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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Compilation issues #117

Open MrDotOne opened 7 months ago

MrDotOne commented 7 months ago

Trying to compile from source the latest version pf PennCNV (1.0.5) on an HPC where i have gcc/8.5.0 and perl/5.14.2. I get a linker error, and i am unsure how to resolve it:

[root@cc-dclrilog63 kext]# make gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm_wrap.o khmm_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm.o khmm.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o kc.o kc.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmmDev.o khmmDev.c gcc -shared -o khmm.so khmm_wrap.o khmm.o kc.o khmmDev.o perl -MExtUtils::Embed -e ldopts -fPIC /usr/bin/ld: cannot find -lnsl collect2: error: ld returned 1 exit status make: *** [Makefile:16: khmm.so] Error 1

Any thoughts would be appreciated.

kaichop commented 7 months ago

can you try install libnsl, like in https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl

On Tue, Mar 5, 2024 at 2:19 PM MrDotOne @.***> wrote:

Trying to compile from source the latest version pf PennCNV (1.0.5) on an HPC where i have gcc/8.5.0 and perl/5.14.2. I get a linker error, and i am unsure how to resolve it:

@. kext]# make gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm_wrap.o khmm_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm.o khmm.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o kc.o kc.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmmDev.o khmmDev.c gcc -shared -o khmm.so khmm_wrap.o khmm.o kc.o khmmDev.o perl -MExtUtils::Embed -e ldopts -fPIC /usr/bin/ld: cannot find -lnsl collect2: error: ld returned 1 exit status make: [Makefile:16: khmm.so] Error 1

Any thoughts would be appreciated.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/117, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

MrDotOne commented 7 months ago

It is already installed:

rpm -qa | grep libnsl libnsl2-1.2.0-2.20180605git4a062cf.el8.i686 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libnsl-2.28-211.el8.x86_64

From: Kai Wang @.> Sent: Tuesday, March 5, 2024 3:14 PM To: WGLab/PennCNV @.> Cc: Weiner, Michael @.>; Author @.> Subject: [EXT] Re: [WGLab/PennCNV] Compilation issues (Issue #117)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

can you try install libnsl, like in https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnslhttps://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl

On Tue, Mar 5, 2024 at 2:19 PM MrDotOne @.***> wrote:

Trying to compile from source the latest version pf PennCNV (1.0.5) on an HPC where i have gcc/8.5.0 and perl/5.14.2. I get a linker error, and i am unsure how to resolve it:

@. kext]# make gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm_wrap.o khmm_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm.o khmm.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o kc.o kc.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmmDev.o khmmDev.c gcc -shared -o khmm.sohttp://khmm.so khmm_wrap.o khmm.o kc.o khmmDev.o perl -MExtUtils::Embed -e ldopts -fPIC /usr/bin/ld: cannot find -lnsl collect2: error: ld returned 1 exit status make: [Makefile:16: khmm.sohttp://khmm.so] Error 1

Any thoughts would be appreciated.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/117<https://github.com/WGLab/PennCNV/issues/117>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI<https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI> . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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kaichop commented 7 months ago

Try install libnsl2-devel which gives header file and library file for gcc to compile together into a shared library.

On Tue, Mar 5, 2024 at 3:16 PM MrDotOne @.***> wrote:

It is already installed:

rpm -qa | grep libnsl libnsl2-1.2.0-2.20180605git4a062cf.el8.i686 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libnsl-2.28-211.el8.x86_64

From: Kai Wang @.> Sent: Tuesday, March 5, 2024 3:14 PM To: WGLab/PennCNV @.> Cc: Weiner, Michael @.>; Author @.> Subject: [EXT] Re: [WGLab/PennCNV] Compilation issues (Issue #117)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

can you try install libnsl, like in

https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl < https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl>

On Tue, Mar 5, 2024 at 2:19 PM MrDotOne @.***> wrote:

Trying to compile from source the latest version pf PennCNV (1.0.5) on an HPC where i have gcc/8.5.0 and perl/5.14.2. I get a linker error, and i am unsure how to resolve it:

@. kext]# make gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm_wrap.o khmm_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm.o khmm.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o kc.o kc.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmmDev.o khmmDev.c gcc -shared -o khmm.sohttp://khmm.so khmm_wrap.o khmm.o kc.o khmmDev.o perl -MExtUtils::Embed -e ldopts -fPIC /usr/bin/ld: cannot find -lnsl collect2: error: ld returned 1 exit status make: [Makefile:16: khmm.sohttp://khmm.so] Error 1

Any thoughts would be appreciated.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/117< https://github.com/WGLab/PennCNV/issues/117>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI < https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI>>

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Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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MrDotOne commented 7 months ago

Got it.

From: Kai Wang @.> Sent: Tuesday, March 5, 2024 3:21 PM To: WGLab/PennCNV @.> Cc: Weiner, Michael @.>; Author @.> Subject: [EXT] Re: [WGLab/PennCNV] Compilation issues (Issue #117)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

Try install libnsl2-devel which gives header file and library file for gcc to compile together into a shared library.

On Tue, Mar 5, 2024 at 3:16 PM MrDotOne @.***> wrote:

It is already installed:

rpm -qa | grep libnsl libnsl2-1.2.0-2.20180605git4a062cf.el8.i686 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libnsl-2.28-211.el8.x86_64

From: Kai Wang @.> Sent: Tuesday, March 5, 2024 3:14 PM To: WGLab/PennCNV @.> Cc: Weiner, Michael @.>; Author @.> Subject: [EXT] Re: [WGLab/PennCNV] Compilation issues (Issue #117)

PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to @.**@.?subject=Report%20a%20Suspicious%20Email>

can you try install libnsl, like in

https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnslhttps://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl < https://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnslhttps://unix.stackexchange.com/questions/627517/centos-8-usr-bin-ld-cannot-find-lnsl>

On Tue, Mar 5, 2024 at 2:19 PM MrDotOne @.***> wrote:

Trying to compile from source the latest version pf PennCNV (1.0.5) on an HPC where i have gcc/8.5.0 and perl/5.14.2. I get a linker error, and i am unsure how to resolve it:

@. kext]# make gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm_wrap.o khmm_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmm.o khmm.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o kc.o kc.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -O -c -o khmmDev.o khmmDev.c gcc -shared -o khmm.sohttp://khmm.sohttp://khmm.so<http://khmm.so> khmm_wrap.o khmm.o kc.o khmmDev.o perl -MExtUtils::Embed -e ldopts -fPIC /usr/bin/ld: cannot find -lnsl collect2: error: ld returned 1 exit status make: [Makefile:16: khmm.sohttp://khmm.sohttp://khmm.so<http://khmm.so>] Error 1

Any thoughts would be appreciated.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/117<https://github.com/WGLab/PennCNV/issues/117< https://github.com/WGLab/PennCNV/issues/117https://github.com/WGLab/PennCNV/issues/117>>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMIhttps://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI < https://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMIhttps://github.com/notifications/unsubscribe-auth/ABNG3OAMVA365YPKIQ4ACJLYWYLFBAVCNFSM6AAAAABEHXBMS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DSOJYGE4TSMI>>

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