trouble installing PennCNV

[LouiseT]

Hi
I am trying to install PennCNV on mac os x 10.8.
The text file is not running so I am trying to re-compile acording to instructions on homepage: http://www.openbioinformatics.org/pe...#_Toc214817843

after typing make I get this error massage:
khmm_wrap.c:288:20: error: string.h: No such file or directory

However string.h is in this folder:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/string.h

which is permanently part of my PATH: $echo $PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/

So what is going wrong?

[shruti]

Hi
I am also trying to install PennCNV in mac (10.6.8)
Was wondering if you were able to install it.
I modified the Makefile as is given on PennCNV site.
on running make I don't get any error but warning

kc.c: In function ‘kcwarn’:
kc.c:200: warning: format not a string literal and no format arguments

However when I run ./detect_cnv.pl
I get the error

PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at kext/khmm.pm line 8
Compilation failed in require at ./detect_cnv.pl line 10.

PennCNV compilation error: Your system architecture is 'darwin-thread-multi-2level', which is not compatible with pre-compiled executables in PennCNV package.
PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.

Not sure what I should check for.

Would be great if you could help me.

Best
shruti

[GenoMax]

It appears that khmm.pm is not being loaded because the directory that has that file is not included in the @INC path.

You can try one of the two methods mentioned at the beginning in this post.

[Karoon]

Same error

Hi
I encountered the same error as "shruti".

$ ./detect_cnv.pl
PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /./kext/ /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at khmm.pm line 8
Compilation failed in require at ./detect_cnv.pl line 10.

PennCNV compilation error: Your system architecture is 'cygwin-thread-multi', which is not compatible with pre-compiled executables in PennCNV package.
PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.

I tried to fix it by adding
use lib "./kext";
use khmm;
in the detect_cnv.pl as suggested in perlmonk, but it didn't work.

Is anyone who did overcome the error?
Thank you.

[GenoMax]

Can you try providing full directory path for "ktext" instead of just ./ for the "use lib" directive?

[Karoon]

Thank you for your reply, GenoMax

This time I have inserted these two lines in detect_cnv.pl
...
BEGIN {($_=$0)=~s{[^\\\/]+$}{};$_||="./"}
use lib $_, $_."kext";
use lib "/cygdrive/c/program files/affymetrix/gw6cnv/kext"; <---here
use khmm; <--- and here
eval {
require "khmm.pm";
};
...

and the result is slightly different but much the same:
$ ./detect_cnv.pl
Can't locate loadable object for module khmm in @INC (@INC contains: /cygdrive/c/program files/affymetrix/gw6cnv/kext ./ ./kext /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at /cygdrive/c/program files/affymetrix/gw6cnv/kext/khmm.pm line 8
Compilation failed in require at ./detect_cnv.pl line 10.
BEGIN failed--compilation aborted at ./detect_cnv.pl line 10.

---
Is there anything wrong ?
( I am not a programming expert at all, as you see.)
Anyway I appreciate your comment very much.

Karoon
Bet Regards

[GenoMax]

I am not a cygwin expert but I think you may need to escape the space in "program files" name.

Try this:

use lib "/cygdrive/c/program\ files/affymetrix/gw6cnv/kext"

[Karoon]

Thank you, GenoMax.
I tried as suggested, but got much the same result
(inserted two lines in the same place in detect_cnv.pl):
---
$ ./detect_cnv.pl
Can't locate loadable object for module khmm in @INC (@INC contains: /cygdrive/c/program files/affymetrix/gw6cnv/kext ./ ./kext /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at /cygdrive/c/program files/affymetrix/gw6cnv/kext/khmm.pm line 8
Compilation failed in require at ./detect_cnv.pl line 10.
BEGIN failed--compilation aborted at ./detect_cnv.pl line 10.----
I am grateful if there are any more suggestions.
Thank you

Karoon
Best Regards

[GenoMax]

Have you already taken into account the instructions for PennCNV install for windows here: http://www.openbioinformatics.org/pe...#_Toc214817843

[Karoon]

Thank you GenoMax,
but I already saw the page and tried as instructed.
Maybe something is wrong with the Makefile, so I am going to check it again.


Karoon
Best Regards

[cicconella]

Hi, I have the same problem as you and even following the instructions here http://penncnv.openbioinformatics.or...#_Toc214817843 I cant solve it.

The same error occurs.

Any lights?

