2023-09-10T08:17:17,845 Created temporary directory: /tmp/pip-build-tracker-agyinpk2 2023-09-10T08:17:17,846 Initialized build tracking at /tmp/pip-build-tracker-agyinpk2 2023-09-10T08:17:17,847 Created build tracker: /tmp/pip-build-tracker-agyinpk2 2023-09-10T08:17:17,847 Entered build tracker: /tmp/pip-build-tracker-agyinpk2 2023-09-10T08:17:17,848 Created temporary directory: /tmp/pip-wheel-djs_i2sr 2023-09-10T08:17:17,851 Created temporary directory: /tmp/pip-ephem-wheel-cache-ajvjvgak 2023-09-10T08:17:17,873 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-10T08:17:17,877 2 location(s) to search for versions of pastml: 2023-09-10T08:17:17,877 * https://pypi.org/simple/pastml/ 2023-09-10T08:17:17,877 * https://www.piwheels.org/simple/pastml/ 2023-09-10T08:17:17,878 Fetching project page and analyzing links: https://pypi.org/simple/pastml/ 2023-09-10T08:17:17,879 Getting page https://pypi.org/simple/pastml/ 2023-09-10T08:17:17,880 Found index url 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2023-09-10T08:17:24,929 Downloading pastml-0.3.3.tar.gz (24 kB) 2023-09-10T08:17:24,982 Added pastml==0.3.3 from https://files.pythonhosted.org/packages/4e/48/eee9ced93fed4f35d2a7fdd14d542856be4479e4ca9ce5da480f17f1c431/pastml-0.3.3.tar.gz to build tracker '/tmp/pip-build-tracker-agyinpk2' 2023-09-10T08:17:24,984 Running setup.py (path:/tmp/pip-wheel-djs_i2sr/pastml_2fd26b25af8e440e9d5218dcab6d93de/setup.py) egg_info for package pastml 2023-09-10T08:17:24,985 Created temporary directory: /tmp/pip-pip-egg-info-fzoa8y0f 2023-09-10T08:17:24,985 Preparing metadata (setup.py): started 2023-09-10T08:17:24,987 Running command python setup.py egg_info 2023-09-10T08:17:25,454 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'platform' 2023-09-10T08:17:25,454 warnings.warn(msg) 2023-09-10T08:17:26,210 Preparing metadata (setup.py): finished with status 'done' 2023-09-10T08:17:26,214 Source in /tmp/pip-wheel-djs_i2sr/pastml_2fd26b25af8e440e9d5218dcab6d93de has version 0.3.3, which satisfies requirement pastml==0.3.3 from https://files.pythonhosted.org/packages/4e/48/eee9ced93fed4f35d2a7fdd14d542856be4479e4ca9ce5da480f17f1c431/pastml-0.3.3.tar.gz 2023-09-10T08:17:26,215 Removed pastml==0.3.3 from https://files.pythonhosted.org/packages/4e/48/eee9ced93fed4f35d2a7fdd14d542856be4479e4ca9ce5da480f17f1c431/pastml-0.3.3.tar.gz from build tracker '/tmp/pip-build-tracker-agyinpk2' 2023-09-10T08:17:26,219 Created temporary directory: /tmp/pip-unpack-817i5t7w 2023-09-10T08:17:26,219 Created temporary directory: /tmp/pip-unpack-s0fd_vk7 2023-09-10T08:17:26,222 Building wheels for collected packages: pastml 2023-09-10T08:17:26,226 Created temporary directory: /tmp/pip-wheel-5z8vxsd9 2023-09-10T08:17:26,226 Building wheel for pastml (setup.py): started 2023-09-10T08:17:26,227 Destination directory: /tmp/pip-wheel-5z8vxsd9 2023-09-10T08:17:26,228 Running command python setup.py bdist_wheel 2023-09-10T08:17:26,668 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'platform' 2023-09-10T08:17:26,669 warnings.warn(msg) 2023-09-10T08:17:27,931 fletcher.c: In function ‘gradient’: 2023-09-10T08:17:27,932 fletcher.c:21:27: warning: unused variable ‘minuslnl’ [-Wunused-variable] 2023-09-10T08:17:27,932 21 | double pluslnl, oldlnl, minuslnl, tmp_p[n], sum=0.0; 2023-09-10T08:17:27,933 | ^~~~~~~~ 2023-09-10T08:17:27,936 fletcher.c: In function ‘mnbrak’: 2023-09-10T08:17:27,936 fletcher.c:143:25: warning: passing argument 4 of ‘SHFT’ from incompatible pointer type [-Wincompatible-pointer-types] 2023-09-10T08:17:27,937 143 | SHFT(bx,cx,&u,&bdum); 2023-09-10T08:17:27,937 | ^~~~~ 2023-09-10T08:17:27,938 | | 2023-09-10T08:17:27,939 | double ** 2023-09-10T08:17:27,939 fletcher.c:11:52: note: expected ‘double *’ but argument is of type ‘double **’ 2023-09-10T08:17:27,940 11 | void SHFT(double* a, double* b, double* c, double* d){ 2023-09-10T08:17:27,941 | ~~~~~~~~^ 2023-09-10T08:17:27,941 fletcher.c:146:26: warning: passing argument 4 of ‘SHFT’ from incompatible pointer type [-Wincompatible-pointer-types] 2023-09-10T08:17:27,942 146 | SHFT(fb,fc,&fu,&cdum); 2023-09-10T08:17:27,943 | ^~~~~ 2023-09-10T08:17:27,943 | | 2023-09-10T08:17:27,944 | double ** 2023-09-10T08:17:27,945 fletcher.c:11:52: note: expected ‘double *’ but argument is of type ‘double **’ 2023-09-10T08:17:27,946 11 | void SHFT(double* a, double* b, double* c, double* d){ 2023-09-10T08:17:27,947 | ~~~~~~~~^ 2023-09-10T08:17:27,947 fletcher.c: In function ‘linmin’: 2023-09-10T08:17:27,948 fletcher.c:235:45: warning: unused variable ‘x_sum’ [-Wunused-variable] 2023-09-10T08:17:27,949 235 | double xx,xmin,fx,fb,fa,bx,ax,*pold,tmp_x,x_sum,f_check; 2023-09-10T08:17:27,949 | ^~~~~ 2023-09-10T08:17:27,950 fletcher.c:235:39: warning: unused variable ‘tmp_x’ [-Wunused-variable] 2023-09-10T08:17:27,950 235 | double xx,xmin,fx,fb,fa,bx,ax,*pold,tmp_x,x_sum,f_check; 2023-09-10T08:17:27,951 | ^~~~~ 2023-09-10T08:17:27,952 fletcher.c:234:7: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-10T08:17:27,952 234 | int i,j; 2023-09-10T08:17:27,953 | ^ 2023-09-10T08:17:27,954 fletcher.c: In function ‘frprmn’: 2023-09-10T08:17:27,954 fletcher.c:271:23: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-10T08:17:27,955 271 | double *g, *h, *xi, sum; 2023-09-10T08:17:27,956 | ^~~ 2023-09-10T08:17:27,956 In file included from fletcher.c:2: 2023-09-10T08:17:27,957 nrutil.h: At top level: 2023-09-10T08:17:27,958 nrutil.h:38:22: warning: ‘iminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,958 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:27,959 | ^~~~~~~~ 2023-09-10T08:17:27,959 nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,960 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:27,960 | ^~~~~~~~ 2023-09-10T08:17:27,961 nrutil.h:34:22: warning: ‘imaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,961 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:27,962 | ^~~~~~~~ 2023-09-10T08:17:27,962 nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,963 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:27,963 | ^~~~~~~~ 2023-09-10T08:17:27,964 nrutil.h:30:23: warning: ‘lminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,965 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:27,965 | ^~~~~~~~ 2023-09-10T08:17:27,966 nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,966 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:27,967 | ^~~~~~~~ 2023-09-10T08:17:27,967 nrutil.h:26:23: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,968 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:27,968 | ^~~~~~~~ 2023-09-10T08:17:27,969 nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,969 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:27,970 | ^~~~~~~~ 2023-09-10T08:17:27,970 nrutil.h:22:24: warning: ‘minarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,971 22 | static double minarg1, minarg2; 2023-09-10T08:17:27,972 | ^~~~~~~ 2023-09-10T08:17:27,972 nrutil.h:22:15: warning: ‘minarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,973 22 | static double minarg1, minarg2; 2023-09-10T08:17:27,974 | ^~~~~~~ 2023-09-10T08:17:27,974 nrutil.h:14:25: warning: ‘dminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,975 