Summary: | sci-libs/arpack-3.5.0 : configure: error: cannot find BLAS libraries | ||
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Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | CONFIRMED --- | ||
Severity: | normal | CC: | anton.kochkov, dschridde+gentoobugs, elliot, frp.bissey, gentoo.2019, sam, silvio.gerli, waebbl-gentoo |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | 696256, 698756, 700196 | ||
Bug Blocks: | |||
Attachments: |
emerge-info.txt
emerge-history.txt environment etc.portage.tbz2 logs.tbz2 sci-libs:arpack-3.5.0:20171121-191437.log temp.tbz2 |
Description
Toralf Förster
2017-11-21 19:21:27 UTC
Created attachment 505522 [details]
emerge-info.txt
Created attachment 505524 [details]
emerge-history.txt
Created attachment 505526 [details]
environment
Created attachment 505528 [details]
etc.portage.tbz2
Created attachment 505530 [details]
logs.tbz2
Created attachment 505532 [details]
sci-libs:arpack-3.5.0:20171121-191437.log
Created attachment 505534 [details]
temp.tbz2
Could you provide config.log? I am fairly sure what kind of problem that is but config.log from arpack would be a nice addition for the diagnostics. (In reply to François Bissey from comment #8) pls look at the attached logs.tbz2 Thanks, I hadn't worked that out. And the problem seems to be of a kind I didn't expect: configure:5227: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall -Wl,-O1 -Wl,--as-needed conftest.c -lblas -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../.. -lgfortran -lm -lquadmath >&5 /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libgfortran.so.3, needed by /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so, not found (try using -rpath or -rpath-link) /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_stop_string@GFORTRAN_1.0' /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_string_len_trim@GFORTRAN_1.0' /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write@GFORTRAN_1.0' /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write_done@GFORTRAN_1.0' /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_character_write@GFORTRAN_1.4' /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_integer_write@GFORTRAN_1.4' collect2: error: ld returned 1 exit status It looks like blas-reference has been compiled with a different version of gfortran. gfortran from gcc-7.2 produce libgfortran.so.4 but libblas has been compiled with .so.3. Rebuilding blas-reference (and lapack-reference afterwards) should solve the issue. Your emerge history confirms that gcc-7.2 was emerged after blas-reference. There is actually quite a number of things that would be affected. emerge -1 blas-reference emerge -1 arpack solves this problema but than another problem appears: checking for cheev_ in -llapack -lblas... no checking for cheev_... no checking for cheev_ in -llapack... no checking for cheev_ in -llapack_rs6k... no configure: error: cannot find LAPACK libraries I re-emerging lapack-reference. I'll update you if it is the last problem. I have to point out that I'm doing: emerge -e world and the problem appears. I think the sequence of the emerge should be more accurate: before the needed packages and than the arpack shouoldn't it? It should have been emerge -1v blas-reference emerge -1v lapack-reference emerge -1v arpack I am not surprised at the result. > I re-emerging lapack-reference. I'll update you if it is the last problem. it worked > > I have to point out that I'm doing: > > emerge -e world > > and the problem appears. I think the sequence of the emerge should be more > accurate: before the needed packages and than the > > arpack > > shouoldn't it? about this? I had the same problem with arpack-3.1.5 (stable). I switched from GCC 6.4.0 to GCC 7.3.0 and started 'emerge -e world'. Emerge couldn't compile arpack and stopped with the error message shown in the first comment. After I executed the statements shown in comment 12, arpack was installed and I could continue with emerge --resume --skipfirst. Thanks to everyone who posted in this thread. The fix shown in comment 12 saved me a couple of hours :-) Seems to be a duplicate of bug #649892 *** Bug 649892 has been marked as a duplicate of this bug. *** Need stabilization of the new BLAS/LAPACK framework soon. So? There is gcc10 patch here https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957007 Whatever this bug is, I can't reproduce it with GCC-10. All blocker bugs finally closed. |