printf '
' | fink --no-use-binary-dist --yes --build-as-nobody rebuild simcoal 2>&1
WARNING: your info file index has not been updated for 17 days. You should
run 'fink selfupdate' to get the latest package descriptions.
The package 'simcoal' will be built without being installed.
Reading build dependency for simcoal-1.0-1...
Reading dependency for simcoal-1.0-1...
Reading build conflict for simcoal-1.0-1...
The package 'dos2unix' will be installed.
Reading dependency for dos2unix-6.0.5-1...
Reading runtime dependency for dos2unix-6.0.5-1...
The following package will be rebuilt:
simcoal
The following additional package will be installed:
dos2unix
Do you want to continue? [Y/n] (assuming default)
Reading buildlock packages...
All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/dos2unix_6.0.5-1_darwin-x86_64.deb
Selecting previously deselected package dos2unix.
(Reading database ... 4967 files and directories currently installed.)
Unpacking dos2unix (from .../dos2unix_6.0.5-1_darwin-x86_64.deb) ...
Setting up dos2unix (6.0.5-1) ...
Setting runtime build-lock...
dpkg-deb -b /sw/build.build/root-fink-buildlock-simcoal-1.0-1 /sw/build.build
dpkg-deb: building package `fink-buildlock-simcoal-1.0-1' in `/sw/build.build/fink-buildlock-simcoal-1.0-1_2014.08.10-21.55.24_darwin-x86_64.deb'.
Installing build-lock package...
/sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-simcoal-1.0-1_2014.08.10-21.55.24_darwin-x86_64.deb
Selecting previously deselected package fink-buildlock-simcoal-1.0-1.
(Reading database ... 4984 files and directories currently installed.)
Unpacking fink-buildlock-simcoal-1.0-1 (from .../fink-buildlock-simcoal-1.0-1_2014.08.10-21.55.24_darwin-x86_64.deb) ...
Setting up fink-buildlock-simcoal-1.0-1 (2014.08.10-21.55.24) ...
sudo -u fink-bld [ENV] sh -c /tmp/fink.okOCc
unzip -o /sw/src/simcoal_linux.zip
Archive: /sw/src/simcoal_linux.zip
inflating: mutation.h
inflating: public.cpp
inflating: public.h
inflating: mutation.cpp
inflating: migrmat.h
inflating: migrmat.cpp
inflating: Makefile
inflating: genealgy.h
inflating: genealgy.cpp
inflating: deme.h
inflating: deme.cpp
inflating: cstring.h
inflating: cstring.cpp
inflating: cond_var.h
inflating: coalmain.h
inflating: coalmain.cpp
inflating: arrays.h
sudo -u fink-bld [ENV] sh -c /tmp/fink.nqUCZ
[ -r /sw/fink/dists/stable/main/finkinfo/sci/simcoal.patch ]
sudo -u fink-bld [ENV] sh -c /tmp/fink.brTtS
dos2unix *.cpp *.h Makefile
dos2unix: converting file coalmain.cpp to Unix format...
dos2unix: converting file cstring.cpp to Unix format...
dos2unix: converting file deme.cpp to Unix format...
dos2unix: converting file genealgy.cpp to Unix format...
dos2unix: converting file migrmat.cpp to Unix format...
dos2unix: converting file mutation.cpp to Unix format...
dos2unix: converting file public.cpp to Unix format...
dos2unix: converting file arrays.h to Unix format...
dos2unix: converting file coalmain.h to Unix format...
dos2unix: converting file cond_var.h to Unix format...
dos2unix: converting file cstring.h to Unix format...
dos2unix: converting file deme.h to Unix format...
dos2unix: converting file genealgy.h to Unix format...
dos2unix: converting file migrmat.h to Unix format...
dos2unix: converting file mutation.h to Unix format...
dos2unix: converting file public.h to Unix format...
dos2unix: converting file Makefile to Unix format...
mac2unix public*
mac2unix: converting file public.cpp to Unix format...
mac2unix: converting file public.h to Unix format...
patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/simcoal.patch
patching file Makefile
patching file arrays.h
patching file coalmain.cpp
patching file cstring.cpp
patching file cstring.h
patching file deme.cpp
patching file genealgy.cpp
patching file genealgy.h
patching file migrmat.cpp
patching file migrmat.h
patching file mutation.cpp
patching file mutation.h
patching file public.cpp
patching file public.h
sudo -u fink-bld [ENV] sh -c /tmp/fink.RjG2X
make
Makefile:29: depend: No such file or directory
g++ -O3 -M *.cpp > depend
g++ -O3 -c coalmain.cpp -o coalmain.o
coalmain.cpp:12:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
coalmain.cpp:106:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
if (!c) return "";
^
coalmain.cpp:128:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
sout="";
^
coalmain.cpp:132:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
if (!c) return "";
^
coalmain.cpp:150:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage ="\nsim_coale.exe usage:\n";
^
coalmain.cpp:151:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n [1] : sim_coal <no arguments>";
^
coalmain.cpp:152:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n The program will prompt you for an input file name to process and the";
^
coalmain.cpp:153:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n number of simulations to perform";
^
coalmain.cpp:154:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n [2] : sim_coal <batch file name>";
^
coalmain.cpp:155:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n The program will open the batch file that should contain, on the first";
^
coalmain.cpp:156:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n line, the number of simulations to perform, and on the following lines";
^
coalmain.cpp:157:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n the names of the input files to process";
^
coalmain.cpp:158:11: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
usage+="\n [3] : sim_coal <file name> <number of simulations to perform>\n";
^
coalmain.cpp:165:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
my_string Path="";
^
coalmain.cpp:239:36: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
outfile_name = infile_name[nf]+".gen";
^
coalmain.cpp:240:46: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
arl_batch_file_name = infile_name[nf]+".arb";
^
coalmain.cpp:243:46: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
paup_batch_file_name = infile_name[nf]+".bat";
^
coalmain.cpp:244:38: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
paup_name = infile_name[nf]+".paup";
^
coalmain.cpp:245:46: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
paup_true_trees_name = infile_name[nf]+"_true_trees.trees";
^
coalmain.cpp:246:45: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
paup_mut_trees_name = infile_name[nf]+"_mut_trees.trees";
^
coalmain.cpp:247:42: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
log_file_name = infile_name[nf]+".log";
^
coalmain.cpp:248:22: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
infile_name[nf]+=".par";
^
coalmain.cpp:562:9: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
if (!gamma_a==0.0 && data_type==DNA) {
^ ~~
coalmain.cpp:562:9: note: add parentheses after the '!' to evaluate the comparison first
if (!gamma_a==0.0 && data_type==DNA) {
^
( )
coalmain.cpp:562:9: note: add parentheses around left hand side expression to silence this warning
if (!gamma_a==0.0 && data_type==DNA) {
^
( )
coalmain.cpp:664:42: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
ArlOut = paup_generic_name + "_" + fcvt(tot_cases, ndiga, &deca, &signa) + ".arp";
^
coalmain.cpp:664:88: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
ArlOut = paup_generic_name + "_" + fcvt(tot_cases, ndiga, &deca, &signa) + ".arp";
^
25 warnings generated.
g++ -O3 -c cstring.cpp -o cstring.o
cstring.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
cstring.cpp:99:56: warning: '&&' within '||' [-Wlogical-op-parentheses]
for(;current==' ' || current=='\t' || current=='\n' && is;){
~~ ~~~~~~~~~~~~~~^~~~~
cstring.cpp:99:56: note: place parentheses around the '&&' expression to silence this warning
for(;current==' ' || current=='\t' || current=='\n' && is;){
^
( )
cstring.cpp:347:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
(*this)="";
^
cstring.cpp:360:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
(*this)="";
^
cstring.cpp:394:18: warning: expression result unused [-Wunused-value]
if(!_nb_char) sub_str; //return empty string.
^~~~~~~
cstring.cpp:464:10: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
(*this)="";
^
cstring.cpp:546:6: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
s="";
^
7 warnings generated.
g++ -O3 -c deme.cpp -o deme.o
deme.cpp:9:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
g++ -O3 -c genealgy.cpp -o genealgy.o
genealgy.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
g++ -O3 -c migrmat.cpp -o migrmat.o
migrmat.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
g++ -O3 -c mutation.cpp -o mutation.o
mutation.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
g++ -O3 -c public.cpp -o public.o
public.cpp:1:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
public.cpp:176:30: warning: while loop has empty body [-Wempty-body]
while (list[++i] < v) ;
^
public.cpp:176:30: note: put the semicolon on a separate line to silence this warning
public.cpp:846:40: warning: for loop has empty body [-Wempty-body]
{ int i; for (i=0; i<n; y[i]=x[i],i++) ; return(0); }
^
public.cpp:846:40: note: put the semicolon on a separate line to silence this warning
public.cpp:849:38: warning: for loop has empty body [-Wempty-body]
{ int i; for (i=0; i<n; x[i]*=a,i++) ; return(0); }
^
public.cpp:849:38: note: put the semicolon on a separate line to silence this warning
4 warnings generated.
echo coalmain.o cstring.o deme.o genealgy.o migrmat.o mutation.o public.o
coalmain.o cstring.o deme.o genealgy.o migrmat.o mutation.o public.o
g++ -O3 *.o -o simcoal
head -n 10 coalmain.cpp > LICENSE
/bin/rm -rf /sw/build.build/root-simcoal-1.0-1
/bin/mkdir -p /sw/build.build/root-simcoal-1.0-1/sw
/bin/mkdir -p /sw/build.build/root-simcoal-1.0-1/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-simcoal-1.0-1
sudo -u fink-bld [ENV] sh -c /tmp/fink.Zd9JS
install -d -m 0755 /sw/build.build/root-simcoal-1.0-1/sw/bin
install -m 0755 simcoal /sw/build.build/root-simcoal-1.0-1/sw/bin
sudo -u fink-bld [ENV] sh -c /tmp/fink.4fwoy
/usr/bin/install -d -m 700 /sw/build.build/root-simcoal-1.0-1/sw/share/doc/simcoal
/bin/cp -r LICENSE /sw/build.build/root-simcoal-1.0-1/sw/share/doc/simcoal/
/bin/chmod -R go=u-w /sw/build.build/root-simcoal-1.0-1/sw/share/doc/simcoal
/bin/rm -f /sw/build.build/root-simcoal-1.0-1/sw/info/dir /sw/build.build/root-simcoal-1.0-1/sw/info/dir.old /sw/build.build/root-simcoal-1.0-1/sw/share/info/dir /sw/build.build/root-simcoal-1.0-1/sw/share/info/dir.old
Reverting ownership of install dir to root
Writing control file...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-simcoal-1.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `simcoal' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/simcoal_1.0-1_darwin-x86_64.deb'.
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-simcoal-1.0-1
(Reading database ... 4985 files and directories currently installed.)
Removing fink-buildlock-simcoal-1.0-1 ...