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:27,976 | ^~~~~~~~ 2023-09-10T08:17:27,976 nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,977 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:27,978 | ^~~~~~~~ 2023-09-10T08:17:27,978 nrutil.h:10:25: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,979 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:27,979 | ^~~~~~~~ 2023-09-10T08:17:27,980 nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,980 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:27,981 | ^~~~~~~~ 2023-09-10T08:17:27,981 nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,982 7 | static double dsqrarg; 2023-09-10T08:17:27,983 | ^~~~~~~ 2023-09-10T08:17:27,983 nrutil.h:4:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:27,984 4 | static double sqrarg; 2023-09-10T08:17:27,985 | ^~~~~~ 2023-09-10T08:17:28,298 fletcher.c: In function ‘brent’: 2023-09-10T08:17:28,299 fletcher.c:191:32: warning: ‘e’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-10T08:17:28,300 191 | if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) { 2023-09-10T08:17:28,300 | ~~~~~^~~~~~ 2023-09-10T08:17:28,301 fletcher.c:169:10: note: ‘e’ was declared here 2023-09-10T08:17:28,302 169 | double e=0.0; 2023-09-10T08:17:28,302 | ^ 2023-09-10T08:17:28,761 fletcherJC.c: In function ‘gradientJC’: 2023-09-10T08:17:28,762 fletcherJC.c:21:47: warning: variable ‘sum’ set but not used [-Wunused-but-set-variable] 2023-09-10T08:17:28,763 21 | double pluslnl, oldlnl, minuslnl, tmp_p[n], sum=0.0, *likp; 2023-09-10T08:17:28,763 | ^~~ 2023-09-10T08:17:28,764 fletcherJC.c:21:37: warning: unused variable ‘tmp_p’ [-Wunused-variable] 2023-09-10T08:17:28,764 21 | double pluslnl, oldlnl, minuslnl, tmp_p[n], sum=0.0, *likp; 2023-09-10T08:17:28,765 | ^~~~~ 2023-09-10T08:17:28,765 fletcherJC.c:21:27: warning: unused variable ‘minuslnl’ [-Wunused-variable] 2023-09-10T08:17:28,766 21 | double pluslnl, oldlnl, minuslnl, tmp_p[n], sum=0.0, *likp; 2023-09-10T08:17:28,766 | ^~~~~~~~ 2023-09-10T08:17:28,767 fletcherJC.c: In function ‘f1dimJC’: 2023-09-10T08:17:28,768 fletcherJC.c:54:32: warning: variable ‘sumfreq’ set but not used [-Wunused-but-set-variable] 2023-09-10T08:17:28,768 54 | double f,*xt,x_sum=0.0,tmp_x,sumfreq,e1,e2,exp1,exp2,*likp; 2023-09-10T08:17:28,769 | ^~~~~~~ 2023-09-10T08:17:28,769 fletcherJC.c:54:26: warning: unused variable ‘tmp_x’ [-Wunused-variable] 2023-09-10T08:17:28,770 54 | double f,*xt,x_sum=0.0,tmp_x,sumfreq,e1,e2,exp1,exp2,*likp; 2023-09-10T08:17:28,770 | ^~~~~ 2023-09-10T08:17:28,771 fletcherJC.c:54:16: warning: variable ‘x_sum’ set but not used [-Wunused-but-set-variable] 2023-09-10T08:17:28,772 54 | double f,*xt,x_sum=0.0,tmp_x,sumfreq,e1,e2,exp1,exp2,*likp; 2023-09-10T08:17:28,772 | ^~~~~ 2023-09-10T08:17:28,773 fletcherJC.c: In function ‘mnbrakJC’: 2023-09-10T08:17:28,774 fletcherJC.c:133:26: warning: passing argument 4 of ‘SHFT2’ from incompatible pointer type [-Wincompatible-pointer-types] 2023-09-10T08:17:28,774 133 | SHFT2(bx,cx,&u,&bdum); 2023-09-10T08:17:28,775 | ^~~~~ 2023-09-10T08:17:28,776 | | 2023-09-10T08:17:28,776 | double ** 2023-09-10T08:17:28,777 fletcherJC.c:11:53: note: expected ‘double *’ but argument is of type ‘double **’ 2023-09-10T08:17:28,778 11 | void SHFT2(double* a, double* b, double* c, double* d){ 2023-09-10T08:17:28,779 | ~~~~~~~~^ 2023-09-10T08:17:28,779 fletcherJC.c:136:27: warning: passing argument 4 of ‘SHFT2’ from incompatible pointer type [-Wincompatible-pointer-types] 2023-09-10T08:17:28,780 136 | SHFT2(fb,fc,&fu,&cdum); 2023-09-10T08:17:28,780 | ^~~~~ 