Package: src:sra-sdk
Version: 3.2.1+dfsg-3
Severity: important
Tags: trixie sid ftbfs
User: debian...@lists.debian.org
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=cmake \
--with python3,javahelper,jh_maven_repo_helper
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf ngs/ngs-java/x86_64-linux-gnu
rm -rf ngs/ngs-bam/x86_64-linux-gnu
rm -f ngs/ngs-bam/Makefile.config
rm -f ngs/ngs-bam/Makefile.config.install.linux.x86_64.prl
rm -f ngs/ngs-bam/Makefile.config.linux.x86_64
[... snipped ...]
-rwxr-xr-x 1 buildd buildd 807504 Apr 16 11:11 abi-load.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 align-cache -> align-cache.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 align-cache.3 ->
align-cache.3.2.1
-rwxr-xr-x 1 buildd buildd 249680 Apr 16 11:11 align-cache.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 align-info -> align-info.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 align-info.3 ->
align-info.3.2.1
-rwxr-xr-x 1 buildd buildd 97320 Apr 16 11:11 align-info.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 bam-load -> bam-load.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 bam-load.3 -> bam-load.3.2.1
-rwxr-xr-x 1 buildd buildd 14124856 Apr 16 11:11 bam-load.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 cache-mgr -> cache-mgr.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 cache-mgr.3 -> cache-mgr.3.2.1
-rwxr-xr-x 1 buildd buildd 124728 Apr 16 11:11 cache-mgr.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 ccextract -> ccextract.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 ccextract.3 -> ccextract.3.2.1
-rwxr-xr-x 1 buildd buildd 272968 Apr 16 11:11 ccextract.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 cg-load -> cg-load.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 cg-load.3 -> cg-load.3.2.1
-rwxr-xr-x 1 buildd buildd 657864 Apr 16 11:11 cg-load.3.2.1
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 check-corrupt ->
check-corrupt.3
lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 check-corrupt.3 ->
check-corrupt.3.2.1
-rwxr-xr-x 1 buildd buildd 247200 Apr 16 11:11 check-corrupt.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 check-redact -> check-redact.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 check-redact.3 ->
check-redact.3.2.1
-rwxr-xr-x 1 buildd buildd 97880 Apr 16 11:11 check-redact.3.2.1
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 compute-coverage ->
compute-coverage.3
lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 compute-coverage-ngs ->
compute-coverage-ngs.3
lrwxrwxrwx 1 buildd buildd 26 Apr 16 11:15 compute-coverage-ngs.3 ->
compute-coverage-ngs.3.2.1
-rwxr-xr-x 1 buildd buildd 2224928 Apr 16 11:14 compute-coverage-ngs.3.2.1
lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 compute-coverage.3 ->
compute-coverage.3.2.1
-rwxr-xr-x 1 buildd buildd 131184 Apr 16 11:11 compute-coverage.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 copycat -> copycat.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 copycat.3 -> copycat.3.2.1
-rwxr-xr-x 1 buildd buildd 484072 Apr 16 11:11 copycat.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 crc32sum -> crc32sum.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 crc32sum.3 -> crc32sum.3.2.1
-rwxr-xr-x 1 buildd buildd 79432 Apr 16 11:11 crc32sum.3.2.1
lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 dump-blob-boundaries ->
dump-blob-boundaries.3
