[Debian-med-packaging] [Bug 1860109] Re: default /etc/ncbi/.ncbirc not read

[Tony Travis]

The BUG appears to be caused when the NCBI environment variable is
undefined. Setting NCBI to the installed location of the default config
file under Ubuntu fixes the problem:

> ajt at beluga:~$ export NCBI=/etc/ncbi
> ajt at beluga:~$ strace blastn |& fgrep .ncbirc
> stat("./.ncbirc", 0x7ffc01d0e2c0)       = -1 ENOENT (No such file or directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> lstat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> openat(AT_FDCWD, "/etc/ncbi/.ncbirc", O_RDONLY) = 3
> stat("./.ncbirc", 0x7ffc01d0eae0)       = -1 ENOENT (No such file or directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
This behaviour is consistent to what NCBI describe:

> https://www.ncbi.nlm.nih.gov/books/NBK279695/

If the NCBI variable is unset, "blastn" looks for "/etc/.ncbirc".
However, the default location the config file is installed to under
Ubuntu is "/etc/ncbi/.ncbirc".

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https://bugs.launchpad.net/bugs/1860109

Title:
  default /etc/ncbi/.ncbirc not read

Status in ncbi-blast+ package in Ubuntu:
  New

Bug description:
  While attempting to use NCBI "blastn" from behind a proxy, I traced
  the execution of "blastn" to check if it was reading the default
  "/etc/ncbi/.ncbirc" config file where I put my proxy config because it
  wasn't working.

  In fact, the default config file is never stat'ed or read:

  > ajt at beluga:~$ strace blastn |& fgrep .ncbirc
  > stat("./.ncbirc", 0x7fff8bbc0200)       = -1 ENOENT (No such file or directory)
  > stat("/home/ajt/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)
  > stat("/etc/.ncbirc", 0x7fff8bbc0200)    = -1 ENOENT (No such file or directory)
  > stat("/usr/bin/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)

  I created a "~/.ncbirc" file, which is read correctly, so I'm using
  that instead.

  ProblemType: Bug
  DistroRelease: Ubuntu 18.04
  Package: ncbi-blast+ 2.6.0-1
  ProcVersionSignature: Ubuntu 5.0.0-37.40~18.04.1-generic 5.0.21
  Uname: Linux 5.0.0-37-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair wl
  ApportVersion: 2.20.9-0ubuntu7.9
  Architecture: amd64
  CurrentDesktop: MATE
  Date: Fri Jan 17 10:52:18 2020
  InstallationDate: Installed on 2019-03-28 (295 days ago)
  InstallationMedia: Ubuntu-MATE 18.04.2 LTS "Bionic Beaver" - Release amd64 (20190210)
  SourcePackage: ncbi-blast+
  UpgradeStatus: No upgrade log present (probably fresh install)

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