2023-09-10T08:17:28,781 | | 2023-09-10T08:17:28,781 | double ** 2023-09-10T08:17:28,782 fletcherJC.c:11:53: note: expected ‘double *’ but argument is of type ‘double **’ 2023-09-10T08:17:28,783 11 | void SHFT2(double* a, double* b, double* c, double* d){ 2023-09-10T08:17:28,783 | ~~~~~~~~^ 2023-09-10T08:17:28,784 fletcherJC.c: In function ‘linminJC’: 2023-09-10T08:17:28,785 fletcherJC.c:225:45: warning: unused variable ‘x_sum’ [-Wunused-variable] 2023-09-10T08:17:28,785 225 | double xx,xmin,fx,fb,fa,bx,ax,*pold,tmp_x,x_sum,f_check,*likp; 2023-09-10T08:17:28,786 | ^~~~~ 2023-09-10T08:17:28,787 fletcherJC.c:225:39: warning: unused variable ‘tmp_x’ [-Wunused-variable] 2023-09-10T08:17:28,788 225 | double xx,xmin,fx,fb,fa,bx,ax,*pold,tmp_x,x_sum,f_check,*likp; 2023-09-10T08:17:28,788 | ^~~~~ 2023-09-10T08:17:28,789 fletcherJC.c: In function ‘frprmnJC’: 2023-09-10T08:17:28,789 fletcherJC.c:268:23: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-10T08:17:28,790 268 | double *g, *h, *xi, sum, *likp; 2023-09-10T08:17:28,790 | ^~~ 2023-09-10T08:17:28,800 In file included from fletcherJC.c:2: 2023-09-10T08:17:28,800 nrutil.h: At top level: 2023-09-10T08:17:28,801 nrutil.h:38:22: warning: ‘iminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,801 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:28,802 | ^~~~~~~~ 2023-09-10T08:17:28,802 nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,803 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:28,803 | ^~~~~~~~ 2023-09-10T08:17:28,804 nrutil.h:34:22: warning: ‘imaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,804 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:28,805 | ^~~~~~~~ 2023-09-10T08:17:28,805 nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,805 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:28,806 | ^~~~~~~~ 2023-09-10T08:17:28,806 nrutil.h:30:23: warning: ‘lminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,807 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:28,807 | ^~~~~~~~ 2023-09-10T08:17:28,808 nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,809 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:28,809 | ^~~~~~~~ 2023-09-10T08:17:28,810 nrutil.h:26:23: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,810 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:28,811 | ^~~~~~~~ 2023-09-10T08:17:28,812 nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,812 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:28,813 | ^~~~~~~~ 2023-09-10T08:17:28,814 nrutil.h:22:24: warning: ‘minarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,814 22 | static double minarg1, minarg2; 2023-09-10T08:17:28,815 | ^~~~~~~ 2023-09-10T08:17:28,815 nrutil.h:22:15: warning: ‘minarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,816 22 | static double minarg1, minarg2; 2023-09-10T08:17:28,816 | ^~~~~~~ 2023-09-10T08:17:28,817 nrutil.h:14:25: warning: ‘dminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,818 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:28,818 | ^~~~~~~~ 2023-09-10T08:17:28,819 nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,819 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:28,820 | ^~~~~~~~ 2023-09-10T08:17:28,820 nrutil.h:10:25: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,821 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:28,822 | ^~~~~~~~ 2023-09-10T08:17:28,822 nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,823 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:28,824 | ^~~~~~~~ 2023-09-10T08:17:28,825 nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,825 