##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:casper.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings casper_2.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/casper.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'casper/DESCRIPTION' ... OK
* this is package 'casper' version '2.43.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'casper' can be installed ... WARNING
Found the following significant warnings:
  cstat.cpp:1111:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1117:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1123:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1131:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1133:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1141:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1143:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
  model.cpp:147:24: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
  seppel.cpp:484:19: warning: 'void operator delete [](void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  variant.cpp:164:52: warning: 'sprintf' argument 3 overlaps destination object 'str' [-Wrestrict]
See 'F:/biocbuild/bbs-3.22-bioc/meat/casper.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) asymmetryCheck.Rd:21: Lost braces
    21 |   \item{...}{Other arguments to be passed on to code{plot}}
       |                                                     ^
checkRd: (-1) qqnormGenomeWide.Rd:35: Lost braces
    35 |   \item{...}{Other arguments to be passed on to code{plot}}
       |                                                     ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/casper.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL casper
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'casper' ...
** this is package 'casper' version '2.43.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c casper.cpp -o casper.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c cstat.cpp -o cstat.o
cstat.cpp: In function 'void free_vector(float*, int, int)':
cstat.cpp:1111:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
 1111 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^
cstat.cpp: In function 'void free_dvector(double*, int, int)':
cstat.cpp:1117:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 8)))' and NULL [-Waddress]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^
cstat.cpp: In function 'void free_ivector(int*, int, int)':
cstat.cpp:1123:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
 1123 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^
cstat.cpp: In function 'void free_dmatrix(double**, int, int, int, int)':
cstat.cpp:1131:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 8)))' and NULL [-Waddress]
 1131 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^
cstat.cpp:1133:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
 1133 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^
cstat.cpp: In function 'void free_imatrix(int**, int, int, int, int)':
cstat.cpp:1141:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 4)))' and NULL [-Waddress]
 1141 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^
cstat.cpp:1143:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
 1143 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^
In function 'void free_dvector(double*, int, int)',
    inlined from 'double f1dim(double)' at cstat.cpp:5501:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double f1dim(double)':
cstat.cpp:5498:13: note: returned from 'double* dvector(int, int)'
 5498 |   xt=dvector(1,ncom);
      |      ~~~~~~~^~~~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void choldc(double**, int, double**, bool*)' at cstat.cpp:1752:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void choldc(double**, int, double**, bool*)':
cstat.cpp:1739:13: note: returned from 'double* dvector(int, int)'
 1739 |   p= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void choldc(double**, int, double**, bool*)' at cstat.cpp:1752:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void choldc(double**, int, double**, bool*)':
cstat.cpp:1739:13: note: returned from 'double* dvector(int, int)'
 1739 |   p= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void nn_bayes(double*, double**, double**, int, double, double*, double**, double, double*, double**)' at cstat.cpp:284:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void nn_bayes(double*, double**, double**, int, double, double*, double**, double, double*, double**)':
cstat.cpp:277:14: note: returned from 'double* dvector(int, int)'
  277 |   z = dvector(1,p);
      |       ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'double nn_integral(double*, double*, double**, double*, double*, double*, double**, double*, int*, int*)' at cstat.cpp:342:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double nn_integral(double*, double*, double**, double*, double*, double*, double**, double*, int*, int*)':
cstat.cpp:329:13: note: returned from 'double* dvector(int, int)'
  329 |   m= dvector(1,*p);
      |      ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void ludc(double**, int, int*, double*)' at cstat.cpp:1947:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void ludc(double**, int, int*, double*)':
cstat.cpp:1901:13: note: returned from 'double* dvector(int, int)'
 1901 |   vv=dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lu_inverse(double**, int, double**)' at cstat.cpp:1999:38:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lu_inverse(double**, int, double**)':
cstat.cpp:1991:34: note: returned from 'double* dvector(int, int)'
 1991 |  indx= ivector(1,n); col= dvector(1,n);
      |                           ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void eigenvals(double**, int, double*)' at cstat.cpp:2033:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void eigenvals(double**, int, double*)':
cstat.cpp:2025:13: note: returned from 'double* dvector(int, int)'
 2025 |   e= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'double dmvnormC(double*, int, double*, double**, double, int)' at cstat.cpp:2494:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvnormC(double*, int, double*, double**, double, int)':
cstat.cpp:2490:13: note: returned from 'double* dvector(int, int)'
 2490 |   z= dvector(1,n); z2= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'double dmvnormC(double*, int, double*, double**, double, int)' at cstat.cpp:2494:36:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvnormC(double*, int, double*, double**, double, int)':
cstat.cpp:2490:31: note: returned from 'double* dvector(int, int)'
 2490 |   z= dvector(1,n); z2= dvector(1,n);
      |                        ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'double dmvtC(double*, int, double*, double**, double, int, int)' at cstat.cpp:2788:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvtC(double*, int, double*, double**, double, int, int)':
cstat.cpp:2784:13: note: returned from 'double* dvector(int, int)'
 2784 |   z= dvector(1,n); z2= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'double dmvtC(double*, int, double*, double**, double, int, int)' at cstat.cpp:2788:36:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvtC(double*, int, double*, double**, double, int, int)':
cstat.cpp:2784:31: note: returned from 'double* dvector(int, int)'
 2784 |   z= dvector(1,n); z2= dvector(1,n);
