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# 8  
Old 09-12-2014
Dear All,

Thank you for your reply. I deleted all the installed packages from mfold and tried to install afresh.

Untar the files in /usr/local

As a superuser, issued the following commands in sequence:

Code:
./configure --prefix=/usr/local

Code:
linux-oc9r:/usr/local/mfold-3.6 # make
make  all-recursive
make[1]: Entering directory `/usr/local/mfold-3.6'
Making all in src
make[2]: Entering directory `/usr/local/mfold-3.6/src'
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-distance.o `test -f 'distance.f' || echo './'`distance.f
/bin/sh: C: command not found
make[2]: [distance-distance.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpin.o `test -f 'bpin.f' || echo './'`bpin.f
/bin/sh: C: command not found
make[2]: [distance-bpin.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpsrch.o `test -f 'bpsrch.f' || echo './'`bpsrch.f
/bin/sh: C: command not found
make[2]: [distance-bpsrch.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o distance distance-distance.o distance-bpin.o distance-bpsrch.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [distance] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct2bp-ct2bp.o `test -f 'ct2bp.f' || echo './'`ct2bp.f
/bin/sh: C: command not found
make[2]: [ct2bp-ct2bp.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct2bp ct2bp-ct2bp.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ct2bp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct_compare-ct_compare.o `test -f 'ct_compare.f' || echo './'`ct_compare.f
/bin/sh: C: command not found
make[2]: [ct_compare-ct_compare.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct_compare ct_compare-ct_compare.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ct_compare] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o efn-efn.o `test -f 'efn.f' || echo './'`efn.f
/bin/sh: C: command not found
make[2]: [efn-efn.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o efn efn-efn.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [efn] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-newtemp.o `test -f 'newtemp.f' || echo './'`newtemp.f
/bin/sh: C: command not found
make[2]: [newtemp-newtemp.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-ion.o `test -f 'ion.f' || echo './'`ion.f
/bin/sh: C: command not found
make[2]: [newtemp-ion.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [newtemp-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none      -o newtemp newtemp-newtemp.o newtemp-ion.o newtemp-dc.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [newtemp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o scorer-scorer.o `test -f 'scorer.f' || echo './'`scorer.f
/bin/sh: C: command not found
make[2]: [scorer-scorer.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o scorer scorer-scorer.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [scorer] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o auxgen-auxgen.o `test -f 'auxgen.f' || echo './'`auxgen.f
/bin/sh: C: command not found
make[2]: [auxgen-auxgen.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o auxgen auxgen-auxgen.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [auxgen] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2plot-sav2plot.o `test -f 'sav2plot.f' || echo './'`sav2plot.f
/bin/sh: C: command not found
make[2]: [sav2plot-sav2plot.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2plot sav2plot-sav2plot.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [sav2plot] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2p_num-sav2p-num.o `test -f 'sav2p-num.f' || echo './'`sav2p-num.f
/bin/sh: C: command not found
make[2]: [sav2p_num-sav2p-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2p_num sav2p_num-sav2p-num.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [sav2p_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o h_num-h-num.o `test -f 'h-num.f' || echo './'`h-num.f
/bin/sh: C: command not found
