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spundhir / PARE

PARE: a computational method to Predict Active Regulatory Elements
http://spundhir.github.io/PARE
GNU General Public License v3.0
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error /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC #1

Closed crazyhottommy closed 8 years ago

crazyhottommy commented 8 years ago

Hi, I got an error when running it on our HPC cluster. what's wrong?

Thanks

/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
/risapps/rhel6/R/3.1.0/lib64/R/bin/exec/R: symbol lookup error: /risapps/rhel6/python/2.7.6/anaconda/lib/libreadline.so.6: undefined symbol: PC
/scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/checkPrerequisite: line 35: [: ==: unary operator expected
Can't locate Statistics/Basic.pm in @INC (@INC contains: /opt/moab/lib/perl5 /opt/moab/lib/perl5 /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/sha
BEGIN failed--compilation aborted at /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/findNFRAll.pl line 24.
Can't locate Statistics/Basic.pm in @INC (@INC contains: /opt/moab/lib/perl5 /opt/moab/lib/perl5 /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/sha
BEGIN failed--compilation aborted at /scratch/genomic_med/mtang1/softwares/spundhir-PARE-63c74f7/bin/commonNFR.pl line 24.
gzip: mybam-PARE-NFR/analysis/my.bam.All.nfr.gz: No such file or directory
mybam-PARE-NFR/analysis/my.bam.All.nfr: No such file or directory
cat: mybam-PARE-NFR/analysis/rep0/my.bam.tmp*: No such file or directory
cat: mybam-PARE-NFR/analysis/rep0/my.bam.tmp*: No such file or directory
my.sorted.bedGraph is not case-sensitive sorted at line 29707282.  Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C,  or bedSort and try again
my_pare.e536160 (END)
spundhir commented 8 years ago

Hi,

Seems to me a problem with R installation (see here https://stat.ethz.ch/pipermail/r-sig-debian/2010-August/001374.html).

This is leading to "[: ==: unary operator expected" error in PARE script, which I accept should not be thrown. I have made a change in the script (checkPrequisite) to quit more nicely.

HTH

crazyhottommy commented 8 years ago

Thanks. It was solved.