lrwxrwxrwx 1 buildd buildd 26 Apr 16 11:15 dump-blob-boundaries.3 ->
dump-blob-boundaries.3.2.1
-rwxr-xr-x 1 buildd buildd 31600 Apr 16 11:11 dump-blob-boundaries.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 dump-ref-fasta ->
dump-ref-fasta.3
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 dump-ref-fasta.3 ->
dump-ref-fasta.3.2.1
-rwxr-xr-x 1 buildd buildd 2098080 Apr 16 11:14 dump-ref-fasta.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 fastconv -> fastconv.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fastconv.3 -> fastconv.3.2.1
-rwxr-xr-x 1 buildd buildd 5042992 Apr 16 11:11 fastconv.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fasterq-dump -> fasterq-dump.3
-rwxr-xr-x 1 buildd buildd 1016680 Apr 16 11:11 fasterq-dump-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 fasterq-dump.3 ->
fasterq-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fasterq-dump.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 fastq-dump -> fastq-dump.3
-rwxr-xr-x 1 buildd buildd 349696 Apr 16 11:11 fastq-dump-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 fastq-dump.3 ->
fastq-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 fastq-dump.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 fastq-load -> fastq-load.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 fastq-load.3 ->
fastq-load.3.2.1
-rwxr-xr-x 1 buildd buildd 859400 Apr 16 11:11 fastq-load.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 general-loader ->
general-loader.3
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 general-loader.3 ->
general-loader.3.2.1
-rwxr-xr-x 1 buildd buildd 1646960 Apr 16 11:11 general-loader.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 helicos-load -> helicos-load.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 helicos-load.3 ->
helicos-load.3.2.1
-rwxr-xr-x 1 buildd buildd 769640 Apr 16 11:11 helicos-load.3.2.1
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 illumina-dump ->
illumina-dump.3
lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 illumina-dump.3 ->
illumina-dump.3.2.1
-rwxr-xr-x 1 buildd buildd 255616 Apr 16 11:11 illumina-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 illumina-load ->
illumina-load.3
lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 illumina-load.3 ->
illumina-load.3.2.1
-rwxr-xr-x 1 buildd buildd 819896 Apr 16 11:11 illumina-load.3.2.1
lrwxrwxrwx 1 buildd buildd 5 Apr 16 11:15 kar -> kar.3
lrwxrwxrwx 1 buildd buildd 6 Apr 16 11:15 kar+ -> kar+.3
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 kar+.3 -> kar+.3.2.1
-rwxr-xr-x 1 buildd buildd 237544 Apr 16 11:11 kar+.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 kar+meta -> kar+meta.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 kar+meta.3 -> kar+meta.3.2.1
-rwxr-xr-x 1 buildd buildd 159056 Apr 16 11:11 kar+meta.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 kar.3 -> kar.3.2.1
-rwxr-xr-x 1 buildd buildd 190712 Apr 16 11:11 kar.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 kdb-index -> kdb-index.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 kdb-index.3 -> kdb-index.3.2.1
-rwxr-xr-x 1 buildd buildd 78448 Apr 16 11:11 kdb-index.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 kdbmeta -> kdbmeta.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 kdbmeta.3 -> kdbmeta.3.2.1
