I am really stuck with something. I have an nf-core module that was working well, then suddenly, I think I updated the bioconda package that it uses, it just hangs for a long time when I try to test with --profile conda (it works fine with --profile singularity).
I am doing:
nf-test test --tag coptr/index --profile conda --update-snapshot
and I get:
🚀 nf-test 0.9.2
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr
Load .nf-test/plugins/nft-bam/0.3.0/nft-bam-0.3.0.jar
Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar
Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
Warning: every snapshot that fails during this test run is re-record.
Test Process COPTR_INDEX
Test [fed7e189] 'coptr index with single fastq' Assertion failed:
assert process.success
| |
| false
COPTR_INDEX
FAILED (7203.831s)
Assertion failed:
1 of 2 assertions failed
Nextflow stdout:
ERROR ~ Error executing process > 'COPTR_INDEX'
Caused by:
Failed to create Conda environment
command: conda env create --prefix /gpfs1/home/r/b/rbarrant/projects/nfcorePipelines/modules/.nf-test/tests/fed7e18906b7e8b55696337c0af814bc/work/conda/environment-b8765177d9aaff5e205b905733f14221 --file /gpfs1/home/r/b/rbarrant/projects/nfcorePipelines/modules/modules/nf-core/coptr/index/tests/../environment.yml
status : 143
message:
Retrieving notices: ...working... done
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
-- Check '/gpfs1/home/r/b/rbarrant/projects/nfcorePipelines/modules/.nf-test/tests/fed7e18906b7e8b55696337c0af814bc/meta/nextflow.log' file for details
Nextflow stderr:
Exception in thread "Thread-2" groovy.lang.GroovyRuntimeException: exception while reading process stream
at org.codehaus.groovy.runtime.ProcessGroovyMethods$TextDumper.run(ProcessGroovyMethods.java:502)
at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.io.IOException: Stream closed
at java.base/java.io.BufferedInputStream.getBufIfOpen(BufferedInputStream.java:168)
at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:334)
at java.base/sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:281)
at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:324)
at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:189)
at java.base/java.io.InputStreamReader.read(InputStreamReader.java:177)
at java.base/java.io.BufferedReader.fill(BufferedReader.java:162)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:329)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:396)
at org.codehaus.groovy.runtime.ProcessGroovyMethods$TextDumper.run(ProcessGroovyMethods.java:495)
... 1 more