      |                        ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void rmvnormC(double*, int, double*, double**)' at cstat.cpp:2733:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void rmvnormC(double*, int, double*, double**)':
cstat.cpp:2730:13: note: returned from 'double* dvector(int, int)'
 2730 |   z= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:499:17:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:493:20: note: returned from 'double* dvector(int, int)'
  493 |     zeroes= dvector(1,*p);
      |             ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:503:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:480:16: note: returned from 'double* dvector(int, int)'
  480 |   b_ls= dvector(1,*p); ypred= dvector(1,*n);
      |         ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:503:40:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:480:38: note: returned from 'double* dvector(int, int)'
  480 |   b_ls= dvector(1,*p); ypred= dvector(1,*n);
      |                               ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:440:17:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:433:20: note: returned from 'double* dvector(int, int)'
  433 |     zeroes= dvector(1,*p);
      |             ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:444:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:418:16: note: returned from 'double* dvector(int, int)'
  418 |   b_ls= dvector(1,*p); ypred= dvector(1,*n);
      |         ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:444:40:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:418:38: note: returned from 'double* dvector(int, int)'
  418 |   b_ls= dvector(1,*p); ypred= dvector(1,*n);
      |                               ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void rmvtC(double*, int, double*, double**, int)' at cstat.cpp:2921:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void rmvtC(double*, int, double*, double**, int)':
cstat.cpp:2918:13: note: returned from 'double* dvector(int, int)'
 2918 |   z= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void polint(double*, double*, int, double, double*, double*)' at cstat.cpp:5136:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void polint(double*, double*, int, double, double*, double*)':
cstat.cpp:5108:13: note: returned from 'double* dvector(int, int)'
 5108 |   d= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void polint(double*, double*, int, double, double*, double*)' at cstat.cpp:5137:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void polint(double*, double*, int, double, double*, double*)':
cstat.cpp:5107:13: note: returned from 'double* dvector(int, int)'
 5107 |   c= dvector(1,n);
      |      ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)' at cstat.cpp:5490:14:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)':
cstat.cpp:5457:15: note: declared here
 5457 | double *pcom,*xicom,(*nrfunc)(double []);
      |               ^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)' at cstat.cpp:5491:14:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer 'pcom' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)':
cstat.cpp:5457:9: note: declared here
 5457 | double *pcom,*xicom,(*nrfunc)(double []);
      |         ^~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5449:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5413:18: note: returned from 'double* dvector(int, int)'
 5413 |   dirinit=dvector(1,n);
      |           ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5450:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5412:15: note: returned from 'double* dvector(int, int)'
 5412 |   thtt=dvector(1,n);
      |        ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
    inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5451:15:
cstat.cpp:1117:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
 1117 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5411:14: note: returned from 'double* dvector(int, int)'
 5411 |   tht=dvector(1,n);
      |       ~~~~~~~^~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c dataframe.cpp -o dataframe.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c discretedf.cpp -o discretedf.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c exon.cpp -o exon.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c fragFunc.c -o fragFunc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c fragment.cpp -o fragment.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c functions.c -o functions.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c hash.c -o hash.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c join_exons.c -o join_exons.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c makeIslands.c -o makeIslands.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c model.cpp -o model.o
model.cpp: In member function 'char* Model::toString()':
model.cpp:147:24: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
  147 |                 sprintf(str, "%s {%s}", str, vstr);
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c model_cmp.cpp -o model_cmp.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c pathCounts.c -o pathCounts.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c procBam.c -o procBam.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcasper.cpp -o rcasper.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c seppel.cpp -o seppel.o
seppel.cpp: In member function 'void Seppel::exploreUnif(int, std::set<Variant*, VariantCmp>*)':
seppel.cpp:484:9: warning: array subscript -1 is outside array bounds of 'void [24]' [-Warray-bounds=]
  484 |         delete [] possiblemodels;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~
seppel.cpp:402:55: note: at offset -8 into object of size 24 allocated by 'operator new'
  402 |   vector<Model*>* possiblemodels = new vector<Model*>();
      |                                                       ^
seppel.cpp:484:19: warning: 'void operator delete [](void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  484 |         delete [] possiblemodels;
      |                   ^~~~~~~~~~~~~~
seppel.cpp:402:55: note: returned from 'void* operator new(std::size_t)'
  402 |   vector<Model*>* possiblemodels = new vector<Model*>();
      |                                                       ^
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c simReads.c -o simReads.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c smartmodeldist.cpp -o smartmodeldist.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c uniqQname.c -o uniqQname.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c variant.cpp -o variant.o
variant.cpp: In member function 'void Variant::toString(char*)':
variant.cpp:164:52: warning: 'sprintf' argument 3 overlaps destination object 'str' [-Wrestrict]
  164 |         for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
      |                                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
variant.cpp:156:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
  156 | void Variant::toString(char *str)
      |                        ~~~~~~^~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++17 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-casper/00new/casper/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (casper)