On 17/01/2020 11:57, Andreas Tille wrote:
[...]
Can you please add some kind of example code that enables us to
reproduce the issue? We could add it to the autopkgtest
https://salsa.debian.org/med-team/ncbi-blastplus/blob/master/debian/tests/run-unit-test
to verify that this issue is solved.
Hi, Andreas.
I'm not sure how this can be tested without tracing attempts by "blastn"
to stat and read /etc/ncbi/.ncbirc, as I showed in my previous email.
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@beluga:~$ export NCBI=/etc/ncbi
ajt@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/
A unit test would need to know where the deb stores ".ncbirc" and strace
the execution of "blastn" to make sure the executable finds the default
config file. If NCBI is unset, it looks for "/etc/.ncbirc". However, the
default location it is installed to under Ubuntu is "/etc/ncbi/.ncbirc".
HTH,
Tony.
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