Your message dated Thu, 10 Apr 2025 02:36:47 +0000
with message-id <[email protected]>
and subject line Bug#1099933: fixed in sra-sdk 3.2.1+dfsg-3
has caused the Debian Bug report #1099933,
regarding autopkgtest requires internet and ca-certificates
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.)
--
1099933: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1099933
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: sra-sdk
Version: 3.0.9+dfsg-7
Severity: normal
Tags: patch
The autopkgtest of sra-sdk requests data from the Internet using https,
however this isn't declared, and there's no requirement to have
ca-certificates.
Log:
autopkgtest [11:11:57]: test run-unit-test: [-----------------------
>>>>>Decompressing test-data archive...
dbGaP-0/
dbGaP-0/SRR2042184.fasta
meta/
meta/prj_phs710EA_test.ngc
meta/SRR6650398_experiment.xml
meta/SRR6650398.bam
meta/SRR2042184_run.xml
meta/SRR2042184_experiment.xml
meta/SRR6650398_illumina_run.xml
meta/SRR7032226_run.xml
meta/SRR7032226_experiment.xml
meta/reference.fna
meta/SRR6650398_fastq_run.xml
public/
public/nannot/
public/wgs/
public/refseq/
public/refseq/NC_000962.3
public/sra/
public/sra/SRR7032226.sra
public/sra/SRR6650398.sra
public/sra/SRR2042184.sra
public/files/
>>>>>Running test-sra...
2025-03-09T15:11:58 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:58 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'trace.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly
signed by the trusted CA !! The certificate is signed with an unacceptable
hash. )
2025-03-09T15:11:58 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:58 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'trace.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly
signed by the trusted CA !! The certificate is signed with an unacceptable
hash. )
2025-03-09T15:11:58 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:58 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'ftp-trace.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not
correctly signed by the trusted CA !! The certificate is signed with an
unacceptable hash. )
2025-03-09T15:11:59 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:59 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'ftp-trace.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not
correctly signed by the trusted CA !! The certificate is signed with an
unacceptable hash. )
2025-03-09T15:11:59 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:59 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'ftp-trace.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not
correctly signed by the trusted CA !! The certificate is signed with an
unacceptable hash. )
2025-03-09T15:11:59 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:59 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'locate.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly
signed by the trusted CA !! The certificate is signed with an unacceptable
hash. )
2025-03-09T15:11:59 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:59 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'sra-download.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not
correctly signed by the trusted CA !! The certificate is signed with an
unacceptable hash. )
2025-03-09T15:11:59 test-sra.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:11:59 test-sra.3.0.9 sys: mbedtls_ssl_get_verify_result for
'sra-download.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not
correctly signed by the trusted CA !! The certificate is signed with an
unacceptable hash. )
>>>>>Running vdb-config...
>>>>>Running cache-mgr...
-----------------------------------
0 cached file(s)
3 complete file(s)
1,800,745 bytes in cached files
1,800,745 bytes used in cached files
0 lock files
>>>>>Running srapath...
/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR2042184.sra
/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR6650398.sra
/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR7032226.sra
>>>>>Running prefetch...
2025-03-09T15:11:59 prefetch.3.0.9:
'/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR2042184.sra' is a local
non-kart file
2025-03-09T15:11:59 prefetch.3.0.9:
'/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR6650398.sra' is a local
non-kart file
2025-03-09T15:12:01 prefetch.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:12:01 prefetch.3.0.9 sys: mbedtls_ssl_get_verify_result for
'locate.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly
signed by the trusted CA !! The certificate is signed with an unacceptable
hash. )
2025-03-09T15:12:01 prefetch.3.0.9:
'/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR6650398.sra' has 0
unresolved dependencies
2025-03-09T15:12:01 prefetch.3.0.9:
'/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR7032226.sra' is a local
non-kart file
2025-03-09T15:12:01 prefetch.3.0.9:
'/tmp/autopkgtest.T7fAqv/autopkgtest_tmp/public/sra/SRR7032226.sra' has 0
unresolved dependencies
>>>>>Running fastq-dump...
