Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#950 closed request (fixed)

spurious failures in yat_pc_test.sh

Reported by: Peter Owned by: Peter
Priority: minor Milestone: yat 0.17.2
Component: test Version: trunk
Keywords: Cc:

Description

The yat_pc_test.sh tries to build against yat using pkg-config. Because it's trying to build with the -static flag, pkg-config is listing all the Libs.private from htslib.pc. On ubuntu that is

Libs.private: -L${libdir} -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -lbz2 -ldeflate -lhts -lm -lpthread

and the linking fails if e.g. libbz2 or libdeflate is not installed. Since those libraries are not really used in yat, the test is overly sensitive. IIRC, there was some thought behind the static, related to capturing problem with cblas linking, but I suggest we change the test case to a more realistic use with using pkg-config linking dynamically.

Change History (4)

comment:1 Changed 13 months ago by Peter

Owner: changed from Jari Häkkinen to Peter
Status: newaccepted

comment:2 Changed 13 months ago by Peter

Milestone: yat 0.18yat 0.17.2

Ticket #952 was marked related.

comment:3 Changed 13 months ago by Peter

Resolution: fixed
Status: acceptedclosed

In 3950:

Double-quote 2nd argument in YAT_SET_CONTAINS to allow expansion of
shell variables.

test/yat_pc_test.sh: remove --static in invocation of pkg-config
(fixes #950)

configure.ac: GSL, htslib and boost libraries that are exposed in
header files are not declared as private in yat.pc (fixes #952).

NEWS: record ticket #952

comment:4 Changed 13 months ago by Peter

Priority: majorminor
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