make[2]: [h_num-h-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o h_num h_num-h-num.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [h_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ss_count-ss-count.o `test -f 'ss-count.f' || echo './'`ss-count.f
/bin/sh: C: command not found
make[2]: [ss_count-ss-count.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ss_count ss_count-ss-count.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ss_count] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm-add-dHdSTm.o `test -f 'add-dHdSTm.f' || echo './'`add-dHdSTm.f
/bin/sh: C: command not found
make[2]: [add_dHdSTm-add-dHdSTm.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm add_dHdSTm-add-dHdSTm.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [add_dHdSTm] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-main.o `test -f 'main.f' || echo './'`main.f
/bin/sh: C: command not found
make[2]: [nafold-main.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-rna.o `test -f 'rna.f' || echo './'`rna.f
/bin/sh: C: command not found
make[2]: [nafold-rna.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-misc.o `test -f 'misc.f' || echo './'`misc.f
/bin/sh: C: command not found
make[2]: [nafold-misc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-efiles.o `test -f 'efiles.f' || echo './'`efiles.f
/bin/sh: C: command not found
make[2]: [nafold-efiles.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-sort.o `test -f 'sort.f' || echo './'`sort.f
/bin/sh: C: command not found
make[2]: [nafold-sort.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [nafold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-bits-gnu.o `test -f 'bits-gnu.f' || echo './'`bits-gnu.f
/bin/sh: C: command not found
make[2]: [nafold-bits-gnu.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-formid.o `test -f 'formid.f' || echo './'`formid.f
/bin/sh: C: command not found
make[2]: [nafold-formid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[2]: [nafold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o nafold  nafold-main.o nafold-rna.o nafold-misc.o nafold-efiles.o nafold-sort.o nafold-dc.o nafold-bits-gnu.o nafold-formid.o nafold-multid.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [nafold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-quik.o `test -f 'quik.f' || echo './'`quik.f
/bin/sh: C: command not found
make[2]: [quikfold-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-rna-quik.o `test -f 'rna-quik.f' || echo './'`rna-quik.f
/bin/sh: C: command not found
make[2]: [quikfold-rna-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-misc-quik.o `test -f 'misc-quik.f' || echo './'`misc-quik.f
/bin/sh: C: command not found
make[2]: [quikfold-misc-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [quikfold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[2]: [quikfold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o quikfold quikfold-quik.o quikfold-rna-quik.o quikfold-misc-quik.o quikfold-dc.o quikfold-multid.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [quikfold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm2-add-dHdSTm2.o `test -f 'add-dHdSTm2.f' || echo './'`add-dHdSTm2.f
/bin/sh: C: command not found
make[2]: [add_dHdSTm2-add-dHdSTm2.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm2 add_dHdSTm2-add-dHdSTm2.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [add_dHdSTm2] Error 127 (ignored)
make[2]: Leaving directory `/usr/local/mfold-3.6/src'
Making all in c++
make[2]: Entering directory `/usr/local/mfold-3.6/c++'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/usr/local/mfold-3.6/c++'
Making all in dat
make[2]: Entering directory `/usr/local/mfold-3.6/dat'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/usr/local/mfold-3.6/dat'
Making all in scripts
make[2]: Entering directory `/usr/local/mfold-3.6/scripts'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/usr/local/mfold-3.6/scripts'
make[2]: Entering directory `/usr/local/mfold-3.6'
make[2]: Leaving directory `/usr/local/mfold-3.6'
make[1]: Leaving directory `/usr/local/mfold-3.6'

