be good to add it to the readme too.

If someone can give this a +1 than I'm merging it. Tokio can start using Mio v0.8 after Feb 26th in compliance with the 6 month policy.

If someone can give this a +1 than I'm merging it. Tokio can start using Mio v0.8 after Feb 26th in compliance with the 6 month policy.


chore(npm): sync README.md from npm-package-template

badges

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Merging #99 into master will not affect coverage as of 257e1fb

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======================================
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  Partial          0       0
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Review entire Coverage Diff as of 257e1fb

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NewNote() will lose color and return to monochrome

When using NewNote() with .WithAccessible(true) it will cause color loss, leaving only black and white. Is there any way to fix this ?
Thks for reply

cannot reproduce it here... could you provide the minimum possible code to reproduce it?
thank you!


Prettify JSON to make more readable

The data in this repo comes from a database (I enter any changes manually and re-publish). I'll merge this pull request, but then immediately republish it in JSON_PRETTY_PRINT format from hereon in. Thanks for the suggestion!


Handle edge case where Arrays and Objects are merged

Handle edge case where the library attempts to merge an array and an object.
merge({foo: {bar: true}}, {foo: ["bar"]})

This fix simply replaces the object with the array that is now at the objects location.

@macdja38 hey! I'd love to make you a collaborator so you can merge this and other PRs and roll a new release! Please signup over at https://github.com/KyleAMathews/deepmerge/issues/25 and let's make this happen!

@macdja38 could you add a new failing test for this issue?  Or make a comment with the output you would expect from your example code above?

@TehShrike I expect to get {foo: ["bar"]} out of the above merge as from what I understand to remain constant with the library's current behavior when the objects are not merge-able the 2nd argument should be applied over top of the first. I'll look into adding a failing test in the morning.

That makes sense to me.
As an aside, it would probably be better to use [Array.isArray](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/isArray) instead of instanceof (isArray is already being used elsewhere in the module).

@TehShrike I thought about that but Array.isArray can fail if the value is null or undefined though I suppose we check that before the code gets to that point.

Array.isArray(null) and Array.isArray(undefined) both return false, so we should be good.

@TehShrike think you could just double check the test before one of us hits that big green merge button?

The test looks good to me.
Looking at it again, I wonder if we could make the "the target isn't an array" case even simpler - if the target isn't an array and we know we're just going to overwrite it, we don't need to iterate over it at all, we can just make a shallow copy and call it good, something like
        if (Array.isArray(target)) {
            dst = dst.concat(target);
            src.forEach(function(e, i) {
                if (typeof dst[i] === 'undefined') {
                    dst[i] = e;
                } else if (typeof e === 'object') {
                    dst[i] = deepmerge(target[i], e);
                } else {
                    if (target.indexOf(e) === -1) {
                        dst.push(e);
                    }
                }
            });
        } else {
            dst = dst.concat(src)
        }

buuuut, I'd kind of like to wait to merge this (or even think about changing the implementation to something like what I pasted above) until after https://github.com/KyleAMathews/deepmerge/pull/37 is merged, as one of the things that happens in that pull request is refactoring the default array merging behavior out into it's own function.
After #37 is merged, I think the implementation could look something like this:
    if (array) {
       return Array.isArray(target) ? arrayMerge(target, source, optionsArgument) : source.slice()
    } /* else ... */

I had another thought - what if the actual expected behavior was that merging { key1: { thingy: 'value' } } and { key1: [ 'array value' ] } would result in { key1: { thingy: 'value', '0': 'array value' } }?
That's not what the current behavior is though, so maybe it doesn't matter much.

(oh, and feel free to give #37 a review to help along its merging!)

I think we should probably deploy this as soon as possible attempting the test on a privious version of this library causes it to throw an exception.
    not ok 3 TypeError: target.indexOf is not a function
      ---
        type:    TypeError
        message: target.indexOf is not a function
        code:    ~
        errno:   ~
        stack:
          - |
            C:\Users\macdja38\deepmerge\index.js:31:31
          - Array.forEach (native)
          - |
            deepmerge (C:\Users\macdja38\deepmerge\index.js:26:13)
          - |
            C:\Users\macdja38\deepmerge\index.js:48:32
          - Array.forEach (native)
          - |
            deepmerge (C:\Users\macdja38\deepmerge\index.js:41:26)
          - |
            C:\Users\macdja38\deepmerge\index.js:30:26
          - Array.forEach (native)
          - |
            deepmerge (C:\Users\macdja38\deepmerge\index.js:26:13)
          - |
            Test.<anonymous> (C:\Users\macdja38\deepmerge\test\merge.js:28:17)
        thrown:  true
      ...

