Source: reapr Version: 1.0.18+dfsg-3 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-b...@lists.alioth.debian.org
Dear Maintainer,
reapr fails to build from source in unstable/amd64:
[…]
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[REAPR smaltmap] Running: smalt index -k 13 -s 2
out.bam.tmp.5905.smaltmap.smalt_index foo1.fasta
# Command line: smalt index -k 13 -s 2 out.bam.tmp.5905.smaltmap.smalt_index
foo1.fasta
# Reading sequences ...
# Writing sequence set ...
# Setting up hash index with collisions ...
# word length = 13 bases, skip step = 2 bases ...
# number of bits for key = 18 with 0 perfect bits
# Counting keys ...
# Counting k-tuples ...
# Allocating k-tuple arrays ...
# Counting k-tuple occurrences ...
# Setting the k-tuple positions in index ...
# Hash table is set up.
# =-=-=-=-= Hash Index Stats =-=-=-=-=
# Hash index with collisions.
# Word length: 13 bases
# Skip step: 2 bases
# Number of hash keys: 262144
# Number of word positions: 499970
# Number of different words: 498076
# Maximum number of words per key: 11
# Number of keys without words: 39377
# =-=-= End of Hash Index Stats =-=-=
# Writing table to file ...
# smalt: Total elapsed wall clock time: 0 seconds
[REAPR smaltmap] Running: smalt sample -u 1000 -o
out.bam.tmp.5905.smaltmap.smalt_sample out.bam.tmp.5905.smaltmap.smalt_index
foofq.1.fastq foofq.2.fastq
# Command line: smalt sample -u 1000 -o
out.bam.tmp.5905.smaltmap.smalt_sample out.bam.tmp.5905.smaltmap.smalt_index
foofq.1.fastq foofq.2.fastq
# Opening read files ...
# Reading reference sequences ...
# Reading hash table ...
# =-=-=-=-= Hash Index Stats =-=-=-=-=
# Hash index with collisions.
# Word length: 13 bases
# Skip step: 2 bases
# Number of hash keys: 262144
# Number of word positions: 499970
# Number of different words: 498076
# Maximum number of words per key: 11
# Number of keys without words: 39377
# =-=-= End of Hash Index Stats =-=-=
# Check of read pairs ok ...
# Mate names match ...
# Sampling insert size distribution ...
# Processed 9999 read pairs.
# smalt: Time spent setting up hash index:0 seconds
# smalt: Time spent mapping reads:1 seconds
# smalt: Total elapsed wall clock time: 1 seconds
[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g
out.bam.tmp.5905.smaltmap.smalt_sample -f samsoft
out.bam.tmp.5905.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk
'$1!~/^#/' | samtools view -S -T foo1.fasta -b - >
out.bam.tmp.5905.smaltmap.raw.bam
# Command line: smalt map -r 0 -x -y 0.5 -g
out.bam.tmp.5905.smaltmap.smalt_sample -f samsoft
out.bam.tmp.5905.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
# Reading distribution of insert sizes from file ...
# Sampled histogram
# Smoothed histogram
# Opening read files ...
# Reading reference sequences ...
# Reading hash table ...
# =-=-=-=-= Hash Index Stats =-=-=-=-=
# Hash index with collisions.
# Word length: 13 bases
# Skip step: 2 bases
# Number of hash keys: 262144
# Number of word positions: 499970
# Number of different words: 498076
# Maximum number of words per key: 11
# Number of keys without words: 39377
# =-=-= End of Hash Index Stats =-=-=
# Processing query reads ...
# Processed 10000 read pairs.
# smalt: Time spent setting up hash index:0 seconds
# smalt: Time spent mapping reads:12 seconds
# smalt: Total elapsed wall clock time: 12 seconds
[REAPR smaltmap] Running: samtools sort out.bam.tmp.5905.smaltmap.raw.bam -O
bam -o out.bam.tmp.5905.smaltmap.raw.bam.sort.bam
[REAPR smaltmap] Running: samtools rmdup
out.bam.tmp.5905.smaltmap.raw.bam.sort.bam out.bam.tmp.5905.smaltmap.rmdup.bam
[bam_rmdup_core] processing reference foo...
[bam_rmdup_core] 1 / 10000 = 0.0001 in library ' '
[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t";
$1=$1; print}' > out.bam.tmp.5905.smaltmap.header
[REAPR smaltmap] Running: samtools view -H
out.bam.tmp.5905.smaltmap.rmdup.bam >> out.bam.tmp.5905.smaltmap.header
[REAPR smaltmap] Running: samtools reheader out.bam.tmp.5905.smaltmap.header
out.bam.tmp.5905.smaltmap.rmdup.bam > out.bam
[REAPR smaltmap] Running: samtools index out.bam
[REAPR smaltmap] Running: rm out.bam.tmp.5905.smaltmap.*
Running reapr version 1.0.18 pipeline:
reapr foo1.fasta out.bam result
[REAPR pipeline] Running facheck
[REAPR pipeline] Running preprocess
[REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases
[REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases
[REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases
[REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339
bases
[REAPR preprocess] Sampled 996854 bases for GC/coverage estimation
[REAPR preprocess] Error in system call:
R CMD BATCH 00.Sample/gc_vs_cov.R 00.Sample/gc_vs_cov.Rout
debian/rules:33: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '«BUILDDIR»'
debian/rules:4: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[…]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
reapr.1.0.18+dfsg-3.unstable.amd64.log.txt.gz
Description: Binary data