-rwxr-xr-x 1 buildd buildd 123624 Apr 16 11:11 kdbmeta.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 latf-load -> latf-load.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 latf-load.3 -> latf-load.3.2.1
-rwxr-xr-x 1 buildd buildd 508272 Apr 16 11:12 latf-load.3.2.1
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 make-read-filter ->
make-read-filter.3
lrwxrwxrwx 1 buildd buildd 22 Apr 16 11:15 make-read-filter.3 ->
make-read-filter.3.2.1
-rwxr-xr-x 1 buildd buildd 158768 Apr 16 11:11 make-read-filter.3.2.1
lrwxrwxrwx 1 buildd buildd 7 Apr 16 11:15 md5cp -> md5cp.3
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 md5cp.3 -> md5cp.3.2.1
-rwxr-xr-x 1 buildd buildd 89720 Apr 16 11:11 md5cp.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 meta-cmp -> meta-cmp.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 meta-cmp.3 -> meta-cmp.3.2.1
-rwxr-xr-x 1 buildd buildd 82024 Apr 16 11:11 meta-cmp.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 meta-copy -> meta-copy.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 meta-copy.3 -> meta-copy.3.2.1
-rwxr-xr-x 1 buildd buildd 81952 Apr 16 11:11 meta-copy.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 meta-repair -> meta-repair.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 meta-repair.3 ->
meta-repair.3.2.1
-rwxr-xr-x 1 buildd buildd 136048 Apr 16 11:11 meta-repair.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 ngs-pileup -> ngs-pileup.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 ngs-pileup.3 ->
ngs-pileup.3.2.1
-rwxr-xr-x 1 buildd buildd 2608704 Apr 16 11:14 ngs-pileup.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 pacbio-correct ->
pacbio-correct.3
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 pacbio-correct.3 ->
pacbio-correct.3.2.1
-rwxr-xr-x 1 buildd buildd 76024 Apr 16 11:11 pacbio-correct.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 pacbio-load -> pacbio-load.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 pacbio-load.3 ->
pacbio-load.3.2.1
-rwxr-xr-x 1 buildd buildd 476952 Apr 16 11:11 pacbio-load.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 pacbio-loadxml ->
pacbio-loadxml.3
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 pacbio-loadxml.3 ->
pacbio-loadxml.3.2.1
-rwxr-xr-x 1 buildd buildd 757368 Apr 16 11:11 pacbio-loadxml.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 pileup-stats -> pileup-stats.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 pileup-stats.3 ->
pileup-stats.3.2.1
-rwxr-xr-x 1 buildd buildd 2848488 Apr 16 11:14 pileup-stats.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 prefetch -> prefetch.3
-rwxr-xr-x 1 buildd buildd 479464 Apr 16 11:11 prefetch-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 prefetch.3 -> prefetch.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 prefetch.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 rcexplain -> rcexplain.3
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 rcexplain.3 -> rcexplain.3.2.1
-rwxr-xr-x 1 buildd buildd 67456 Apr 16 11:11 rcexplain.3.2.1
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 read-filter-redact ->
read-filter-redact.3
lrwxrwxrwx 1 buildd buildd 24 Apr 16 11:15 read-filter-redact.3 ->
read-filter-redact.3.2.1
-rwxr-xr-x 1 buildd buildd 111192 Apr 16 11:11 read-filter-redact.3.2.1
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 ref-variation ->
ref-variation.3
lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 ref-variation.3 ->