7 | static double dsqrarg; 2023-09-10T08:17:28,826 | ^~~~~~~ 2023-09-10T08:17:28,826 nrutil.h:4:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:28,827 4 | static double sqrarg; 2023-09-10T08:17:28,828 | ^~~~~~ 2023-09-10T08:17:29,169 fletcherJC.c: In function ‘brentJC’: 2023-09-10T08:17:29,170 fletcherJC.c:181:32: warning: ‘e’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-10T08:17:29,170 181 | if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) { 2023-09-10T08:17:29,171 | ~~~~~^~~~~~ 2023-09-10T08:17:29,171 fletcherJC.c:159:10: note: ‘e’ was declared here 2023-09-10T08:17:29,172 159 | double e=0.0; 2023-09-10T08:17:29,172 | ^ 2023-09-10T08:17:29,664 golden.c:4: warning: "SIGMA" redefined 2023-09-10T08:17:29,665 4 | #define SIGMA 1e-5 2023-09-10T08:17:29,665 | 2023-09-10T08:17:29,666 In file included from golden.c:1: 2023-09-10T08:17:29,667 asrml.h:26: note: this is the location of the previous definition 2023-09-10T08:17:29,668 26 | #define SIGMA 1.0e-3 2023-09-10T08:17:29,668 | 2023-09-10T08:17:29,929 lik.c: In function ‘calc_lik_bfgs’: 2023-09-10T08:17:29,931 lik.c:13:122: warning: unused variable ‘sum_mu’ [-Wunused-variable] 2023-09-10T08:17:29,932 13 | double mul, expmul, sum = 0., prob_left = 0., prob_right = 0., bl, smallest, scaled_lk, logroot, prob_sons[MAXPOLY], sum_mu; 2023-09-10T08:17:29,933 | ^~~~~~ 2023-09-10T08:17:29,933 lik.c:13:51: warning: unused variable ‘prob_right’ [-Wunused-variable] 2023-09-10T08:17:29,934 13 | double mul, expmul, sum = 0., prob_left = 0., prob_right = 0., bl, smallest, scaled_lk, logroot, prob_sons[MAXPOLY], sum_mu; 2023-09-10T08:17:29,935 | ^~~~~~~~~~ 2023-09-10T08:17:29,936 lik.c:13:35: warning: unused variable ‘prob_left’ [-Wunused-variable] 2023-09-10T08:17:29,937 13 | double mul, expmul, sum = 0., prob_left = 0., prob_right = 0., bl, smallest, scaled_lk, logroot, prob_sons[MAXPOLY], sum_mu; 2023-09-10T08:17:29,938 | ^~~~~~~~~ 2023-09-10T08:17:29,939 lik.c:12:13: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-10T08:17:29,939 12 | int i, j, k, ii; 2023-09-10T08:17:29,940 | ^ 2023-09-10T08:17:30,509 make_tree.c: In function ‘parse_double’: 2023-09-10T08:17:30,509 make_tree.c:137:9: warning: ‘return’ with no value, in function returning non-void [-Wreturn-type] 2023-09-10T08:17:30,510 137 | return; 2023-09-10T08:17:30,511 | ^~~~~~ 2023-09-10T08:17:30,511 make_tree.c:131:5: note: declared here 2023-09-10T08:17:30,512 131 | int parse_double(char *in_str, int begin, int end, double *location) { 2023-09-10T08:17:30,513 | ^~~~~~~~~~~~ 2023-09-10T08:17:30,523 make_tree.c: In function ‘parse_nh_string’: 2023-09-10T08:17:30,523 make_tree.c:584:12: warning: too many arguments for format [-Wformat-extra-args] 2023-09-10T08:17:30,524 584 | printf("\n*** BASIC STATISTICS ***\n\n", in_str); 2023-09-10T08:17:30,525 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-10T08:17:30,525 make_tree.c:487:54: warning: unused variable ‘collapsed_internal’ [-Wunused-variable] 2023-09-10T08:17:30,526 487 | int collapsed_one = 0, uncollapsed_terminal = 0, collapsed_internal = 0; 2023-09-10T08:17:30,526 | ^~~~~~~~~~~~~~~~~~ 2023-09-10T08:17:30,528 make_tree.c:487:28: warning: unused variable ‘uncollapsed_terminal’ [-Wunused-variable] 2023-09-10T08:17:30,529 487 | int collapsed_one = 0, uncollapsed_terminal = 0, collapsed_internal = 0; 2023-09-10T08:17:30,529 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-10T08:17:30,530 make_tree.c:487:9: warning: unused variable ‘collapsed_one’ [-Wunused-variable] 2023-09-10T08:17:30,531 487 | int collapsed_one = 0, uncollapsed_terminal = 