2025-03-09T15:12:02 fastq-dump.3.0.9 sys: encryption failed while validating
token within cryptographic module - Verification issue 0x4008 for this
certificate: ( cert. version : 3 serial number : 00 issuer name
: C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification
Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy
Class 2 Certification Authority issued on : 2004-06-29 17:06:20
expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA
key size : 2048 bits basic constraints : CA=true )
2025-03-09T15:12:02 fastq-dump.3.0.9 sys: mbedtls_ssl_get_verify_result for
'locate.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly
signed by the trusted CA !! The certificate is signed with an unacceptable
hash. )
Failed to call external services.
autopkgtest [11:12:03]: test run-unit-test: -----------------------]
autopkgtest [11:12:03]: test run-unit-test: - - - - - - - - - - results - - -
- - - - - - -
run-unit-test FAIL non-zero exit status 64
Trivial patch:
diff -Nru sra-sdk-3.0.9+dfsg/debian/tests/control
sra-sdk-3.0.9+dfsg/debian/tests/control
--- sra-sdk-3.0.9+dfsg/debian/tests/control 2024-10-17 22:48:06.000000000
-0400
+++ sra-sdk-3.0.9+dfsg/debian/tests/control 2025-03-09 10:33:36.000000000
-0400
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
+Depends: @, ca-certificates
+Restrictions: allow-stderr, needs-internet
--- End Message ---
--- Begin Message ---
Source: sra-sdk
Source-Version: 3.2.1+dfsg-3
Done: Aaron M. Ucko <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sra-sdk, 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.
Aaron M. Ucko <[email protected]> (supplier of updated sra-sdk 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: Wed, 09 Apr 2025 21:31:32 -0400
Source: sra-sdk
Architecture: source
Version: 3.2.1+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 1084404 1087096 1099933
Changes:
sra-sdk (3.2.1+dfsg-3) unstable; urgency=medium
.
* Upload to unstable.
* debian/salsa-ci.yml: Disable use of experimental (build-)deps again.
.
sra-sdk (3.2.1+dfsg-2) experimental; urgency=medium
.
* debian/control: Build-depend on python3-setuptools.
* debian/patches/fix_arm64_build.patch: Correct parenthesis placement.
* debian/patches/setuptools.patch (new): Substitute setuptools for
distutils (retired) in ngs/ngs-python/setup.py.
* debian/rules:
- Set PIP_BREAK_SYSTEM_PACKAGES for upstream's test suite.
- Substitute pybuild for direct setup.py invocation and clean up after
it.
* .gitignore: Add .pc (belatedly) and .pybuild.
.
sra-sdk (3.2.1+dfsg-1) experimental; urgency=medium
.
[ Andreas Tille ]
* New upstream version 3.1.1.
* Fix Python3.12 string syntax
Closes: #1087096
* Do not fail if clean target debian/libngs-jni.links does not exist
.
[ Aaron M. Ucko ]
* New upstream version 3.2.1.
* debian/control:
- Tighten libncbi-vdb-dev build dependency as usual; add one on
python3-vdb (provided by ncbi-vdb-data for now, to be split off
post-Trixie.)
- Drop vestigial build dependency on libfuse-dev. (Closes: #1084404.)
* debian/copyright: Update GPL logistics (see #1080497) and bm and
spdlog paths.
* debian/patches: Update accordingly. Notably:
- label_online_tests.patch: Add a couple dozen additional tests.
- missing_include.patch: Drop, superfluous at this point.
- support_libre2-11.patch: Cover new additions to
fastq_defline_matcher.hpp.
- use_debian_packaged_re2.patch: Cover new test-sharq-reader.
* debian/rules:
- Stop generating and installing debian.kfg, taken over by
ncbi-vdb-data.
- Clean up additional build output.
* debian/salsa-ci.yml: Reenable use of experimental (build-)deps for now.
* debian/tests/control: Per Stefano Rivera (thanks!), declare a
dependency on ca-certificates and the need for Internet access.
(Closes: #1099933.)
* .gitignore: Add, belatedly.
* Standards-Version: 4.7.2 (routine-update)
Checksums-Sha1:
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e69709d24f8b14573413b868b9e45084d5ee6ee1 3794904
sra-sdk_3.2.1+dfsg-3.debian.tar.xz
Checksums-Sha256:
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sra-sdk_3.2.1+dfsg-3.debian.tar.xz
Files:
a34833d499170503b6a9ec2b3cbfb07a 3003 science optional sra-sdk_3.2.1+dfsg-3.dsc
15e92455fb8fa9330666435047601cc0 3794904 science optional
sra-sdk_3.2.1+dfsg-3.debian.tar.xz
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