Code:
linux-oc9r:/usr/local/mfold-3.6 # make install
Making install in src                                                                                                                                                                   
make[1]: Entering directory `/usr/local/mfold-3.6/src'                                                                                                                                  
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-distance.o `test -f 'distance.f' || echo './'`distance.f                                                           
/bin/sh: C: command not found                                                                                                                                                           
make[1]: [distance-distance.o] Error 127 (ignored)                                                                                                                                      
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpin.o `test -f 'bpin.f' || echo './'`bpin.f                                                                       
/bin/sh: C: command not found                                                                                                                                                           
make[1]: [distance-bpin.o] Error 127 (ignored)                                                                                                                                          
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpsrch.o `test -f 'bpsrch.f' || echo './'`bpsrch.f                                                                 
/bin/sh: C: command not found                                                                                                                                                           
make[1]: [distance-bpsrch.o] Error 127 (ignored)                                                                                                                                        
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o distance distance-distance.o distance-bpin.o distance-bpsrch.o  -lpng -lm                                                    
make[1]: C: Command not found                                                                                                                                                           
make[1]: [distance] Error 127 (ignored)                                                                                                                                                 
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct2bp-ct2bp.o `test -f 'ct2bp.f' || echo './'`ct2bp.f                                                                       
/bin/sh: C: command not found                                                                                                                                                           
make[1]: [ct2bp-ct2bp.o] Error 127 (ignored)                                                                                                                                            
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct2bp ct2bp-ct2bp.o  -lpng -lm                                                                                               
make[1]: C: Command not found
make[1]: [ct2bp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct_compare-ct_compare.o `test -f 'ct_compare.f' || echo './'`ct_compare.f
/bin/sh: C: command not found
make[1]: [ct_compare-ct_compare.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct_compare ct_compare-ct_compare.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [ct_compare] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o efn-efn.o `test -f 'efn.f' || echo './'`efn.f
/bin/sh: C: command not found
make[1]: [efn-efn.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o efn efn-efn.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [efn] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-newtemp.o `test -f 'newtemp.f' || echo './'`newtemp.f
/bin/sh: C: command not found
make[1]: [newtemp-newtemp.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-ion.o `test -f 'ion.f' || echo './'`ion.f
/bin/sh: C: command not found
make[1]: [newtemp-ion.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[1]: [newtemp-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none      -o newtemp newtemp-newtemp.o newtemp-ion.o newtemp-dc.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [newtemp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o scorer-scorer.o `test -f 'scorer.f' || echo './'`scorer.f
/bin/sh: C: command not found
make[1]: [scorer-scorer.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o scorer scorer-scorer.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [scorer] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o auxgen-auxgen.o `test -f 'auxgen.f' || echo './'`auxgen.f
/bin/sh: C: command not found
