[Debian-med-packaging] Bug#860876: reapr: FTBFS: Error in system call: R CMD BATCH 00.Sample/gc_vs_cov.R 00.Sample/gc_vs_cov.Rout
Chris Lamb
lamby at debian.org
Fri Apr 21 08:04:02 UTC 2017
Source: reapr
Version: 1.0.18+dfsg-3
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bugs at lists.alioth.debian.org
Dear Maintainer,
reapr fails to build from source in unstable/amd64:
[…]
foo 810152 A M +
foo 811506 G R +
foo 813494 A M +
foo 814035 G T -
foo 814476 A W +
foo 819399 T K +
foo 820171 T W +
foo 820445 G C -
foo 822178 C G -
foo 822504 C T -
foo 823378 C M +
foo 823591 CG - -
foo 824229 C M +
foo 824579 C T -
foo 824858 C M +
foo 826101 T K +
foo 827593 C G -
foo 827794 T Y +
foo 828228 A M +
foo 828367 T K +
foo 828788 C M +
foo 829002 C Y +
foo 830345 C M +
foo 831018 C A -
foo 831459 T K +
foo 832413 A T -
foo 832782 T Y +
foo 832908 T Y +
foo 833130 T - -
foo 833142 G S +
foo 833241 G A -
foo 836727 A T -
foo 836829 G S +
foo 838452 T G -
foo 838543 A T -
foo 838605 C M +
foo 838954 G C -
foo 841829 G K +
foo 842324 - TC +
foo 842996 - C +
foo 844390 C A -
foo 844793 A C -
foo 844925 C A -
foo 845082 G C -
foo 846202 G R +
foo 846707 A G -
foo 848713 G A -
foo 849372 C S +
foo 849742 G A -
foo 850499 C - -
foo 850927 GT - -
foo 851084 - G +
foo 852247 A R +
foo 852972 C A -
foo 854808 T W +
foo 855956 G K +
foo 856225 G A -
foo 856582 T K +
foo 857351 C M +
foo 857504 AC - -
foo 858324 A T -
foo 858858 T C -
foo 859488 T Y +
foo 862441 T Y +
foo 863827 C Y +
foo 864165 C A -
foo 865997 C M +
foo 866370 G S +
foo 867653 G S +
foo 867722 C Y +
foo 868696 C M +
foo 869005 T W +
foo 869791 T Y +
foo 875339 C Y +
foo 875347 C M +
foo 875584 T G -
foo 876780 C T -
foo 878368 A C -
foo 878916 - CAG +
foo 879005 A R +
foo 880112 G T -
foo 881021 - T -
foo 881175 T W +
foo 882168 - GGG +
foo 882223 - G -
foo 883033 TG - -
foo 883381 C G -
foo 884378 C - -
foo 885075 A M +
foo 885190 A W +
foo 885568 A W +
foo 885827 T Y +
foo 887610 TG - -
foo 889139 G R +
foo 890978 T - -
foo 891500 C Y +
foo 892257 G C -
foo 892642 G R +
foo 892644 T W +
foo 892757 C A -
foo 893222 T - -
foo 893348 T W +
foo 894161 - C -
foo 894447 A G -
foo 894614 A W +
foo 897817 T W +
foo 899408 C S +
foo 902450 A T -
foo 902970 AT - -
foo 905836 G K +
foo 906524 GA - -
foo 907484 A W +
foo 907537 C M +
foo 908515 G R +
foo 908642 C T -
foo 911145 T C -
foo 912220 T Y +
foo 912682 C Y +
foo 914260 C S +
foo 914757 T Y +
foo 916413 G C -
foo 916783 T G -
foo 917033 G C -
foo 917218 A - -
foo 918225 G - -
foo 918459 A - -
foo 918732 A M +
foo 919640 TC - -
foo 920824 T W +
foo 920836 G C -
foo 924560 G R +
foo 924659 GA - -
foo 925868 T A -
foo 928254 T G -
foo 928369 - A -
foo 928641 - AG +
foo 929857 C M +
foo 930211 T W +
foo 930935 C T -
foo 931986 A M +
foo 932852 G T -
foo 933965 T A -
foo 935564 A W +
foo 936034 T Y +
foo 936221 AC - -
foo 936670 C S +
foo 936704 T A -
foo 936786 T W +
foo 939218 C S +
foo 939312 A W +
foo 939467 A W +
foo 939934 C S +
foo 941603 C Y +
foo 942910 A W +
foo 944654 T Y +
foo 945301 A C -
foo 945770 C T -
foo 946078 G S +
foo 948833 G K +
foo 948999 A W +
foo 949193 A R +
foo 950276 C M +
foo 950414 A W +
foo 951285 G C -
foo 953158 G R +
foo 953287 A W +
foo 954150 C G -
foo 954258 G - -
foo 955396 CC - -
foo 956490 - AC +
foo 958129 A R +
foo 959027 T A -
foo 959964 A W +
foo 962042 A G -
foo 962742 C G -
foo 963306 T W +
foo 963422 G K +
foo 964082 G S +
foo 965561 C S +
foo 966531 T K +
foo 967324 T W +
foo 968419 - C -
foo 969054 G - -
foo 969158 G S +
foo 972658 C M +
foo 974266 T W +
foo 974629 G K +
foo 975034 A R +
foo 975636 T W +
foo 977078 - A -
foo 978321 G T -
foo 978595 C G -
foo 979090 C M +
foo 983855 TA - -
foo 985725 T A -
foo 988497 C Y +
foo 990171 C M +
foo 990804 - CA -
foo 990941 T W +
foo 991797 A W +
foo 992469 A M +
foo 994610 C Y +
foo 998107 - T +
foo 999725 G R +
[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
`. `'` lamby at debian.org / chris-lamb.co.uk
`-
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