[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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