make[1]: [auxgen-auxgen.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o auxgen auxgen-auxgen.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [auxgen] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2plot-sav2plot.o `test -f 'sav2plot.f' || echo './'`sav2plot.f
/bin/sh: C: command not found
make[1]: [sav2plot-sav2plot.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2plot sav2plot-sav2plot.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [sav2plot] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2p_num-sav2p-num.o `test -f 'sav2p-num.f' || echo './'`sav2p-num.f
/bin/sh: C: command not found
make[1]: [sav2p_num-sav2p-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2p_num sav2p_num-sav2p-num.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [sav2p_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o h_num-h-num.o `test -f 'h-num.f' || echo './'`h-num.f
/bin/sh: C: command not found
make[1]: [h_num-h-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o h_num h_num-h-num.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [h_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ss_count-ss-count.o `test -f 'ss-count.f' || echo './'`ss-count.f
/bin/sh: C: command not found
make[1]: [ss_count-ss-count.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ss_count ss_count-ss-count.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [ss_count] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm-add-dHdSTm.o `test -f 'add-dHdSTm.f' || echo './'`add-dHdSTm.f
/bin/sh: C: command not found
make[1]: [add_dHdSTm-add-dHdSTm.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm add_dHdSTm-add-dHdSTm.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [add_dHdSTm] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-main.o `test -f 'main.f' || echo './'`main.f
/bin/sh: C: command not found
make[1]: [nafold-main.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-rna.o `test -f 'rna.f' || echo './'`rna.f
/bin/sh: C: command not found
make[1]: [nafold-rna.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-misc.o `test -f 'misc.f' || echo './'`misc.f
/bin/sh: C: command not found
make[1]: [nafold-misc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-efiles.o `test -f 'efiles.f' || echo './'`efiles.f
/bin/sh: C: command not found
make[1]: [nafold-efiles.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-sort.o `test -f 'sort.f' || echo './'`sort.f
/bin/sh: C: command not found
make[1]: [nafold-sort.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[1]: [nafold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-bits-gnu.o `test -f 'bits-gnu.f' || echo './'`bits-gnu.f
/bin/sh: C: command not found
make[1]: [nafold-bits-gnu.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-formid.o `test -f 'formid.f' || echo './'`formid.f
/bin/sh: C: command not found
make[1]: [nafold-formid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[1]: [nafold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o nafold  nafold-main.o nafold-rna.o nafold-misc.o nafold-efiles.o nafold-sort.o nafold-dc.o nafold-bits-gnu.o nafold-formid.o nafold-multid.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [nafold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-quik.o `test -f 'quik.f' || echo './'`quik.f
/bin/sh: C: command not found
make[1]: [quikfold-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-rna-quik.o `test -f 'rna-quik.f' || echo './'`rna-quik.f
/bin/sh: C: command not found
make[1]: [quikfold-rna-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-misc-quik.o `test -f 'misc-quik.f' || echo './'`misc-quik.f
/bin/sh: C: command not found
make[1]: [quikfold-misc-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[1]: [quikfold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[1]: [quikfold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o quikfold quikfold-quik.o quikfold-rna-quik.o quikfold-misc-quik.o quikfold-dc.o quikfold-multid.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [quikfold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm2-add-dHdSTm2.o `test -f 'add-dHdSTm2.f' || echo './'`add-dHdSTm2.f
/bin/sh: C: command not found
make[1]: [add_dHdSTm2-add-dHdSTm2.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm2 add_dHdSTm2-add-dHdSTm2.o  -lpng -lm 
make[1]: C: Command not found
make[1]: [add_dHdSTm2] Error 127 (ignored)
make[2]: Entering directory `/usr/local/mfold-3.6/src'
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-distance.o `test -f 'distance.f' || echo './'`distance.f
/bin/sh: C: command not found
make[2]: [distance-distance.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpin.o `test -f 'bpin.f' || echo './'`bpin.f
/bin/sh: C: command not found
make[2]: [distance-bpin.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o distance-bpsrch.o `test -f 'bpsrch.f' || echo './'`bpsrch.f
/bin/sh: C: command not found