ref-variation.3.2.1
-rwxr-xr-x 1 buildd buildd 3020016 Apr 16 11:14 ref-variation.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 rowwritetest -> rowwritetest.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 rowwritetest.3 ->
rowwritetest.3.2.1
-rwxr-xr-x 1 buildd buildd 88592 Apr 16 11:11 rowwritetest.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sam-dump -> sam-dump.3
-rwxr-xr-x 1 buildd buildd 834512 Apr 16 11:11 sam-dump-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sam-dump.3 -> sam-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sam-dump.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 samview -> samview.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 samview-util -> samview-util.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 samview-util.3 ->
samview-util.3.2.1
-rwxr-xr-x 1 buildd buildd 64176 Apr 16 11:11 samview-util.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 samview.3 -> samview.3.2.1
-rwxr-xr-x 1 buildd buildd 305696 Apr 16 11:11 samview.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 schema-replace ->
schema-replace.3
lrwxrwxrwx 1 buildd buildd 20 Apr 16 11:15 schema-replace.3 ->
schema-replace.3.2.1
-rwxr-xr-x 1 buildd buildd 82928 Apr 16 11:11 schema-replace.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sff-dump -> sff-dump.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sff-dump.3 -> sff-dump.3.2.1
-rwxr-xr-x 1 buildd buildd 234512 Apr 16 11:11 sff-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sff-load -> sff-load.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sff-load.3 -> sff-load.3.2.1
-rwxr-xr-x 1 buildd buildd 818504 Apr 16 11:11 sff-load.3.2.1
lrwxrwxrwx 1 buildd buildd 7 Apr 16 11:15 sharq -> sharq.3
lrwxrwxrwx 1 buildd buildd 11 Apr 16 11:15 sharq.3 -> sharq.3.2.1
-rwxr-xr-x 1 buildd buildd 44902232 Apr 16 11:13 sharq.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sortreadtest -> sortreadtest.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 sortreadtest.3 ->
sortreadtest.3.2.1
-rwxr-xr-x 1 buildd buildd 79784 Apr 16 11:11 sortreadtest.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-info -> sra-info.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-info.3 -> sra-info.3.2.1
-rwxr-xr-x 1 buildd buildd 2904864 Apr 16 11:11 sra-info.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 sra-pileup -> sra-pileup.3
-rwxr-xr-x 1 buildd buildd 443160 Apr 16 11:11 sra-pileup-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 sra-pileup.3 ->
sra-pileup.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-pileup.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 sra-search -> sra-search.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 sra-search.3 ->
sra-search.3.2.1
-rwxr-xr-x 1 buildd buildd 4340304 Apr 16 11:14 sra-search.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-sort -> sra-sort.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 sra-sort-cg -> sra-sort-cg.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 sra-sort-cg.3 ->
sra-sort-cg.3.2.1
-rwxr-xr-x 1 buildd buildd 808784 Apr 16 11:11 sra-sort-cg.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-sort.3 -> sra-sort.3.2.1
-rwxr-xr-x 1 buildd buildd 808816 Apr 16 11:11 sra-sort.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sra-stat -> sra-stat.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sra-stat.3 -> sra-stat.3.2.1
