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Bug 680036 - dev-python/pandas-0.24.1 parallel make fails - ld: .../work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o: file not recognized: File truncated
Summary: dev-python/pandas-0.24.1 parallel make fails - ld: .../work/pandas-0.24.1-pyt...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2019-03-11 13:31 UTC by Thomas Beutin
Modified: 2020-03-09 12:44 UTC (History)
5 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,397.86 KB, text/plain)
2019-03-11 13:32 UTC, Thomas Beutin
Details
build-python2_7.log (build-python2_7.log,197.29 KB, text/plain)
2019-03-11 13:32 UTC, Thomas Beutin
Details
build-python3_6.log (build-python3_6.log,199.78 KB, text/plain)
2019-03-11 13:32 UTC, Thomas Beutin
Details
emerge-info.log (emerge-info.log,9.74 KB, text/plain)
2019-03-11 13:33 UTC, Thomas Beutin
Details

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Description Thomas Beutin 2019-03-11 13:31:41 UTC
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/timestamps.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/tslibs/timestamps.cpython-36m-x86_64-linux-gnu.so
/mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o: file not recognized: File truncated
collect2: error: ld returned 1 exit status
x86_64-pc-linux-gnu-gcc -march=sandybridge -fomit-frame-pointer -O2 -pipe -fPIC -Ipandas/_libs/tslibs/src -Ipandas/_libs/tslibs -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c pandas/_libs/tslibs/src/datetime/np_datetime_strings.c -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -Wno-unused-function
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/strptime.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/tslibs/strptime.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -march=sandybridge -fomit-frame-pointer -O2 -pipe -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c pandas/_libs/src/parser/tokenizer.c -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/src/parser/tokenizer.o -Wno-unused-function
x86_64-pc-linux-gnu-gcc -march=sandybridge -fomit-frame-pointer -O2 -pipe -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -Ipandas/_libs/tslibs/src -Ipandas/_libs/tslibs -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c pandas/_libs/tslibs/src/datetime/np_datetime.c -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o -Wno-unused-function
x86_64-pc-linux-gnu-gcc -march=sandybridge -fomit-frame-pointer -O2 -pipe -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c pandas/_libs/src/parser/io.c -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/src/parser/io.o -Wno-unused-function
x86_64-pc-linux-gnu-gcc -march=sandybridge -fomit-frame-pointer -O2 -pipe -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -Ipandas/_libs/tslibs/src -Ipandas/_libs/tslibs -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c pandas/_libs/tslibs/src/datetime/np_datetime_strings.c -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -Wno-unused-function
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/hashtable.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/hashtable.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/parsers.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/src/parser/tokenizer.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/src/parser/io.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/parsers.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/index.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime.o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/index.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/groupby.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/groupby.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/sparse.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/sparse.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/window.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/window.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/algos.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/algos.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/interval.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/interval.cpython-36m-x86_64-linux-gnu.so
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=sandybridge -fomit-frame-pointer -O2 -pipe /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/temp.linux-x86_64-3.6/pandas/_libs/join.o -L/usr/lib64 -lpython3.6m -o /mnt/gentoo/tmp/portage/dev-python/pandas-0.24.1/work/pandas-0.24.1-python3_6/lib/pandas/_libs/join.cpython-36m-x86_64-linux-gnu.so
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1
 * ERROR: dev-python/pandas-0.24.1::gentoo failed (compile phase):
 *   (no error message)


I'll attach all build*.log files.

emerge --info '=dev-python/pandas-0.24.1::gentoo' will be attached, too.
Comment 1 Thomas Beutin 2019-03-11 13:32:04 UTC
Created attachment 568570 [details]
build.log
Comment 2 Thomas Beutin 2019-03-11 13:32:32 UTC
Created attachment 568572 [details]
build-python2_7.log
Comment 3 Thomas Beutin 2019-03-11 13:32:54 UTC
Created attachment 568574 [details]
build-python3_6.log
Comment 4 Thomas Beutin 2019-03-11 13:33:12 UTC
Created attachment 568576 [details]
emerge-info.log
Comment 5 Andrew 2020-02-24 08:26:07 UTC
I've got exactly the same error with pandas-0.24.2.
Comment 6 Larry the Git Cow gentoo-dev 2020-03-09 12:44:58 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8b2102355a1bf6bea86984f5194f4bbfa6aff465

commit 8b2102355a1bf6bea86984f5194f4bbfa6aff465
Author:     Benda Xu <heroxbd@gentoo.org>
AuthorDate: 2020-03-09 12:39:12 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2020-03-09 12:44:48 +0000

    dev-python/pandas: version bump.
    
    upstream have fixed the parallel issue by forcing the build system to
    be mostly serial.
    
    3 s3 tests fails because dev-python/s3fs is not new enough (>=0.3).
    
    drop amd64-linux x86-linux keywords because the dependencies are not
    met.
    
    Reported-By: Thomas Beutin, Andrew
    Closes: https://bugs.gentoo.org/680036
    Package-Manager: Portage-2.3.88, Repoman-2.3.18
    Signed-off-by: Benda Xu <heroxbd@gentoo.org>

 dev-python/pandas/Manifest            |   1 +
 dev-python/pandas/pandas-1.0.1.ebuild | 164 ++++++++++++++++++++++++++++++++++
 2 files changed, 165 insertions(+)