make[2]: [distance-bpsrch.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o distance distance-distance.o distance-bpin.o distance-bpsrch.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [distance] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct2bp-ct2bp.o `test -f 'ct2bp.f' || echo './'`ct2bp.f
/bin/sh: C: command not found
make[2]: [ct2bp-ct2bp.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct2bp ct2bp-ct2bp.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ct2bp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ct_compare-ct_compare.o `test -f 'ct_compare.f' || echo './'`ct_compare.f
/bin/sh: C: command not found
make[2]: [ct_compare-ct_compare.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ct_compare ct_compare-ct_compare.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ct_compare] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o efn-efn.o `test -f 'efn.f' || echo './'`efn.f
/bin/sh: C: command not found
make[2]: [efn-efn.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o efn efn-efn.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [efn] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-newtemp.o `test -f 'newtemp.f' || echo './'`newtemp.f
/bin/sh: C: command not found
make[2]: [newtemp-newtemp.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-ion.o `test -f 'ion.f' || echo './'`ion.f
/bin/sh: C: command not found
make[2]: [newtemp-ion.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none    -c -o newtemp-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [newtemp-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none      -o newtemp newtemp-newtemp.o newtemp-ion.o newtemp-dc.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [newtemp] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o scorer-scorer.o `test -f 'scorer.f' || echo './'`scorer.f
/bin/sh: C: command not found
make[2]: [scorer-scorer.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o scorer scorer-scorer.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [scorer] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o auxgen-auxgen.o `test -f 'auxgen.f' || echo './'`auxgen.f
/bin/sh: C: command not found
make[2]: [auxgen-auxgen.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o auxgen auxgen-auxgen.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [auxgen] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2plot-sav2plot.o `test -f 'sav2plot.f' || echo './'`sav2plot.f
/bin/sh: C: command not found
make[2]: [sav2plot-sav2plot.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2plot sav2plot-sav2plot.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [sav2plot] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o sav2p_num-sav2p-num.o `test -f 'sav2p-num.f' || echo './'`sav2p-num.f
/bin/sh: C: command not found
make[2]: [sav2p_num-sav2p-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o sav2p_num sav2p_num-sav2p-num.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [sav2p_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o h_num-h-num.o `test -f 'h-num.f' || echo './'`h-num.f
/bin/sh: C: command not found
make[2]: [h_num-h-num.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o h_num h_num-h-num.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [h_num] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ss_count-ss-count.o `test -f 'ss-count.f' || echo './'`ss-count.f
/bin/sh: C: command not found
make[2]: [ss_count-ss-count.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o ss_count ss_count-ss-count.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [ss_count] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm-add-dHdSTm.o `test -f 'add-dHdSTm.f' || echo './'`add-dHdSTm.f
/bin/sh: C: command not found
make[2]: [add_dHdSTm-add-dHdSTm.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm add_dHdSTm-add-dHdSTm.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [add_dHdSTm] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-main.o `test -f 'main.f' || echo './'`main.f
/bin/sh: C: command not found
make[2]: [nafold-main.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-rna.o `test -f 'rna.f' || echo './'`rna.f
/bin/sh: C: command not found
make[2]: [nafold-rna.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-misc.o `test -f 'misc.f' || echo './'`misc.f
/bin/sh: C: command not found
make[2]: [nafold-misc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-efiles.o `test -f 'efiles.f' || echo './'`efiles.f
/bin/sh: C: command not found
make[2]: [nafold-efiles.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-sort.o `test -f 'sort.f' || echo './'`sort.f
/bin/sh: C: command not found
make[2]: [nafold-sort.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [nafold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-bits-gnu.o `test -f 'bits-gnu.f' || echo './'`bits-gnu.f
/bin/sh: C: command not found
make[2]: [nafold-bits-gnu.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-formid.o `test -f 'formid.f' || echo './'`formid.f
/bin/sh: C: command not found