-rwxr-xr-x 1 buildd buildd 347472 Apr 16 11:11 sra-stat.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 srapath -> srapath.3
-rwxr-xr-x 1 buildd buildd 256120 Apr 16 11:11 srapath-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 srapath.3 -> srapath.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 srapath.3.2.1 -> sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 sratools -> sratools.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 sratools.3 -> sratools.3.2.1
-rwxr-xr-x 1 buildd buildd 5471720 Apr 16 11:11 sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 srf-load -> srf-load.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 srf-load.3 -> srf-load.3.2.1
-rwxr-xr-x 1 buildd buildd 999560 Apr 16 11:11 srf-load.3.2.1
lrwxrwxrwx 1 buildd buildd 15 Apr 16 11:15 test-download ->
test-download.3
lrwxrwxrwx 1 buildd buildd 19 Apr 16 11:15 test-download.3 ->
test-download.3.2.1
-rwxr-xr-x 1 buildd buildd 93648 Apr 16 11:11 test-download.3.2.1
lrwxrwxrwx 1 buildd buildd 24 Apr 16 11:15 test-read-write-cursor ->
test-read-write-cursor.3
lrwxrwxrwx 1 buildd buildd 28 Apr 16 11:15 test-read-write-cursor.3 ->
test-read-write-cursor.3.2.1
-rwxr-xr-x 1 buildd buildd 75488 Apr 16 11:11 test-read-write-cursor.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 test-sra -> test-sra.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 test-sra.3 -> test-sra.3.2.1
-rwxr-xr-x 1 buildd buildd 343496 Apr 16 11:11 test-sra.3.2.1
lrwxrwxrwx 1 buildd buildd 8 Apr 16 11:15 testld -> testld.3
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 testld.3 -> testld.3.2.1
-rwxr-xr-x 1 buildd buildd 76472 Apr 16 11:11 testld.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 txt2kdb -> txt2kdb.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 txt2kdb.3 -> txt2kdb.3.2.1
-rwxr-xr-x 1 buildd buildd 83256 Apr 16 11:11 txt2kdb.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 var-expand -> var-expand.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 var-expand.3 ->
var-expand.3.2.1
-rwxr-xr-x 1 buildd buildd 2049376 Apr 16 11:14 var-expand.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 vdb-config -> vdb-config.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 vdb-config.3 ->
vdb-config.3.2.1
-rwxr-xr-x 1 buildd buildd 2655424 Apr 16 11:13 vdb-config.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-copy -> vdb-copy.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-copy.3 -> vdb-copy.3.2.1
-rwxr-xr-x 1 buildd buildd 329728 Apr 16 11:11 vdb-copy.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-decrypt -> vdb-decrypt.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 vdb-decrypt.3 ->
vdb-decrypt.3.2.1
-rwxr-xr-x 1 buildd buildd 121584 Apr 16 11:11 vdb-decrypt.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-diff -> vdb-diff.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-diff.3 -> vdb-diff.3.2.1
-rwxr-xr-x 1 buildd buildd 155224 Apr 16 11:11 vdb-diff.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-dump -> vdb-dump.3
-rwxr-xr-x 1 buildd buildd 887840 Apr 16 11:11 vdb-dump-orig.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-dump.3 -> vdb-dump.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-dump.3.2.1 ->
sratools.3.2.1
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-encrypt -> vdb-encrypt.3
lrwxrwxrwx 1 buildd buildd 17 Apr 16 11:15 vdb-encrypt.3 ->
vdb-encrypt.3.2.1
