Bug#1114262: marked as done (pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2)

Debian Bug Tracking System Fri, 05 Dec 2025 06:43:34 -0800

Your message dated Fri, 05 Dec 2025 14:40:18 +0000
with message-id <[email protected]>
and subject line Bug#1114262: fixed in pigx-rnaseq 0.1.1-2
has caused the Debian Bug report #1114262,
regarding pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary 
subprocess returned exit status 2
to be marked as done.


This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)


-- 
1114262: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114262
Debian Bug Tracking System
Contact [email protected] with problems

--- Begin Message ---

Package: src:pigx-rnaseq
Version: 0.1.1-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:pigx-rnaseq, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf pigx-common
rm -f config.log test.sh
rm -rf tests/output
rm -f Makefile.in aclocal.m4 build-aux/install-sh build-aux/missing 
build-aux/test-driver
rm -f scripts/jquery.min.js
rm -f conftest.tar confdefs.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
        rm -f debian/debhelper-build-stamp

[... snipped ...]

    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf; Input 
files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
    wildcards: sample=UHR_Rep2
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1
[Fri Sep  5 00:06:02 2025]
Finished job 12.
28 of 49 steps (57%) done
Select jobs to execute...

[Fri Sep  5 00:06:02 2025]
rule salmon_quant:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz
    output: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log
    jobid: 10
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf; Input 
files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz
    wildcards: sample=UHR_Rep1
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1
[Fri Sep  5 00:06:04 2025]
Finished job 10.
29 of 49 steps (59%) done
Select jobs to execute...

[Fri Sep  5 00:06:04 2025]
rule count_reads:
    input: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
    output: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv
    log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep2.count_reads.log
    jobid: 34
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; 
Input files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
    wildcards: sample=UHR_Rep2
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts//count_reads.R UHR_Rep2 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam
 /<<PKGBUILDDIR>>/tests/sample_data/sample.gtf         False Union True 
unspecific         exon gene_id 2000000 >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1
[Fri Sep  5 00:06:06 2025]
Finished job 28.
30 of 49 steps (61%) done
Select jobs to execute...

[Fri Sep  5 00:06:06 2025]
rule salmon_quant:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz
    output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log
    jobid: 3
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf; Input files 
updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
    wildcards: sample=HBR_Rep1
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

[Fri Sep  5 00:06:06 2025]
Finished job 32.
31 of 49 steps (63%) done
Select jobs to execute...

[Fri Sep  5 00:06:06 2025]
rule salmon_quant:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz
    output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log
    jobid: 6
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf; Input files 
updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
    wildcards: sample=HBR_Rep2
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

[Fri Sep  5 00:06:07 2025]
Finished job 30.
32 of 49 steps (65%) done
Select jobs to execute...

[Fri Sep  5 00:06:07 2025]
rule salmon_quant:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz
    output: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log
    jobid: 8
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf; Input 
files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
    wildcards: sample=HBR_Rep3
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

[Fri Sep  5 00:06:07 2025]
Finished job 26.
33 of 49 steps (67%) done
Select jobs to execute...

[Fri Sep  5 00:06:07 2025]
rule coverage_megadepth:
    input: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
    output: 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw
    log: 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log
    jobid: 43
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; 
Input files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
    wildcards: sample=UHR_Rep2
    resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2


    /usr/bin/megadepth  
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam
 --threads 2 --bigwig --prefix 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1
    
Building DAG of jobs...
[Fri Sep  5 00:06:07 2025]
Finished job 43.
34 of 49 steps (69%) done
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...

[Fri Sep  5 00:06:07 2025]
rule salmon_quant:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin, 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz
    output: /<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log
    jobid: 14
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files 
updated by another job: 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, 
/<<PKGBUILDDIR>>/tests/output/salmon_index/pos.bin
    wildcards: sample=UHR_Rep3
    resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723

[Fri Sep  5 00:06:07 2025]
Finished job 36.
35 of 49 steps (71%) done
Select jobs to execute...

