[Debian-med-packaging] Bug#792510: blast_formatter: need internet access even if run locally

[Yann Dumont]

Package: ncbi-blast+
Version: 2.2.30-4
Severity: important

Dear Maintainer,

I am currently have some connection issues, so I realized that blast_formatter
failled when internet connection is off.

This is what I obtain :

Error: (311.22) SOCK#1000[?]: [SOCK::Connect]  Failed
SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
Error: (303.7) [URL_Connect;
http//www.ncbi.nlm.nih.gov:80/Service/dispd.cgi?service=ID2&address=netbookyann(127.0.1.1)&platform=x86_64
-unknown-linux-gnu]  Failed to connect: Unknown
Error: (310.5) [ID2]  Service not found
Error: (315.2) CConn_Streambuf::CConn_Streambuf():  NULL connector: Unknown
Error: (311.22) SOCK#2000[?]: [SOCK::Connect]  Failed
SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
Error: (303.7) [URL_Connect;
http//www.ncbi.nlm.nih.gov:80/Service/dispd.cgi?service=ID2&address=netbookyann(127.0.1.1)&platform=x86_64
-unknown-linux-gnu]  Failed to connect: Unknown
Error: (310.5) [ID2]  Service not found
Error: (315.2) CConn_Streambuf::CConn_Streambuf():  NULL connector: Unknown
Error: (311.22) SOCK#3000[?]: [SOCK::Connect]  Failed
SOCK_gethostbyname("www.ncbi.nlm.nih.gov")
Error: (303.7) [URL_Connect;
http//www.ncbi.nlm.nih.gov:80/Service/dispd.cgi?service=ID2&address=netbookyann(127.0.1.1)&platform=x86_64
-unknown-linux-gnu]  Failed to connect: Unknown
Error: (310.5) [ID2]  Service not found
Error: (315.2) CConn_Streambuf::CConn_Streambuf():  NULL connector: Unknown
Error: NCBI C++ Exception:
    T0 "/home/amu/src/ncbi-blast+/build-area/ncbi-
blast+-2.2.30/c++/src/objtools/data_loaders/genbank/id2/reader_id2.cpp", line
257: Error: ncbi::objects::CId2Reader::x_ConnectAtSlot() - cannot open
connection: ID2
    T0 "/home/amu/src/ncbi-blast+/build-area/ncbi-
blast+-2.2.30/c++/src/objtools/data_loaders/genbank/reader_id2_base.cpp", line
1279: Error: ncbi::objects::CId2ReaderBase::x_ProcessPacket() - failed to send
request: NULL

None of these messages appears when I am connected.
Since the formatter still creates the results'files, that are empty, it could
lead false negative results if you don't mind the warnings.

I am using formatter in a bash script, just after a blastx query that generate
a ASN file. None of the files are on internet. There is no matter with this ASN
file since when I generate it with internet connection off, then run formatter
with connection on, everything is OK. But when I do the opposite (blastx with
net on then formatter with net off), it fails.

Best regards,

Yann Dumont



-- System Information:
Debian Release: stretch/sid
  APT prefers testing-updates
  APT policy: (900, 'testing-updates'), (850, 'testing'), (800, 'stable-updates'), (800, 'stable'), (700, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.0.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages ncbi-blast+ depends on:
ii  libbz2-1.0  1.0.6-8
ii  libc6       2.19-18
ii  libgcc1     1:5.1.1-12
ii  libgomp1    5.1.1-12
ii  libpcre3    2:8.35-7
ii  libstdc++6  5.1.1-12
ii  ncbi-data   6.1.20120620-8
ii  perl        5.20.2-6
ii  python      2.7.9-1
ii  zlib1g      1:1.2.8.dfsg-2+b1

ncbi-blast+ recommends no packages.

ncbi-blast+ suggests no packages.

-- no debconf information