-rwxr-xr-x 1 buildd buildd 119960 Apr 16 11:11 vdb-encrypt.3.2.1
lrwxrwxrwx 1 buildd buildd 10 Apr 16 11:15 vdb-lock -> vdb-lock.3
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-lock.3 -> vdb-lock.3.2.1
-rwxr-xr-x 1 buildd buildd 68336 Apr 16 11:11 vdb-lock.3.2.1
lrwxrwxrwx 1 buildd buildd 9 Apr 16 11:15 vdb-sql -> vdb-sql.3
lrwxrwxrwx 1 buildd buildd 13 Apr 16 11:15 vdb-sql.3 -> vdb-sql.3.2.1
-rwxr-xr-x 1 buildd buildd 5296480 Apr 16 11:11 vdb-sql.3.2.1
lrwxrwxrwx 1 buildd buildd 12 Apr 16 11:15 vdb-unlock -> vdb-unlock.3
lrwxrwxrwx 1 buildd buildd 16 Apr 16 11:15 vdb-unlock.3 ->
vdb-unlock.3.2.1
-rwxr-xr-x 1 buildd buildd 68344 Apr 16 11:11 vdb-unlock.3.2.1
lrwxrwxrwx 1 buildd buildd 14 Apr 16 11:15 vdb-validate -> vdb-validate.3
lrwxrwxrwx 1 buildd buildd 18 Apr 16 11:15 vdb-validate.3 ->
vdb-validate.3.2.1
-rwxr-xr-x 1 buildd buildd 261640 Apr 16 11:11 vdb-validate.3.2.1
cd debian/tmp/usr/bin && \
for bin in *-orig.* ; do \
base=${bin%-orig.*} && \
vbase=$(readlink "$(readlink $base)") && \
vdriver=$(readlink "$vbase") && \
mv -v $bin $base-orig && \
ln -snfv ${vdriver%%.[0-9]*} $vbase || exit $? ; \
done && \
for bin in *[a-z+] ; do \
bin2=$(readlink $bin) ; \
bin3=$(readlink "$bin2") ; \
case $bin2 in \
$bin.* ) rm -v $bin2 && mv -v $bin3 $bin || exit $? ;; \
esac ; \
done
renamed 'fasterq-dump-orig.3.2.1' -> 'fasterq-dump-orig'
'fasterq-dump.3.2.1' -> 'sratools'
renamed 'fastq-dump-orig.3.2.1' -> 'fastq-dump-orig'
'fastq-dump.3.2.1' -> 'sratools'
renamed 'prefetch-orig.3.2.1' -> 'prefetch-orig'
'prefetch.3.2.1' -> 'sratools'
renamed 'sam-dump-orig.3.2.1' -> 'sam-dump-orig'
'sam-dump.3.2.1' -> 'sratools'
renamed 'sra-pileup-orig.3.2.1' -> 'sra-pileup-orig'
'sra-pileup.3.2.1' -> 'sratools'
renamed 'srapath-orig.3.2.1' -> 'srapath-orig'
'srapath.3.2.1' -> 'sratools'
renamed 'vdb-dump-orig.3.2.1' -> 'vdb-dump-orig'
'vdb-dump.3.2.1' -> 'sratools'
removed 'abi-dump.3'
renamed 'abi-dump.3.2.1' -> 'abi-dump'
removed 'abi-load.3'
renamed 'abi-load.3.2.1' -> 'abi-load'
removed 'align-cache.3'
renamed 'align-cache.3.2.1' -> 'align-cache'
removed 'align-info.3'
renamed 'align-info.3.2.1' -> 'align-info'
removed 'bam-load.3'
renamed 'bam-load.3.2.1' -> 'bam-load'
removed 'cache-mgr.3'
renamed 'cache-mgr.3.2.1' -> 'cache-mgr'
removed 'ccextract.3'
renamed 'ccextract.3.2.1' -> 'ccextract'
removed 'cg-load.3'
renamed 'cg-load.3.2.1' -> 'cg-load'
removed 'check-corrupt.3'
renamed 'check-corrupt.3.2.1' -> 'check-corrupt'
removed 'check-redact.3'
renamed 'check-redact.3.2.1' -> 'check-redact'
removed 'compute-coverage.3'
renamed 'compute-coverage.3.2.1' -> 'compute-coverage'
removed 'compute-coverage-ngs.3'
renamed 'compute-coverage-ngs.3.2.1' -> 'compute-coverage-ngs'
removed 'copycat.3'
renamed 'copycat.3.2.1' -> 'copycat'
removed 'crc32sum.3'
renamed 'crc32sum.3.2.1' -> 'crc32sum'
removed 'dump-blob-boundaries.3'
renamed 'dump-blob-boundaries.3.2.1' -> 'dump-blob-boundaries'
removed 'dump-ref-fasta.3'
renamed 'dump-ref-fasta.3.2.1' -> 'dump-ref-fasta'
removed 'fastconv.3'
renamed 'fastconv.3.2.1' -> 'fastconv'
removed 'fasterq-dump.3'
renamed 'fasterq-dump.3.2.1' -> 'fasterq-dump'
removed 'fastq-dump.3'
renamed 'fastq-dump.3.2.1' -> 'fastq-dump'
removed 'fastq-load.3'
renamed 'fastq-load.3.2.1' -> 'fastq-load'
removed 'general-loader.3'
renamed 'general-loader.3.2.1' -> 'general-loader'
removed 'helicos-load.3'
renamed 'helicos-load.3.2.1' -> 'helicos-load'
removed 'illumina-dump.3'