0, collapsed_internal = 0; 2023-09-10T08:17:30,531 | ^~~~~~~~~~~~~ 2023-09-10T08:17:30,532 make_tree.c:486:10: warning: unused variable ‘str’ [-Wunused-variable] 2023-09-10T08:17:30,533 486 | char str[MAXLNAME]; 2023-09-10T08:17:30,533 | ^~~ 2023-09-10T08:17:30,534 make_tree.c: In function ‘complete_parse_nh’: 2023-09-10T08:17:30,534 make_tree.c:605:9: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-10T08:17:30,535 605 | int i; 2023-09-10T08:17:30,535 | ^ 2023-09-10T08:17:31,456 marginal_approxi.c: In function ‘calc_correct’: 2023-09-10T08:17:31,457 marginal_approxi.c:20:12: warning: variable ‘local_numpos’ set but not used [-Wunused-but-set-variable] 2023-09-10T08:17:31,457 20 | double local_numpos, tmp_correct = 10.0, local_cor; 2023-09-10T08:17:31,458 | ^~~~~~~~~~~~ 2023-09-10T08:17:31,459 marginal_approxi.c:19:15: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-10T08:17:31,459 19 | int i, j, k, tmpnum, node_start; 2023-09-10T08:17:31,460 | ^ 2023-09-10T08:17:31,461 marginal_approxi.c: In function ‘order_marginal’: 2023-09-10T08:17:31,462 marginal_approxi.c:73:9: warning: variable ‘pupko’ set but not used [-Wunused-but-set-variable] 2023-09-10T08:17:31,462 73 | int pupko; 2023-09-10T08:17:31,463 | ^~~~~ 2023-09-10T08:17:31,463 marginal_approxi.c:70:22: warning: unused variable ‘jj’ [-Wunused-variable] 2023-09-10T08:17:31,464 70 | int i, j, k, ii, jj, tmpnum, zerostate[nbanno], zero_count = 0, node_start; 2023-09-10T08:17:31,465 | ^~ 2023-09-10T08:17:31,465 marginal_approxi.c:70:18: warning: unused variable ‘ii’ [-Wunused-variable] 2023-09-10T08:17:31,466 70 | int i, j, k, ii, jj, tmpnum, zerostate[nbanno], zero_count = 0, node_start; 2023-09-10T08:17:31,467 | ^~ 2023-09-10T08:17:31,468 marginal_approxi.c: In function ‘make_samples’: 2023-09-10T08:17:31,468 marginal_approxi.c:156:9: warning: unused variable ‘true_count’ [-Wunused-variable] 2023-09-10T08:17:31,469 156 | int true_count = 0; 2023-09-10T08:17:31,470 | ^~~~~~~~~~ 2023-09-10T08:17:31,525 marginal_approxi.c: In function ‘calc_correct’: 2023-09-10T08:17:31,526 marginal_approxi.c:53:12: warning: ‘tmpnum’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-10T08:17:31,527 53 | if (i < tmpnum) { 2023-09-10T08:17:31,528 | ^ 2023-09-10T08:17:31,528 marginal_approxi.c:19:18: note: ‘tmpnum’ was declared here 2023-09-10T08:17:31,529 19 | int i, j, k, tmpnum, node_start; 2023-09-10T08:17:31,530 | ^~~~~~ 2023-09-10T08:17:32,070 marginal_lik.c: In function ‘down_like_marginal’: 2023-09-10T08:17:32,070 marginal_lik.c:12:23: warning: unused variable ‘sumlog’ [-Wunused-variable] 2023-09-10T08:17:32,071 12 | double curr_scaler, sumlog; 2023-09-10T08:17:32,072 | ^~~~~~ 2023-09-10T08:17:32,073 marginal_lik.c:11:17: warning: unused variable ‘tmp_factor’ [-Wunused-variable] 2023-09-10T08:17:32,073 11 | int factor=0, tmp_factor; 2023-09-10T08:17:32,074 | ^~~~~~~~~~ 2023-09-10T08:17:32,075 marginal_lik.c:11:7: warning: unused variable ‘factor’ [-Wunused-variable] 2023-09-10T08:17:32,075 11 | int factor=0, tmp_factor; 2023-09-10T08:17:32,076 | ^~~~~~ 2023-09-10T08:17:32,077 marginal_lik.c:9:127: warning: unused variable ‘tmp_br’ [-Wunused-variable] 2023-09-10T08:17:32,078 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,078 | ^~~~~~ 2023-09-10T08:17:32,079 marginal_lik.c:9:123: warning: unused variable ‘bl’ [-Wunused-variable] 2023-09-10T08:17:32,080 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,080 | ^~ 2023-09-10T08:17:32,080 marginal_lik.c:9:108: warning: unused variable ‘root_my_BL’ [-Wunused-variable] 2023-09-10T08:17:32,081 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,081 | ^~~~~~~~~~ 2023-09-10T08:17:32,082 marginal_lik.c:9:99: warning: unused variable ‘logroot’ [-Wunused-variable] 2023-09-10T08:17:32,082 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,083 | ^~~~~~~ 2023-09-10T08:17:32,083 marginal_lik.c:9:85: warning: unused variable ‘scaled_lk’ [-Wunused-variable] 2023-09-10T08:17:32,083 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,084 | ^~~~~~~~~ 2023-09-10T08:17:32,085 marginal_lik.c:9:31: warning: unused variable ‘prob_up’ [-Wunused-variable] 2023-09-10T08:17:32,085 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,086 | ^~~~~~~ 2023-09-10T08:17:32,086 marginal_lik.c:9:15: warning: unused variable ‘expmul’ [-Wunused-variable] 2023-09-10T08:17:32,087 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,088 | ^~~~~~ 2023-09-10T08:17:32,089 marginal_lik.c:9:10: warning: unused variable ‘mul’ [-Wunused-variable] 2023-09-10T08:17:32,090 9 | double mul, expmul, sum=0., prob_up=0., prob_down=0., prob_down_son=0., smallest, scaled_lk=0., logroot, root_my_BL=0., bl, tmp_br, sum_mu; 2023-09-10T08:17:32,090 | ^~~ 2023-09-10T08:17:32,216 marginal_lik.c:44:15: warning: ‘my_id’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-10T08:17:32,217 44 | if(i!=my_id){ 2023-09-10T08:17:32,218 | ^ 2023-09-10T08:17:32,218 marginal_lik.c:13:46: note: ‘my_id’ was declared here 2023-09-10T08:17:32,219 13 | int curr_scaler_pow, piecewise_scaler_pow, my_id, node_start; 2023-09-10T08:17:32,220 | ^~~~~ 2023-09-10T08:17:32,479 In file included from nrutil.c:2: 2023-09-10T08:17:32,479 nrutil.h:38:22: warning: ‘iminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,480 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:32,481 | ^~~~~~~~ 2023-09-10T08:17:32,482 nrutil.h:38:12: warning: ‘iminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,482 38 | static int iminarg1, iminarg2; 2023-09-10T08:17:32,483 | ^~~~~~~~ 2023-09-10T08:17:32,484 nrutil.h:34:22: warning: ‘imaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,485 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:32,485 | ^~~~~~~~ 2023-09-10T08:17:32,486 nrutil.h:34:12: warning: ‘imaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,487 34 | static int imaxarg1, imaxarg2; 2023-09-10T08:17:32,487 | ^~~~~~~~ 2023-09-10T08:17:32,488 nrutil.h:30:23: warning: ‘lminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,489 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:32,489 | ^~~~~~~~ 2023-09-10T08:17:32,490 nrutil.h:30:13: warning: ‘lminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,490 30 | static long lminarg1, lminarg2; 2023-09-10T08:17:32,491 | ^~~~~~~~ 2023-09-10T08:17:32,491 nrutil.h:26:23: warning: ‘lmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,491 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:32,492 | ^~~~~~~~ 2023-09-10T08:17:32,492 nrutil.h:26:13: warning: ‘lmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,493 26 | static long lmaxarg1, lmaxarg2; 2023-09-10T08:17:32,493 | ^~~~~~~~ 2023-09-10T08:17:32,494 nrutil.h:22:24: warning: ‘minarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,494 22 | static double minarg1, minarg2; 2023-09-10T08:17:32,494 | ^~~~~~~ 2023-09-10T08:17:32,495 nrutil.h:22:15: warning: ‘minarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,495 22 | static double minarg1, minarg2; 2023-09-10T08:17:32,496 | ^~~~~~~ 2023-09-10T08:17:32,496 nrutil.h:18:24: warning: ‘maxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,497 18 | static double maxarg1, maxarg2; 2023-09-10T08:17:32,497 | ^~~~~~~ 2023-09-10T08:17:32,498 nrutil.h:18:15: warning: ‘maxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,499 18 | static double maxarg1, maxarg2; 2023-09-10T08:17:32,500 | ^~~~~~~ 2023-09-10T08:17:32,500 nrutil.h:14:25: warning: ‘dminarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,501 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:32,501 | ^~~~~~~~ 2023-09-10T08:17:32,502 nrutil.h:14:15: warning: ‘dminarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,503 14 | static double dminarg1, dminarg2; 2023-09-10T08:17:32,503 | ^~~~~~~~ 2023-09-10T08:17:32,504 nrutil.h:10:25: warning: ‘dmaxarg2’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,505 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:32,506 | ^~~~~~~~ 2023-09-10T08:17:32,506 nrutil.h:10:15: warning: ‘dmaxarg1’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,507 10 | static double dmaxarg1, dmaxarg2; 2023-09-10T08:17:32,508 | ^~~~~~~~ 2023-09-10T08:17:32,508 nrutil.h:7:15: warning: ‘dsqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,509 7 | static double dsqrarg; 2023-09-10T08:17:32,510 | ^~~~~~~ 2023-09-10T08:17:32,510 nrutil.h:4:15: warning: ‘sqrarg’ defined but not used [-Wunused-variable] 2023-09-10T08:17:32,511 4 | static double sqrarg; 2023-09-10T08:17:32,511 | ^~~~~~ 2023-09-10T08:17:32,706 output_states.c: In function ‘output_state_anc_PP’: 2023-09-10T08:17:32,707 output_states.c:11:12: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-10T08:17:32,709 11 | double sum = 0.0; 2023-09-10T08:17:32,709 | ^~~ 2023-09-10T08:17:32,710 output_states.c:10:15: warning: unused variable ‘count’ [-Wunused-variable] 2023-09-10T08:17:32,711 10 | int i, j, count = 0, node_start, num = 0; 2023-09-10T08:17:32,712 | ^~~~~ 2023-09-10T08:17:33,767 runpastml.c: In function ‘runpastml’: 2023-09-10T08:17:33,768 runpastml.c:117:17: warning: passing argument 1 of ‘sprintf’ from incompatible pointer type [-Wincompatible-pointer-types] 2023-09-10T08:17:33,769 117 | sprintf(stderr, "Model must be either JC or F81, not %s", model); 2023-09-10T08:17:33,770 | ^~~~~~ 2023-09-10T08:17:33,771 | | 2023-09-10T08:17:33,771 | FILE * 2023-09-10T08:17:33,772 In file included from asrml.h:2, 2023-09-10T08:17:33,772 from runpastml.c:1: 2023-09-10T08:17:33,773 /usr/include/stdio.h:358:38: note: expected ‘char * restrict’ but argument is of type ‘FILE *’ 2023-09-10T08:17:33,773 358 | extern int sprintf (char *__restrict __s, 2023-09-10T08:17:33,774 | ~~~~~~~~~~~~~~~~~^~~ 2023-09-10T08:17:34,451 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-10T08:17:34,452 !! 2023-09-10T08:17:34,453 ******************************************************************************** 2023-09-10T08:17:34,454 Please avoid running ``setup.py`` directly. 2023-09-10T08:17:34,454 Instead, use pypa/build, pypa/installer or other 2023-09-10T08:17:34,455 standards-based tools. 2023-09-10T08:17:34,455 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-10T08:17:34,456 ******************************************************************************** 2023-09-10T08:17:34,457 !! 2023-09-10T08:17:34,457 self.initialize_options() 2023-09-10T08:17:34,957 Building wheel for pastml (setup.py): finished with status 'done' 2023-09-10T08:17:34,960 Created wheel for pastml: filename=pastml-0.3.3-cp311-cp311-linux_armv7l.whl size=83207 sha256=8304a9df73e22caf19b1a4f0298e34b65de742c1083cc2024906b9e509125849 2023-09-10T08:17:34,961 Stored in directory: /tmp/pip-ephem-wheel-cache-ajvjvgak/wheels/11/6b/62/8aca7fb0341766c9497d33a12c0de8b6c011058c9315e8033a 2023-09-10T08:17:34,970 Successfully built pastml 2023-09-10T08:17:34,978 Removed build tracker: '/tmp/pip-build-tracker-agyinpk2'