-profile 'error while loading shared libraries: libiconv.so.2'

[jfy133]

Describe the bug
The pipeline when ran with -r dev flag and the conda profile crashes at output_documentation after adapter removal with the following error:

Command error: /projects1/users/fellows/nextflow/eager2/my_test/work/conda/nf-core-eager-2.0.1-21a7e9f4e1525113a0a8843adce834c8/lib/R/bin/exec/R: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory

To Reproduce
run the same command and data in #67 .

Expected behaviour
The conda environment to download the a working R environment.

Additional context
Please provide me with the following files:
nextflow.log.2.txt
eager2_Rsharedlibrary_erorr.zip

[apeltzer]

After adding a test case for conda, I can reproduce this, unfortunately:

https://travis-ci.org/nf-core/eager/jobs/449852941

I'll investigate whats the problem here...

[apeltzer]

Fixed in Release 2.0.2 :-)

[apeltzer]

alex@aragorn ~/tmp> nextflow run nf-core/eager -r 2.0.2 -profile test,conda --pairedEnd
N E X T F L O W  ~  version 18.10.1
Launching `nf-core/eager` [festering_shannon] - revision: c44b88110d [2.0.2]
=========================================
 nf-core/eager v2.0.0dev
=========================================
Pipeline Name  : nf-core/eager
Pipeline Version: 2.0.2
Run Name       : festering_shannon
Reads          : data/*{1,2}.fastq.gz
Fasta Ref      : https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta
Data Type      : Paired-End
Max Memory     : 6 GB
Max CPUs       : 2
Max Time       : 2d
Output dir     : ./results
Working dir    : /home/alex/tmp/work
Container Engine: null
Current home   : /home/alex
Current user   : alex
Current path   : /home/alex/tmp
Script dir     : /home/alex/.nextflow/assets/nf-core/eager
Config Profile : test,conda
=========================================
[warm up] executor > local
Creating Conda env: /home/alex/.nextflow/assets/nf-core/eager/environment.yml [cache /home/alex/tmp/work/conda/nf-core-eager-2.0.2-66fcfa315360652366a34058a3a2edf4]
[e0/591717] Submitted process > get_software_versions
[78/42b903] Submitted process > output_documentation
[e8/16c82e] Submitted process > makeBWAIndex (Mammoth_MT_Krause.fasta)
[88/2bfad7] Submitted process > makeSeqDict (Mammoth_MT_Krause.fasta)
[b4/ce21f5] Submitted process > makeFastaIndex (Mammoth_MT_Krause.fasta)
[e7/18f415] Submitted process > adapter_removal (JK2782_TGGCCGATCAACGA_L008)
[4e/a22d9a] Submitted process > fastqc (JK2782_TGGCCGATCAACGA_L008)
[16/6a0a8b] Submitted process > fastqc_after_clipping (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.combined.prefixed.fq)
[ff/938b49] Submitted process > bwa (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand)
[b3/31203b] Submitted process > samtools_idxstats (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted)
[bc/ec104f] Submitted process > samtools_filter (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted.bam)
[10/3be9c4] Submitted process > damageprofiler (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted)
[d8/034919] Submitted process > dedup (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted.bam.filtered)
[97/882e0c] Submitted process > qualimap (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted.bam.filtered)
[01/c98b51] Submitted process > preseq (JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.sorted.bam.filtered)
[5a/0186fd] Submitted process > multiqc
[nf-core/eager] Pipeline Complete

[jfy133]

I can confirm with v2.0.2 the bug is solved! Thanks for the speedy work!