renamed 'illumina-dump.3.2.1' -> 'illumina-dump'
removed 'illumina-load.3'
renamed 'illumina-load.3.2.1' -> 'illumina-load'
removed 'kar.3'
renamed 'kar.3.2.1' -> 'kar'
removed 'kar+.3'
renamed 'kar+.3.2.1' -> 'kar+'
removed 'kar+meta.3'
renamed 'kar+meta.3.2.1' -> 'kar+meta'
removed 'kdb-index.3'
renamed 'kdb-index.3.2.1' -> 'kdb-index'
removed 'kdbmeta.3'
renamed 'kdbmeta.3.2.1' -> 'kdbmeta'
removed 'latf-load.3'
renamed 'latf-load.3.2.1' -> 'latf-load'
removed 'make-read-filter.3'
renamed 'make-read-filter.3.2.1' -> 'make-read-filter'
removed 'md5cp.3'
renamed 'md5cp.3.2.1' -> 'md5cp'
removed 'meta-cmp.3'
renamed 'meta-cmp.3.2.1' -> 'meta-cmp'
removed 'meta-copy.3'
renamed 'meta-copy.3.2.1' -> 'meta-copy'
removed 'meta-repair.3'
renamed 'meta-repair.3.2.1' -> 'meta-repair'
removed 'ngs-pileup.3'
renamed 'ngs-pileup.3.2.1' -> 'ngs-pileup'
removed 'pacbio-correct.3'
renamed 'pacbio-correct.3.2.1' -> 'pacbio-correct'
removed 'pacbio-load.3'
renamed 'pacbio-load.3.2.1' -> 'pacbio-load'
removed 'pacbio-loadxml.3'
renamed 'pacbio-loadxml.3.2.1' -> 'pacbio-loadxml'
removed 'pileup-stats.3'
renamed 'pileup-stats.3.2.1' -> 'pileup-stats'
removed 'prefetch.3'
renamed 'prefetch.3.2.1' -> 'prefetch'
removed 'rcexplain.3'
renamed 'rcexplain.3.2.1' -> 'rcexplain'
removed 'read-filter-redact.3'
renamed 'read-filter-redact.3.2.1' -> 'read-filter-redact'
removed 'ref-variation.3'
renamed 'ref-variation.3.2.1' -> 'ref-variation'
removed 'rowwritetest.3'
renamed 'rowwritetest.3.2.1' -> 'rowwritetest'
removed 'sam-dump.3'
renamed 'sam-dump.3.2.1' -> 'sam-dump'
removed 'samview.3'
renamed 'samview.3.2.1' -> 'samview'
removed 'samview-util.3'
renamed 'samview-util.3.2.1' -> 'samview-util'
removed 'schema-replace.3'
renamed 'schema-replace.3.2.1' -> 'schema-replace'
removed 'sff-dump.3'
renamed 'sff-dump.3.2.1' -> 'sff-dump'
removed 'sff-load.3'
renamed 'sff-load.3.2.1' -> 'sff-load'
removed 'sharq.3'
renamed 'sharq.3.2.1' -> 'sharq'
removed 'sortreadtest.3'
renamed 'sortreadtest.3.2.1' -> 'sortreadtest'
removed 'sra-info.3'
renamed 'sra-info.3.2.1' -> 'sra-info'
removed 'sra-pileup.3'
renamed 'sra-pileup.3.2.1' -> 'sra-pileup'
removed 'sra-search.3'
renamed 'sra-search.3.2.1' -> 'sra-search'
removed 'sra-sort.3'
renamed 'sra-sort.3.2.1' -> 'sra-sort'
removed 'sra-sort-cg.3'
renamed 'sra-sort-cg.3.2.1' -> 'sra-sort-cg'
removed 'sra-stat.3'
renamed 'sra-stat.3.2.1' -> 'sra-stat'
removed 'srapath.3'
renamed 'srapath.3.2.1' -> 'srapath'
removed 'sratools.3'
renamed 'sratools.3.2.1' -> 'sratools'
removed 'srf-load.3'
renamed 'srf-load.3.2.1' -> 'srf-load'
removed 'test-download.3'
renamed 'test-download.3.2.1' -> 'test-download'
removed 'test-read-write-cursor.3'
renamed 'test-read-write-cursor.3.2.1' -> 'test-read-write-cursor'
removed 'test-sra.3'
renamed 'test-sra.3.2.1' -> 'test-sra'
removed 'testld.3'
renamed 'testld.3.2.1' -> 'testld'
removed 'txt2kdb.3'
renamed 'txt2kdb.3.2.1' -> 'txt2kdb'
removed 'var-expand.3'
renamed 'var-expand.3.2.1' -> 'var-expand'
removed 'vdb-config.3'
renamed 'vdb-config.3.2.1' -> 'vdb-config'
removed 'vdb-copy.3'
renamed 'vdb-copy.3.2.1' -> 'vdb-copy'
removed 'vdb-decrypt.3'
renamed 'vdb-decrypt.3.2.1' -> 'vdb-decrypt'
removed 'vdb-diff.3'
renamed 'vdb-diff.3.2.1' -> 'vdb-diff'
removed 'vdb-dump.3'
renamed 'vdb-dump.3.2.1' -> 'vdb-dump'
removed 'vdb-encrypt.3'
renamed 'vdb-encrypt.3.2.1' -> 'vdb-encrypt'
removed 'vdb-lock.3'