It's an awkward bug, but it's not a regression and it's been around for quite a while.  I'm for getting it fixed, but I don't think we should feel rushed.  Better to fix it right once than fix it one way now, have more discussions later, and decide to fix it a different way.


C lportfolio

Hi @charleslamb212 ! It looks like you are making changes to the current example repository. You'll need to create one on your own account and publish from there. Thanks for trying out the templates!

I am so sorry for the mistake! Thanks for reaching out.
On Mon, Mar 6, 2023 at 11:03 AM Alfredo Deza @.***>
wrote:

Closed #34
https://github.com/education/codespaces-project-template-js/pull/34.
—
Reply to this email directly, view it on GitHub
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or unsubscribe
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ARROW-15215: [C++] Consolidate kernel data-copy utilities between replace_with_mask, case_when, coalesce, choose, fill_null_forward, fill_null_backward

Consolidate kernel data-copy utilities between replace_with_mask, case_when, coalesce, choose, fill_null_forward, fill_null_backward in one place

Should this be marked as draft for now?

Should this be marked as draft for now?

Yes, for now

@ursabot please benchmark lang=C++


*: detect leaky goroutines, fix leaks

gexpect.Interact leaks. This adds ReadLine method to wait for the leaky
goroutine to accept an EOF.
Fixes coreos#4258.
Reference: https://github.com/coreos/etcd/pull/4261#issuecomment-174198945.

@heyitsanthony Please review. Later we can have better way to do this rather than copy and paste main_test.go script. Thanks,

@heyitsanthony Just removed those two lines. PTAL.
e2e test passed:
https://semaphoreci.com/coreos/etcd/branches/pull-request-4261/builds/3
Thanks!

Is this actually fixed by removing Interact? It still needs Interact so the child doesn't stall forever on stdout/stderr. Cf. https://gist.github.com/heyitsanthony/ed5e09a665680e40be11

@heyitsanthony I see. I will fix it. Thanks!

@heyitsanthony Please review again.

I attempted to replicate Interact method synchronizing the stdin stream.
I separated leaky goroutine checking functions into a separate package.

Thanks for feedback!

Not 100% sure here, but I think all this needs is a proc.Wait() in etcdProcessCluster.Close(). Those goroutines shouldn't leak when the process is gone since the pipe closes and the copy hits EOF.

@heyitsanthony This still leaks with p.proc.Cmd.Wait():
func (epc *etcdProcessCluster) Close() (err error) {
	for _, p := range epc.procs {
		if p == nil {
			continue
		}
		os.RemoveAll(p.cfg.dataDirPath)
		p.proc.Cmd.Wait()
		if curErr := p.proc.Close(); curErr != nil {
			if err != nil {
				err = fmt.Errorf("%v; %v", err, curErr)
			} else {
				err = curErr
			}
		}
		<-p.donec
	}
	return err
}

