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BioC 3.5: BUILD BIN report for puma on veracruz2

This page was generated on 2017-08-16 13:28:00 -0400 (Wed, 16 Aug 2017).

Package 1029/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
puma 3.18.0
Xuejun Liu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/puma
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: puma
Version: 3.18.0
Command: rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R puma.buildbin-libdir
StartedAt: 2017-08-16 10:57:36 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 10:58:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 30.0 seconds
RetCode: 0
Status:  OK 
PackageFile: puma_3.18.0.tgz
PackageFileSize: 3.548 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf puma.buildbin-libdir && mkdir puma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh puma_3.18.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R puma.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=puma.buildbin-libdir puma_3.18.0.tar.gz'
>>>>>>> 

* installing *source* package ‘puma’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
PMmultimgmos.c:425:23: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER i,j;
                      ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cregistration.c -o cregistration.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c donlp2.c -o donlp2.o
donlp2.c:270:5: warning: '/*' within block comment [-Wcomment]
    /*  bloc                                                                  */
    ^
donlp2.c:471:39: warning: unused variable 'gxi' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                                      ^
donlp2.c:471:28: warning: unused variable 'bd0' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                           ^
donlp2.c:471:43: warning: unused variable 'hxi' [-Wunused-variable]
    static DDOUBLE   tol1 ,bd0,infiny,gxi,hxi,term;
                                          ^
donlp2.c:470:26: warning: unused variable 'k' [-Wunused-variable]
    static IINTEGER  i,j,k;
                         ^
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive  
^
donlp2.c:2090:21: warning: unused variable 'eval_err' [-Wunused-variable]
    static LLOGICAL eval_err;
                    ^
donlp2.c:2076:22: warning: unused variable 'l' [-Wunused-variable]
    static IINTEGER  l,l0,i,j,k,csssig,csirup,csreg,cschgx;
                     ^
donlp2.c:4123:27: warning: unused variable 'term1' [-Wunused-variable]
    static DDOUBLE   term,term1;
                          ^
donlp2.c:4127:5: warning: unused label 'L100' [-Wunused-label]
    L100:
    ^˜˜˜˜
donlp2.c:4412:24: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER  i,j;
                       ^
donlp2.c:5027:28: warning: unused variable 'l' [-Wunused-variable]
    static IINTEGER  i,j,k,l,i1,icur,ipiv;
                           ^
donlp2.c:5755:48: warning: unused variable 'term2' [-Wunused-variable]
                    su1,su2,condr,infiny,term1,term2,
                                               ^
donlp2.c:6418:9: warning: unused label 'L500' [-Wunused-label]
        L500:
        ^˜˜˜˜
donlp2.c:7153:5: warning: unused label 'L20' [-Wunused-label]
    L20:
    ^˜˜˜
donlp2.c:7878:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:7916:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
donlp2.c:8009:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:8044:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
donlp2.c:8141:16: warning: unused variable 'j' [-Wunused-variable]
    IINTEGER i,j;
               ^
donlp2.c:8177:14: warning: unused variable 'i' [-Wunused-variable]
    IINTEGER i;
             ^
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gme.c -o gme.o
gme.c:268:6: warning: unused variable 'finishflag' [-Wunused-variable]
        int finishflag = 1;
            ^
gme.c:265:6: warning: unused variable 'niter' [-Wunused-variable]
        int niter = 1, nx;
            ^
gme.c:354:9: warning: unused variable 'xxx' [-Wunused-variable]
    int xxx=(2+in_param->num_prctile)*in_param->numofgenes*in_param->chips;
        ^
gme.c:347:15: warning: unused variable 'k' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                     ^
gme.c:349:10: warning: unused variable 'alphai' [-Wunused-variable]
        double  alphai, c, d,alpha_temp,kk_gene;
                ^
gme.c:347:20: warning: unused variable 'px' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                          ^
gme.c:347:18: warning: unused variable 'q' [-Wunused-variable]
        int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
                        ^
gme.c:349:23: warning: unused variable 'alpha_temp' [-Wunused-variable]
        double  alphai, c, d,alpha_temp,kk_gene;
                             ^
gme.c:894:10: warning: unused variable 'res_isoform' [-Wunused-variable]
    SEXP res_isoform=NULL;
         ^
gme.c:897:11: warning: unused variable 't' [-Wunused-variable]
        int i, j,t,t1;
                 ^
gme.c:897:13: warning: unused variable 't1' [-Wunused-variable]
        int i, j,t,t1;
                   ^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:114: warning: '&&' within '||' [-Wlogical-op-parentheses]
                   while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
                                                                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ipplr_c.c:255:114: note: place parentheses around the '&&' expression to silence this warning
                   while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
                                                                                                                               ^
                                                                            (                                                          )
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c multimgmos.c -o multimgmos.o
multimgmos.c:264:8: warning: unused variable 'Rf_pf' [-Wunused-variable]
        FILE *pf=NULL;
              ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:285:13: note: expanded from macro 'pf'
#define pf              Rf_pf
                        ^
multimgmos.c:660:23: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER i,j;
                      ^
multimgmos.c:773:9: warning: unused variable 's5' [-Wunused-variable]
        double s5[MAX_NUM_PROBE]={0.0};
               ^
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
        double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
                                                                                                     ^˜˜
                                                                                                     {  }
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c newx.c -o newx.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
        double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                                                   ^
pplr_c.c:442:38: warning: unused variable 'var_c' [-Wunused-variable]
    double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
                                     ^
pplr_c.c:444:35: warning: unused variable 'lam_temp' [-Wunused-variable]
    double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
                                  ^
pplr_c.c:444:12: warning: unused variable 'mu_temp' [-Wunused-variable]
    double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
           ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:181:24: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^
pumaclust_c.c:181:24: note: use function 'fabs' instead
        while (foptold-fopt > abs(in_param.eps*fopt))
                              ^˜˜
                              fabs
pumaclust_c.c:384:13: warning: unused variable 't2' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                   ^
pumaclust_c.c:384:30: warning: unused variable 'expr_temp' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                                    ^
pumaclust_c.c:384:9: warning: unused variable 't1' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
               ^
pumaclust_c.c:384:41: warning: unused variable 'var_temp' [-Wunused-variable]
        double t1, t2, **mujd=NULL, expr_temp, var_temp;
                                               ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
pumaclustii_c.c:972:21: warning: unused variable 'j' [-Wunused-variable]
    static IINTEGER j;
                    ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c user_eval.c -o user_eval.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/puma.buildbin-libdir/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (puma)


>>>>>>> 
>>>>>>> FIXING LINKS FOR puma.buildbin-libdir/puma/libs//puma.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "puma.buildbin-libdir/puma/libs//puma.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "puma.buildbin-libdir/puma/libs//puma.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "puma.buildbin-libdir/puma/libs//puma.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "puma.buildbin-libdir/puma/libs//puma.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "puma.buildbin-libdir/puma/libs//puma.so"