[Fri Sep  5 00:06:07 2025]
rule coverage_megadepth:
    input: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai
    output: 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw
    log: 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log
    jobid: 39
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; 
Input files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam,
 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai
    wildcards: sample=HBR_Rep1
    resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2


    /usr/bin/megadepth  
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam
 --threads 2 --bigwig --prefix 
/<<PKGBUILDDIR>>/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1
    
[Fri Sep  5 00:06:07 2025]
Finished job 39.
36 of 49 steps (73%) done
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-r /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-r /<<PKGBUILDDIR>>/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=6000, mem_mib=5723
Select jobs to execute...
/usr/bin/salmon quant -i /<<PKGBUILDDIR>>/tests/output/salmon_index -l A -p 8 
-1 /<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 
/<<PKGBUILDDIR>>/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g 
/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1
[Fri Sep  5 00:06:08 2025]
Finished job 3.
37 of 49 steps (76%) done
[Fri Sep  5 00:06:08 2025]
Finished job 6.
38 of 49 steps (78%) done
[Fri Sep  5 00:06:08 2025]
Finished job 14.
39 of 49 steps (80%) done
[Fri Sep  5 00:06:08 2025]
Finished job 8.
40 of 49 steps (82%) done
Select jobs to execute...

[Fri Sep  5 00:06:08 2025]
rule counts_from_SALMON:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, 
/<<PKGBUILDDIR>>/tests/output/colData.tsv
    output: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv,
 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv,
 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv,
 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv
    log: /<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_import_counts.log
    jobid: 23
    reason: Missing output files: /<<PKGBUILDDIR>>/tests/out 
[too-long-redacted] _output/UHR_Rep1/quant.genes.sf
    resources: tmpdir=/tmp, mem_mb=200, mem_mib=191

/usr/bin/Rscript --vanilla 
/<<PKGBUILDDIR>>/scripts//counts_matrix_from_SALMON.R 
/<<PKGBUILDDIR>>/tests/output/salmon_output 
/<<PKGBUILDDIR>>/tests/output/feature_counts 
/<<PKGBUILDDIR>>/tests/output/colData.tsv >> 
/<<PKGBUILDDIR>>/tests/output/logs/salmon/salmon_import_counts.log 2>&1

[Fri Sep  5 00:06:08 2025]
rule multiqc:
    input: /<<PKGBUILDDIR>>/tests/output/salmon_output/HBR_R 
[too-long-redacted] 3_Aligned.sortedByCoord.out.bam
    output: /<<PKGBUILDDIR>>/tests/output/multiqc/multiqc_report.html
    log: /<<PKGBUILDDIR>>/tests/output/logs/multiqc.hisat2.log
    jobid: 2
    reason: Missing output files: /<<PKGBUILDDIR>>/tests/out 
[too-long-redacted] salmon_output/UHR_Rep1/quant.sf
    resources: tmpdir=/tmp, mem_mb=500, mem_mib=477

/usr/bin/multiqc  -f -o /<<PKGBUILDDIR>>/tests/output/multiqc 
/<<PKGBUILDDIR>>/tests/output >> 
/<<PKGBUILDDIR>>/tests/output/logs/multiqc.hisat2.log 2>&1
[Fri Sep  5 00:06:10 2025]
Finished job 2.
41 of 49 steps (84%) done
[Fri Sep  5 00:06:13 2025]
Finished job 34.
42 of 49 steps (86%) done
Select jobs to execute...

[Fri Sep  5 00:06:13 2025]
rule collate_read_counts:
    input: /<<PKGBUILDDIR>>/tests/output/colData.tsv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv
    output: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
    log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/collate_read_counts.log
    jobid: 25
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; 
Input files updated by another job: 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/colData.tsv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv
    resources: tmpdir=/tmp, mem_mb=200, mem_mib=191

/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/collate_read_counts.R 
/<<PKGBUILDDIR>>/tests/output/mapped_reads/hisat2 
/<<PKGBUILDDIR>>/tests/output/colData.tsv 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/collate_read_counts.log 2>&1
[Fri Sep  5 00:06:14 2025]
Finished job 25.
43 of 49 steps (88%) done
Select jobs to execute...

