mzR.so: undefined symbol: _intel_fast_memcpy

[lhedjazi]

Dear all,
I am unable to install mzR package due to "undefined symbol: _intel_fast_memcpy" . I am including the whole error and my sessionInfo() below. I have followed all the discussion about the issues with mzR and tried to re-install mzR in different ways (e.g. indicating the mirror site, from source) but the problem persists. I will be grateful to get some guidance on how to solve this issue.
Best regards,
Lyamine

** R
** inst
** preparing package for lazy loading
Creating a generic function for 'close' from package 'base' in package 'mzR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/san2/home/mqtlican/local/lib64/R/library/mzR/libs/mzR.so':
/san2/home/mqtlican/local/lib64/R/library/mzR/libs/mzR.so: undefined symbol: _intel_fast_memcpy
Error: loading failed
Execution halted

ERROR: loading failed

---

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.20.0

loaded via a namespace (and not attached):
[1] tools_3.2.1

[lgatto]

I assume this is the output from biocLite("mzR").

What compiler are you using?

[lhedjazi]

Thanks for your reply,
Yes this is the output of |biocLite("mzR") but I tried also to install
previous versions and also from source: same error.|
Using compiler gcc version 4.3.4
I am trying to run it on a cluster on which I don't have root access.

Many thanks,
Lyamine

Le 20/10/2015 12:36, Laurent Gatto a écrit :

I assume this is the output from |biocLite("mzR")|.

What compiler are you using?

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ICAN Institute for Cardiometabolism And Nutrition
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75013 Paris - France
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[lhedjazi]

Thanks for your reply,
Using compiler gcc version 4.3.4
I am trying to run it on a cluster on which I don't have root access.

Many thanks,
Lyamine

Le 20/10/2015 12:36, Laurent Gatto a écrit :

I assume this is the output from |biocLite("mzR")|.

What compiler are you using?

—
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#28 (comment)
Bug from
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Lyamine Hedjazi (PhD)
ICAN Institute for Cardiometabolism And Nutrition
Pierre & Marie Curie Medical School
75013 Paris - France
tel: +33 (0)1 40 77 98 51
ICAN conference series http://ican-institute.org/

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[lgatto]

Here are some hopefully useful instructions I found that might be relevant

The following is only an issue if you are not linking against the standard Intel libraries, either as a result of specifying -nostdlib on the command line or as a result of calling the linker directly rather than from the Intel C++ Compiler driver.

The Intel C++ Compiler uses two routines _intel_fast_memcpy and _intel_fast_memset to perform memcpy and memset operations that are not macro expanded to __builtin_memcpy and __builtin_memset in the source code. These are found in libirc. If you use the gcc compiler to link your application or if you directly call the linker, ld, you might find these unresolved symbols. For this reason, Intel recomends using the Intel C++ Compiler for linking, using the same compiler options used during the compilation phase. However, if you see these as undefined externals, either add -lirc to your link line, or change your includes so that memcpy and memset will be macro expanded to the builtin forms and recompile. The Intel C++ Compiler for IA-32 based applications calls a routine intel_proc_init from the main routine of any program to ensure that the processor is correctly set up. This routine is also found in libirc. These routines used further entry points from glibc, so -lirc needs to be placed before -lc on your command line.

This link also suggest to use -lintlc.

I would suggest you get in touch with your sysadmin.

[lhedjazi]

Thanks a lot for your help.
I will contact my sysadmin with your suggestions.

Best,
Lyamine

Le 20/10/2015 13:03, Laurent Gatto a écrit :

Here are some hopefully useful instructions I found that might be relevant

The following is only an issue if you are not linking against the
standard Intel libraries, either as a result of specifying
-nostdlib on the command line or as a result of calling the linker
directly rather than from the Intel C++ Compiler driver.

The Intel C++ Compiler uses two routines _intel_fast_memcpy and
_intel_fast_memset to perform memcpy and memset operations that
are not macro expanded to __builtin_memcpy and __builtin_memset in
the source code. These are found in libirc. If you use the gcc
compiler to link your application or if you directly call the
linker, ld, you might find these unresolved symbols. For this
reason, Intel recomends using the Intel C++ Compiler for linking,
using the same compiler options used during the compilation phase.
However, if you see these as undefined externals, either add -lirc
to your link line, or change your includes so that memcpy and
memset will be macro expanded to the builtin forms and recompile.
The Intel C++ Compiler for IA-32 based applications calls a
routine intel_proc_init from the main routine of any program to
ensure that the processor is correctly set up. This routine is
also found in libirc. These routines used further entry points
from glibc, so -lirc needs to be pl aced before -lc on your
command line.

This link
http://hpchcl.blogspot.co.uk/2013/12/how-to-resolve-undefined-reference-to.html
also suggest to use |-lintlc|.

I would suggest you get in touch with your sysadmin.

—
Reply to this email directly or view it on GitHub
#28 (comment)
Bug from
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Lyamine Hedjazi (PhD)
ICAN Institute for Cardiometabolism And Nutrition
Pierre & Marie Curie Medical School
75013 Paris - France
tel: +33 (0)1 40 77 98 51
ICAN conference series http://ican-institute.org/

---

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https://www.avast.com/antivirus

[lhedjazi]

Thanks a lot for your help.
I will contact my sysadmin with your suggestions.

Best,
Lyamine

Le 20/10/2015 13:03, Laurent Gatto a écrit :

Here are some hopefully useful instructions I found that might be relevant

The following is only an issue if you are not linking against the
standard Intel libraries, either as a result of specifying
-nostdlib on the command line or as a result of calling the linker
directly rather than from the Intel C++ Compiler driver.

The Intel C++ Compiler uses two routines _intel_fast_memcpy and
_intel_fast_memset to perform memcpy and memset operations that
are not macro expanded to __builtin_memcpy and __builtin_memset in
the source code. These are found in libirc. If you use the gcc
compiler to link your application or if you directly call the
linker, ld, you might find these unresolved symbols. For this
reason, Intel recomends using the Intel C++ Compiler for linking,
using the same compiler options used during the compilation phase.
However, if you see these as undefined externals, either add -lirc
to your link line, or change your includes so that memcpy and
memset will be macro expanded to the builtin forms and recompile.
The Intel C++ Compiler for IA-32 based applications calls a
routine intel_proc_init from the main routine of any program to
ensure that the processor is correctly set up. This routine is
also found in libirc. These routines used further entry points
from glibc, so -lirc needs to be pl aced before -lc on your
command line.

This link
http://hpchcl.blogspot.co.uk/2013/12/how-to-resolve-undefined-reference-to.html
also suggest to use |-lintlc|.

I would suggest you get in touch with your sysadmin.

—
Reply to this email directly or view it on GitHub
#28 (comment)
Bug from
https://github.com/notifications/beacon/AKpGwfZeDXHoTBcds4ex34Ztcz_2azsKks5o9hcUgaJpZM4GSBoa.gif

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Lyamine Hedjazi (PhD)
ICAN Institute for Cardiometabolism And Nutrition
Pierre & Marie Curie Medical School
75013 Paris - France
tel: +33 (0)1 40 77 98 51
ICAN conference series http://ican-institute.org/

---

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https://www.avast.com/antivirus

[lgatto]

Closing for now. Please re-open if necessary.