Too many goroutines running after all test(s).
1 instances of:
syscall.Syscall(0x0, 0x3, 0xc820128000, 0x8000, 0x2800000000, 0x19, 0x1)
	/usr/local/go/src/syscall/asm_linux_amd64.s:18 +0x5
syscall.read(0x3, 0xc820128000, 0x8000, 0x8000, 0x7f5bf51abc38, 0x0, 0x0)
	/usr/local/go/src/syscall/zsyscall_linux_amd64.go:783 +0x5f
syscall.Read(0x3, 0xc820128000, 0x8000, 0x8000, 0xc820128000, 0x0, 0x0)
	/usr/local/go/src/syscall/syscall_unix.go:160 +0x4d
os.(*File).read(0xc820030040, 0xc820128000, 0x8000, 0x8000, 0x717760, 0x0, 0x0)
	/usr/local/go/src/os/file_unix.go:211 +0x53
os.(*File).Read(0xc820030040, 0xc820128000, 0x8000, 0x8000, 0x8000, 0x0, 0x0)
	/usr/local/go/src/os/file.go:95 +0x8a
io.copyBuffer(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030040, 0xc820128000, 0x8000, 0x8000, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:381 +0x247
io.Copy(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030040, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:351 +0x64
created by github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect.(*ExpectSubprocess).Interact
	/home/gyuho/go/src/github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect/gexpect.go:353 +0x145
1 instances of:
syscall.Syscall(0x0, 0x4, 0xc820164000, 0x8000, 0x2800000000, 0x0, 0x40db64)
	/usr/local/go/src/syscall/asm_linux_amd64.s:18 +0x5
syscall.read(0x4, 0xc820164000, 0x8000, 0x8000, 0x0, 0x0, 0x0)
	/usr/local/go/src/syscall/zsyscall_linux_amd64.go:783 +0x5f
syscall.Read(0x4, 0xc820164000, 0x8000, 0x8000, 0xc820164000, 0x0, 0x0)
	/usr/local/go/src/syscall/syscall_unix.go:160 +0x4d
os.(*File).read(0xc820030058, 0xc820164000, 0x8000, 0x8000, 0x717760, 0x0, 0x0)
	/usr/local/go/src/os/file_unix.go:211 +0x53
os.(*File).Read(0xc820030058, 0xc820164000, 0x8000, 0x8000, 0x8000, 0x0, 0x0)
	/usr/local/go/src/os/file.go:95 +0x8a
io.copyBuffer(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030058, 0xc820164000, 0x8000, 0x8000, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:381 +0x247
io.Copy(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030058, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:351 +0x64
created by github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect.(*ExpectSubprocess).Interact
	/home/gyuho/go/src/github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect/gexpect.go:353 +0x145
1 instances of:
syscall.Syscall(0x0, 0x5, 0xc820154000, 0x8000, 0x4de3b8, 0x74a600, 0x0)
	/usr/local/go/src/syscall/asm_linux_amd64.s:18 +0x5
syscall.read(0x5, 0xc820154000, 0x8000, 0x8000, 0x40cd55, 0x0, 0x0)
	/usr/local/go/src/syscall/zsyscall_linux_amd64.go:783 +0x5f
syscall.Read(0x5, 0xc820154000, 0x8000, 0x8000, 0xc820148608, 0x0, 0x0)
	/usr/local/go/src/syscall/syscall_unix.go:160 +0x4d
os.(*File).read(0xc820030070, 0xc820154000, 0x8000, 0x8000, 0x88, 0x0, 0x0)
	/usr/local/go/src/os/file_unix.go:211 +0x53
os.(*File).Read(0xc820030070, 0xc820154000, 0x8000, 0x8000, 0x88, 0x0, 0x0)
	/usr/local/go/src/os/file.go:95 +0x8a
io.copyBuffer(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030070, 0xc820154000, 0x8000, 0x8000, 0x88, 0x0, 0x0)
	/usr/local/go/src/io/io.go:381 +0x247
io.Copy(0x7f5bf51ab750, 0xc820030010, 0x7f5bf51ab518, 0xc820030070, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:351 +0x64
created by github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect.(*ExpectSubprocess).Interact
	/home/gyuho/go/src/github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect/gexpect.go:353 +0x145
exit status 1
FAIL	github.com/coreos/etcd/e2e	2.726s

The Wait() has to follow the Close(). proc.Close() kills the process via kill and the Wait() reaps the process. I'll play around with it some tonight; I'm not sure whether the deferred wait from Interact will interfere in a bad way.

@heyitsanthony Think still fails.
=== RUN   TestBasicOpsClientTLS
--- PASS: TestBasicOpsClientTLS (3.51s)
PASS
Too many goroutines running after all test(s).
1 instances of:
syscall.Syscall(0x0, 0x5, 0xc82014e000, 0x8000, 0x2820010940, 0x0, 0x0)
	/usr/local/go/src/syscall/asm_linux_amd64.s:18 +0x5
syscall.read(0x5, 0xc82014e000, 0x8000, 0x8000, 0x0, 0x0, 0x0)
	/usr/local/go/src/syscall/zsyscall_linux_amd64.go:783 +0x5f
syscall.Read(0x5, 0xc82014e000, 0x8000, 0x8000, 0xc82014e000, 0x0, 0x0)
	/usr/local/go/src/syscall/syscall_unix.go:160 +0x4d
os.(*File).read(0xc820030070, 0xc82014e000, 0x8000, 0x8000, 0x717760, 0x0, 0x0)
	/usr/local/go/src/os/file_unix.go:211 +0x53
os.(*File).Read(0xc820030070, 0xc82014e000, 0x8000, 0x8000, 0x8000, 0x0, 0x0)
	/usr/local/go/src/os/file.go:95 +0x8a
io.copyBuffer(0x7fa8ca5b4750, 0xc820030010, 0x7fa8ca5b4518, 0xc820030070, 0xc82014e000, 0x8000, 0x8000, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:381 +0x247
io.Copy(0x7fa8ca5b4750, 0xc820030010, 0x7fa8ca5b4518, 0xc820030070, 0x0, 0x0, 0x0)
	/usr/local/go/src/io/io.go:351 +0x64
created by github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect.(*ExpectSubprocess).Interact
	/home/gyuho/go/src/github.com/coreos/etcd/Godeps/_workspace/src/github.com/coreos/gexpect/gexpect.go:353 +0x145
exit status 1
FAIL	github.com/coreos/etcd/e2e	3.510s

I will play with it more too. Thanks for helping me on this. It will be great for me to learn!