[Fri Sep  5 00:06:14 2025]
rule report1:
    input: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, 
/<<PKGBUILDDIR>>/tests/output/colData.tsv
    output: 
/<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html
    log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log
    jobid: 45
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html; Input 
files updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv, 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
    wildcards: analysis=analysis1
    resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815

/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/runDeseqReport.R 
--logo=/<<PKGBUILDDIR>>/images/Logo_PiGx.png --prefix='analysis1' 
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd 
--countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
 --colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv 
--gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf 
--caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates=''  
--workdir=/<<PKGBUILDDIR>>/tests/output/report/hisat2 --organism='' 
--description='This analysis is part of the pigx-rnaseq build-time tests.' 
--selfContained='True' >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log 2>&1

[Fri Sep  5 00:06:14 2025]
rule norm_counts_deseq:
    input: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, 
/<<PKGBUILDDIR>>/tests/output/colData.tsv
    output: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt,
 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv
    log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/norm_counts_deseq.log
    jobid: 38
    reason: Missing output files: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt,
 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv;
 Input files updated by another job: /<<PKGBUILDDIR>>/tests/output/colData.tsv, 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
    resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954

/usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/norm_counts_deseq.R 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv 
/<<PKGBUILDDIR>>/tests/output/colData.tsv 
/<<PKGBUILDDIR>>/tests/output/feature_counts/normalized/hisat2 >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1
[Fri Sep  5 00:06:14 2025]
Error in rule report1:
    jobid: 45
    input: 
/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, 
/<<PKGBUILDDIR>>/tests/output/colData.tsv
    output: 
/<<PKGBUILDDIR>>/tests/output/report/hisat2/analysis1.deseq.report.html
    log: /<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log (check 
log file(s) for error details)
    shell:
        /usr/bin/Rscript --vanilla /<<PKGBUILDDIR>>/scripts/runDeseqReport.R 
--logo=/<<PKGBUILDDIR>>/images/Logo_PiGx.png --prefix='analysis1' 
--reportFile=/<<PKGBUILDDIR>>/scripts/deseqReport.Rmd 
--countDataFile=/<<PKGBUILDDIR>>/tests/output/feature_counts/raw_counts/hisat2/counts.tsv
 --colDataFile=/<<PKGBUILDDIR>>/tests/output/colData.tsv 
--gtfFile=/<<PKGBUILDDIR>>/tests/sample_data/sample.gtf 
--caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates=''  
--workdir=/<<PKGBUILDDIR>>/tests/output/report/hisat2 --organism='' 
--description='This analysis is part of the pigx-rnaseq build-time tests.' 
--selfContained='True' >> 
/<<PKGBUILDDIR>>/tests/output/logs/hisat2/analysis1.report.log 2>&1
        (one of the commands exited with non-zero exit code; note that 
snakemake uses bash strict mode!)

[Fri Sep  5 00:06:15 2025]
Finished job 23.
44 of 49 steps (90%) done
[Fri Sep  5 00:06:19 2025]
Finished job 38.
45 of 49 steps (92%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-09-05T000521.751761.snakemake.log
ERROR: could not find report for SALMON at transcript level
make[1]: *** [debian/rules:40: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

--- End Message ---

--- Begin Message ---

Source: pigx-rnaseq
Source-Version: 0.1.1-2
Done: Andreas Tille <[email protected]>

We believe that the bug you reported is fixed in the latest version of
pigx-rnaseq, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated pigx-rnaseq package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Fri, 05 Dec 2025 14:16:48 +0100
Source: pigx-rnaseq
Architecture: source
Version: 0.1.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1114262
Changes:
 pigx-rnaseq (0.1.1-2) unstable; urgency=medium
 .
   * Team upload.
   * d/watch: version=5
   * Make sure snakemake does not pick wrong HOME
     Closes: #1114262
   * Standards-Version: 4.7.2 (routine-update)
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pigx-rnaseq_0.1.1-2.debian.tar.xz
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Files:
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 c7cd1de1c97871eda97f21fd1d87c208 15496 science optional 
pigx-rnaseq_0.1.1-2.debian.tar.xz
 ac633982c5bf83baceab6292c6d28fba 26642 science optional 
pigx-rnaseq_0.1.1-2_amd64.buildinfo

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--- End Message ---

Bug#1114262: marked as done (pigx-rnaseq: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2)

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