make[2]: [nafold-formid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o nafold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[2]: [nafold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o nafold  nafold-main.o nafold-rna.o nafold-misc.o nafold-efiles.o nafold-sort.o nafold-dc.o nafold-bits-gnu.o nafold-formid.o nafold-multid.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [nafold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-quik.o `test -f 'quik.f' || echo './'`quik.f
/bin/sh: C: command not found
make[2]: [quikfold-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-rna-quik.o `test -f 'rna-quik.f' || echo './'`rna-quik.f
/bin/sh: C: command not found
make[2]: [quikfold-rna-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-misc-quik.o `test -f 'misc-quik.f' || echo './'`misc-quik.f
/bin/sh: C: command not found
make[2]: [quikfold-misc-quik.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-dc.o `test -f 'dc.f' || echo './'`dc.f
/bin/sh: C: command not found
make[2]: [quikfold-dc.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o quikfold-multid.o `test -f 'multid.f' || echo './'`multid.f
/bin/sh: C: command not found
make[2]: [quikfold-multid.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o quikfold quikfold-quik.o quikfold-rna-quik.o quikfold-misc-quik.o quikfold-dc.o quikfold-multid.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [quikfold] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o add_dHdSTm2-add-dHdSTm2.o `test -f 'add-dHdSTm2.f' || echo './'`add-dHdSTm2.f
/bin/sh: C: command not found
make[2]: [add_dHdSTm2-add-dHdSTm2.o] Error 127 (ignored)
C -O3 -Wall -fno-automatic -ffixed-line-length-none     -o add_dHdSTm2 add_dHdSTm2-add-dHdSTm2.o  -lpng -lm 
make[2]: C: Command not found
make[2]: [add_dHdSTm2] Error 127 (ignored)
 /usr/bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c boxplot_ng ct_boxplot_ng overlay_boxplot_ng sir_graph mfold_datdir '/usr/local/bin'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/usr/local/mfold-3.6/src'
make[1]: Leaving directory `/usr/local/mfold-3.6/src'
Making install in c++
make[1]: Entering directory `/usr/local/mfold-3.6/c++'
make[2]: Entering directory `/usr/local/mfold-3.6/c++'
 /usr/bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c efn2 '/usr/local/bin'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/usr/local/mfold-3.6/c++'
make[1]: Leaving directory `/usr/local/mfold-3.6/c++'
Making install in dat
make[1]: Entering directory `/usr/local/mfold-3.6/dat'
make[2]: Entering directory `/usr/local/mfold-3.6/dat'
make[2]: Nothing to be done for `install-exec-am'.
 /usr/bin/mkdir -p '/usr/local/share/mfold'
 /usr/bin/install -c -m 644 asint1x2.dg dangle.dg miscloop.dg sint4.dg stack.dg triloop.dg tstacki.dg asint2x3.dg loop.dg sint2.dg sint6.dg tloop.dg tstackh.dg asint1x2.dh dangle.dh miscloop.dh sint4.dh stack.dh triloop.dh tstacki.dh asint2x3.dh loop.dh sint2.dh sint6.dh tloop.dh tstackh.dh asint1x2.dgd loop.dgd sint4.dgd tloop.dgd tstacki.dgd asint2x3.dgd miscloop.dgd sint6.dgd triloop.dgd dangle.dgd sint2.dgd stack.dgd tstackh.dgd asint1x2.dhd '/usr/local/share/mfold'
 /usr/bin/install -c -m 644 loop.dhd sint4.dhd tloop.dhd tstacki.dhd asint2x3.dhd miscloop.dhd sint6.dhd triloop.dhd dangle.dhd sint2.dhd stack.dhd tstackh.dhd asint1x2.dat int11.dat miscloop.dat tloop.dat tstackh.dat coaxial.dat int21.dat sint2.dat triloop.dat tstacki.dat coaxstack.dat int22.dat sint4.dat tstackcoax.dat tstackm.dat dangle.dat loop.dat stack.dat tstack.dat back.gif home.gif l_purple.gif mfold-server-credit-sm.gif ddG.gif l_blue.gif l_red.gif rna.gif end2.gif '/usr/local/share/mfold'
 /usr/bin/install -c -m 644 l_brown.gif l_yellow.gif shield_t.gif end-break.gif l_cyan.gif mail.gif Flower.gif l_green.gif mfold5.gif green.gif l_grey.gif mfold-server-credit.gif split_ct.awk form1-doc.html formats.html boxplot.col boxplot-3.0.col ct_boxplot.col overlay_boxplot.col sir_graph.col sir_graph.1.col '/usr/local/share/mfold'
make[2]: Leaving directory `/usr/local/mfold-3.6/dat'
make[1]: Leaving directory `/usr/local/mfold-3.6/dat'
Making install in scripts
make[1]: Entering directory `/usr/local/mfold-3.6/scripts'
make[2]: Entering directory `/usr/local/mfold-3.6/scripts'
 /usr/bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c h-num mfold mfold_quik reformat-seq.sh filter-sort myps2img.bash '/usr/local/bin'
make  install-exec-hook
make[3]: Entering directory `/usr/local/mfold-3.6/scripts'
cd /usr/local/bin && ln -s -f myps2img.bash myps2pdf.bash
cd /usr/local/bin && ln -s -f myps2img.bash myps2jpg.bash
cd /usr/local/bin && ln -s -f myps2img.bash myps2png.bash
make[3]: Leaving directory `/usr/local/mfold-3.6/scripts'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/usr/local/mfold-3.6/scripts'
make[1]: Leaving directory `/usr/local/mfold-3.6/scripts'
make[1]: Entering directory `/usr/local/mfold-3.6'
make[2]: Entering directory `/usr/local/mfold-3.6'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/usr/local/mfold-3.6'
make[1]: Leaving directory `/usr/local/mfold-3.6'