This reliably works for me, let me know if it works for you:
_, err := etcdp.proc.ExpectRegex(readyStr)
readyC <- err
etcdp.proc.ReadLine()
etcdp.proc.Interact()
etcdp.proc.ReadLine()
close(etcdp.donec)

A somewhat sloppy explanation: the fds close after the process gets reaped since the pty evaporates once the slave dies, not before, and so Wait does not gate the reader goroutine. However, since the file is a pipe, reads are serialized; if the goroutine is already reading, another read will wait for the goroutine read to complete (I'm not sure if FIFO ordering among several concurrent reads on one pipe is POSIX or simply a linux quirk). Hence a ReadLine after Interact will wait for the leaky goroutine to accept an EOF.

@heyitsanthony Thanks a lot. Just pushed the changes as you suggest and I don't see any leaky goroutines any more. I also added comments based on your explanation. Thanks for the great explanation.
PTAL.

@xiang90 Just addressed. Thanks for feedback. PTAL.

LGTM except https://github.com/coreos/etcd/pull/4261#discussion_r50626423.
Defer to @heyitsanthony

lgtm

Thanks a lot team!


Pulseq plot

Could you please fix the following line to allow the plotting of the sequence (line 118, sequence.py)
#t0 += core.calc_duration.calc_duration(block) #changed this line to fix plot issues
Suggested change:
#t0 += calc_duration(block) #changed this line to fix plot issues

Thanks, fixed!


[Feedback requested] Update slider example in SDC Catalog app - What do you think?

Problem:
The current slider is intended for numerical entry and this is not a good example of when to use the slider. For numerical entry it is more usable to use a text field.
Proposed solution:

Update the example in SDC catalog app of when to use the slider with
Example 1: "How are you feeling today?" Great, fine, neutral, okay, bad. (slider with only 1-5 ticks)
Example 2: In a scale from 1-5, how happy are you with X? (1 - very unhappy, 2-unhappy, 3-neutral, 4-happy, 5-very happy)
Update corresponding documentation in the design guidelines

Feedback requested
Do you have an example of when you'd use a slider in your deployment? Please share it with us, would love to better understand when and why you'd want to use a slider.
Research required:

Can we customize the slider so that text appears instead of number values?

Design mocks:
(work in progress)

No further research planned. Closing issue

i think we do any here it'll be guided by extensions in the sdc ig.


Potential preview issues

We recently did a Bump @nuxtjs/prismic from 1.2.4 to 1.2.6 on our project and noticed Prismic previews stopped working. No other code on the project changed.
We reverted this bump and sure enough the previews started working again, any ideas as to what might be happening here?
Some additional details:

We're previewing on localhost
All previews broke
Followed the troubleshooting guide here: https://user-guides.prismic.io/en/articles/3403530-troubleshooting-previews

Hey @MariuszDabrowski, thank you so much for letting us know!
Can you share your version of Nuxt & Node also? Thanks!

"nuxt": "^2.15.3"
"node": "14.15.1"

Thanks! I'll investigate that next week, in the meantime for your intention here are the two change we introduced since 1.2.4:

https://github.com/nuxt-community/prismic-module/commit/5e443508e1c69540f63a512675ce5a35ab428df8#diff-0702cfb7026ef4a87ca46003aa83c63e6a33be6a91edf840e50b77f0b6c2e73d
https://github.com/nuxt-community/prismic-module/commit/6f60b21d596306585391ffde7a662b1a87fdbf11#diff-0702cfb7026ef4a87ca46003aa83c63e6a33be6a91edf840e50b77f0b6c2e73d

Hey,
I took some time today to reproduce the issue on a simple project using<EMAIL_ADDRESS>with<EMAIL_ADDRESS>and<EMAIL_ADDRESS> Unfortunately, I didn't manage to reproduce the issue on both a local server (nuxt) and a production build (nuxt generate over Netlify).
I'll close this issue for now. Please reopen it if you're still experiencing it, I'd be happy to dig into it further if you can share your complete package.json and nuxt.config.js file along your Prismic repository name. A minimal reproduction would also greatly help.
If anyone's experiencing the issue Marius raised here please also notify me so I can prioritize that one 🙂


Translation: redis-dev-services

Hello everyone,
I would like to inform you that I am working on the translation of the file:
redis-dev-services

Hello @dellamas ! I just finished the translation and stumbled upon your isse. Can I pull mine?

Hi @vandrep , yes you can translate. I'll work on another one, you can complete this one without any problems. Thank you very much for your collaboration!