Thank you

[Karoon]

I managed to successfully install PennCNV

Hi cicconella,

I read the same webpage ( http://penncnv.openbioinformatics.or...#_Toc214817843 ) again and did exactly as instructed in "Compilation in Windows" section (a year ago).
That is, I installed MinGW and MSYS, and compiled from the sourcecodes. I don't know why it worked, but anyway I did exactly as the instruction in the webpage says.
I already installed PennCNV and finished analyses a year ago and do not remember well the details of installation. I am writing this answer looking back my programming note which was recorded at that time.

I appreciate GenoMax for kind answers.

Good luck,
Karoon

[shinvkuo]

Recently, I encountered the same questions in Linux. I solved the problem by following instructions from http://penncnv.openbioinformatics.or...on-from-source (Installation trouble shooting at the bottom of this page).
The related scripts how I solved it are as follows:
$ locate khmm.so
/home/biosoft/penncnv/kext/5.10.1/x86_64-linux-thread-multi/khmm.so
/home/biosoft/penncnv/kext/5.14.2/x86_64-linux-thread-multi/khmm.so
## Here, we could see that the compatiable perl versions for Linux (*.so) are 5.10.1 and 5.14.2. Thus, I used perlbrew to install the corresponding perl version.
$ wget -O - https://raw.githubusercontent.com/gu...rlbrew-install | sh
$ source ~/perl5/perlbrew/etc/bashrc
$ perlbrew install perl-5.14.2 --thread --multi
$ perlbrew use perl-5.14.2
$ cd /home/biosoft/penncnv/example && perl ../detect_cnv.pl -test -hmm example.hmm -pfb example.pfb -conf -log ex1.log -out ex1.rawcnv father.txt mother.txt offspring.txt ## Success without error!
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file ex1.log
NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from example.pfb ... Done with 93129 records
NOTICE: Reading LRR and BAF values for from father.txt ... Done with 93129 records in 4 chromosomes
NOTICE: Data from chromosome X will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from father.txt by 0.0221
NOTICE: Median-adjusting BAF values for all autosome markers from father.txt by 0.0029
NOTICE: quality summary for father.txt: LRR_mean=0.0027 LRR_median=0.0000 LRR_SD=0.1335 BAF_mean=0.5063 BAF_median=0.5000 BAF_SD=0.0390 BAF_DRIFT=0.000037 WF=0.0184 GCWF=0.0136
NOTICE: Reading LRR and BAF values for from mother.txt ... Done with 93129 records in 4 chromosomes
NOTICE: Data from chromosome X will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from mother.txt by -0.0199
NOTICE: Median-adjusting BAF values for all autosome markers from mother.txt by 0.0324
NOTICE: quality summary for mother.txt: LRR_mean=0.0039 LRR_median=0.0000 LRR_SD=0.1374 BAF_mean=0.5044 BAF_median=0.5000 BAF_SD=0.0418 BAF_DRIFT=0.000140 WF=0.0100 GCWF=0.0028
NOTICE: Reading LRR and BAF values for from offspring.txt ... Done with 93129 records in 4 chromosomes
NOTICE: Data from chromosome X will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from offspring.txt by -0.0087
NOTICE: Median-adjusting BAF values for all autosome markers from offspring.txt by 0.0260
NOTICE: quality summary for offspring.txt: LRR_mean=0.0028 LRR_median=0.0000 LRR_SD=0.1263 BAF_mean=0.5045 BAF_median=0.5000 BAF_SD=0.0429 BAF_DRIFT=0.000293 WF=-0.0171 GCWF=-0.0100
08:34:14 root@localhost /home/biosoft/penncnv/example
I think the solution for other platform like windows will be similar to this. Hope it help you all!

Good luck,
Xinwu Guo

[hyeonjipark]

Thank you GenoMax,
but I already saw the page and tried as instructed.
Maybe something is wrong with the Makefile, so I am going to check it again.


Karoon
Best Regards

What change the Makefile?
I try to install PennCNV in linux server, but again to again error. T.T

This error ......

hyeonji/src/PennCNV-1.0.3$ perl detect_cnv.pl
PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /data/hyeonji/src/mirdeep2_0_0_7/lib/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at kext/khmm.pm line 11.
Compilation failed in require at detect_cnv.pl line 10.

PennCNV compilation error: Your system architecture is 'x86_64-linux-gnu-thread-multi', which is not compatible with pre-compiled executables in PennCNV package.
PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.

I guess that probelm is no change Makefile. How solved you?

Thanks,
Hyeonji