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

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)