Found some website discussing the problem and tried to resolve but no success:
Code:
http://mfold.rna.albany.edu/?q=node/120

Code:
http://www.bioinfo.rpi.edu/zukerm/comments/2006.html

I am also attaching the Makefile with this reply.
Regards
Makefile.txt (23.1 KB) 
# 9  
Old 09-12-2014
OK, I see something from comparing your output to mine. Your fortran compile lines look like:

Code:
C -O3 -Wall -fno-automatic -ffixed-line-length-none   -c -o ...

There's something kind of important missing:

Code:
gfortran -C -O3 -Wall -fno-automatic -ffixed-line-length-none  -g -O2 -c -o ...

From your configure log:
Code:
configure:4331: checking for g77
configure:4361: result: no
configure:4331: checking for xlf
configure:4361: result: no
configure:4331: checking for f77
configure:4361: result: no
configure:4331: checking for frt
configure:4361: result: no
configure:4331: checking for pgf77
configure:4361: result: no
configure:4331: checking for cf77
configure:4361: result: no
configure:4331: checking for fort77
configure:4361: result: no
configure:4331: checking for fl32
configure:4361: result: no
configure:4331: checking for af77
configure:4361: result: no
configure:4331: checking for xlf90
configure:4361: result: no
configure:4331: checking for f90
configure:4361: result: no
configure:4331: checking for f90
configure:4361: result: no
configure:4331: checking for pgf90
configure:4361: result: no
configure:4331: checking for pghpf
configure:4361: result: no
configure:4331: checking for epcf90
configure:4361: result: no
configure:4331: checking for gfortran
configure:4361: result: no
configure:4331: checking for g95
configure:4361: result: no
configure:4331: checking for xlf95
configure:4361: result: no
configure:4331: checking for f95
configure:4361: result: no
configure:4331: checking for fort
configure:4361: result: no
configure:4331: checking for ifort
configure:4361: result: no
configure:4331: checking for ifc
configure:4361: result: no
configure:4331: checking for efc
configure:4361: result: no
configure:4331: checking for pgfortran
configure:4361: result: no
configure:4331: checking for pgf95
configure:4361: result: no
configure:4331: checking for lf95
configure:4361: result: no
configure:4331: checking for ftn
configure:4361: result: no
configure:4331: checking for nagfor
configure:4361: result: no
configure:4384: checking for Fortran 77 compiler version
configure:4393:  --version >&5
./configure: line 4395: --version: command not found

So it tried to find fortran, didn't, and then got confused, not realizing it didn't find fortran. I on the other hand apparently had fortran and had no idea I did Smilie

Make sure you have fortran installed. It's part of the gnu compiler collection but isn't always installed with the rest.

If you have a kind of Fortran ./configure wasn't looking for, you can perhaps force it with F77="/path/to/myfortrancompiler" ./configure --prefix=...
# 10  
Old 09-15-2014
Dear Corona688,

I really thank you for your help and patience in troubleshooting the problem.
It was indeed a fortran problem and as soon as I installed gfortran, the program started to work.
Again I really really appreciate your help SmilieSmilieSmilieSmilie

Regards
Biochemist

---------- Post updated at 10:31 AM ---------- Previous update was at 10:08 AM ----------

Some more happiness and kudos for Corona688 and Unix.com team.

SmilieSmilieSmilieSmilieSmilie

SmilieSmilieSmilieSmilieSmilie

Regards
Biochemist
This User Gave Thanks to biochemist For This Post:
Corona688
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i installed x windows redhat linux 9.0 in my pc. but the problem is when i run cc command for c programme .....bash:cc: command not found printed ...........i set the path for bash ............with the help of PATH=$PATH....................still it is not working .........please guide me. (4 Replies)
Discussion started by: mishra_sk_in
4 Replies

10. Shell Programming and Scripting

how can i check in csh if command found or not found ?

hello all im trying to use in sun Solaris the information received from the top command now i several machines that dont have install the top program so when im running the script im geting error saying after im running this code : set MemoryInfo = `top | grep Memory` if (... (2 Replies)
Discussion started by: umen
2 Replies
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