Hi all,
I'm adding an package (scanpy) to our Python-3.6.3-foss-2017b.eb:
('scanpy', '1.4.3', {
'source_urls': ['https://pypi.python.org/packages/source/s/scanpy'],
'checksums': [
'2ae88098c6caa403e2a83eb8ea0b8971f9fada53385f0f5ccda4f34fce1590cc', #
scanpy-1.4.3..tar.gz ],
}),
But the compilation fails with:
[...]c-blosc/internal-complibs/zstd-1.3.8/legacy/zstd_v01.c:1882:35:
warning: �dumpsLength’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
seqState.dumpsEnd = dumps +
dumpsLength;/apps/prod/easybuild/sl7.x86_64/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold:
error: cannot find
-l-lm/apps/prod/easybuild/sl7.x86_64/software/binutils/2.28-GCCcore-6.4.0/bin/ld.gold:
error: cannot find -l-lpthread
collect2: error: ld returned 1 exit status* Using Python 3.6.3
(default, Jul 18 2019, 08:51:15)* USE_PKGCONFIG: True* Found HDF5
headers at
``/apps/prod/easybuild/sl7.x86_64/software/HDF5/1.10.1-foss-2017b/include``,
library at
``/apps/prod/easybuild/sl7.x86_64/software/HDF5/1.10.1-foss-2017b/lib``.*
Found LZO 2 headers at
``/apps/prod/easybuild/sl7.x86_64/software/LZO/2.10-GCCcore-6.4.0/include``,
the library is located in the standard system search dirs.* Skipping
detection of LZO 1 since LZO 2 has already been found.* Found bzip2
headers at
``/apps/prod/easybuild/sl7.x86_64/software/bzip2/1.0.6-GCCcore-6.4.0/include``,
library at ``/usr/lib64``.* Could not find blosc headers and library;
using internal sources.
SSE2 detected and enabled
AVX2 detected and enabled
error: Setup script exited with error: command 'g++' failed with exit status 1
This was already ask/answered in the mailing list a while ago:
> > /sysapps/cluster/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold:
error: cannot find -lc
> > /sysapps/cluster/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold:
error: cannot find -lm
> > /sysapps/cluster/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold:
error: cannot find -lpthread
> > /lib/../lib64/crt1.o(.text+0x12): error: undefined reference to
'__libc_csu_fini'
> > /lib/../lib64/crt1.o(.text+0x19): error: undefined reference to
'__libc_csu_init'
> > /lib/../lib64/crt1.o(.text+0x25): error: undefined reference to
'__libc_start_main'
> > collect2: error: ld returned 1 exit status
> It seems like you don't have glibc-static installed on your system?
But in my case glibc-static IS installed.
I'm getting a little crazy trying to understand the problem, so I come here
to ask for help...
Anyone?
TIA,
Arnau