renamed 'vdb-lock.3.2.1' -> 'vdb-lock'
removed 'vdb-sql.3'
renamed 'vdb-sql.3.2.1' -> 'vdb-sql'
removed 'vdb-unlock.3'
renamed 'vdb-unlock.3.2.1' -> 'vdb-unlock'
removed 'vdb-validate.3'
renamed 'vdb-validate.3.2.1' -> 'vdb-validate'
mkdir debian/tmp/usr/lib/sra-toolkit
mv debian/tmp/usr/bin/sratools debian/tmp/usr/lib/sra-toolkit
for x in debian/tmp/usr/bin/*-orig; do \
mv -v $x debian/tmp/usr/lib/sra-toolkit ; \
ln -snfv ../lib/sra-toolkit/sratools ${x%-orig} ; \
done
renamed 'debian/tmp/usr/bin/fasterq-dump-orig' ->
'debian/tmp/usr/lib/sra-toolkit/fasterq-dump-orig'
'debian/tmp/usr/bin/fasterq-dump' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/fastq-dump-orig' ->
'debian/tmp/usr/lib/sra-toolkit/fastq-dump-orig'
'debian/tmp/usr/bin/fastq-dump' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/prefetch-orig' ->
'debian/tmp/usr/lib/sra-toolkit/prefetch-orig'
'debian/tmp/usr/bin/prefetch' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/sam-dump-orig' ->
'debian/tmp/usr/lib/sra-toolkit/sam-dump-orig'
'debian/tmp/usr/bin/sam-dump' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/sra-pileup-orig' ->
'debian/tmp/usr/lib/sra-toolkit/sra-pileup-orig'
'debian/tmp/usr/bin/sra-pileup' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/srapath-orig' ->
'debian/tmp/usr/lib/sra-toolkit/srapath-orig'
'debian/tmp/usr/bin/srapath' -> '../lib/sra-toolkit/sratools'
renamed 'debian/tmp/usr/bin/vdb-dump-orig' ->
'debian/tmp/usr/lib/sra-toolkit/vdb-dump-orig'
'debian/tmp/usr/bin/vdb-dump' -> '../lib/sra-toolkit/sratools'
dh_install
# remove susipcious file which is not executable and conflicts with package
magic
rm -f debian/*/usr/bin/magic
pybuild --install --name ngs -d ngs/ngs-python
I: pybuild base:311: dh_auto_install --buildsystem=cmake
--builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ngs/build
--destdir=/<<PKGBUILDDIR>>/debian/python3-ngs --
dh_auto_install: error: "debian/control" not found. Are you sure you are in the
correct directory?
Compilation failed in require at /usr/bin/dh_auto_install line 12.
BEGIN failed--compilation aborted at /usr/bin/dh_auto_install line 12.
E: pybuild pybuild:389: install: plugin cmake failed with: exit code=25:
dh_auto_install --buildsystem=cmake
--builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ngs/build
--destdir=/<<PKGBUILDDIR>>/debian/python3-ngs --
make[1]: *** [debian/rules:113: override_dh_install] Error 13
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:24: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202504/
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:sra-sdk, so that this is still
visible in the BTS web page for this package.
Notes:
* When a package is built with the nocheck profile, it means:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- DEB_BUILD_PROFILES=nocheck
(Build-Depends marked <!nocheck> are not installed)
- The contents of the package is allowed to be different than normal
* This category of bugs was going to be RC for trixie, but
according to the Release Managers it's a little bit late in the
release cycle to introduce a bunch of RC bugs of this type.
* In addition to the above, this package also fails when
using DEB_BUILD_OPTIONS=nocheck alone. In this mode:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- Build-Depends marked <!nocheck> are installed as normal
- The contents of the package should not change compared
to a regular build
Thanks.
