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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings casper_2.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.40.0’
* 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 for sufficient/correct file permissions ... 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 unsigned int)nl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1117:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long unsigned int)nl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1123:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long unsigned int)nl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1131:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1133:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long unsigned int)nrl) * 8)))' and NULL [-Waddress]
  cstat.cpp:1141:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))' and NULL [-Waddress]
  cstat.cpp:1143:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((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 ‘/home/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.6Mb
* 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 loading without being on the library search path ... 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 ... WARNING
File ‘casper/libs/casper.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Objects: ‘fragFunc.o’, ‘hash.o’, ‘join_exons.o’, ‘makeIslands.o’,
      ‘model.o’, ‘pathCounts.o’, ‘procBam.o’, ‘simReads.o’,
      ‘simReadsfunc.o’, ‘uniqQname.o’, ‘variant.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL casper
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘casper’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c casper.cpp -o casper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -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 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 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 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 unsigned int)i) * 8)))) + ((sizetype)(((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 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 unsigned int)i) * 8)))) + ((sizetype)(((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 unsigned int)nrl) * 8)))' and NULL [-Waddress]
 1143 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c dataframe.cpp -o dataframe.o
In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/map:62,
                 from variant.h:3,
                 from variant_cmp.h:1,
                 from model.h:1,
                 from model_cmp.h:1,
                 from dataframe.h:1,
                 from dataframe.cpp:2:
In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_unique_pos(const key_type&) [with _Key = Variant*; _Val = Variant*; _KeyOfValue = std::_Identity<Variant*>; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]',
    inlined from 'std::pair<std::_Rb_tree_iterator<_Val>, bool> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique(_Arg&&) [with _Arg = Variant* const&; _Key = Variant*; _Val = Variant*; _KeyOfValue = std::_Identity<Variant*>; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_tree.h:2167:28,
    inlined from 'std::pair<typename std::_Rb_tree<_Key, _Key, std::_Identity<_Tp>, _Compare, typename __gnu_cxx::__alloc_traits<_Alloc>::rebind<_Key>::other>::const_iterator, bool> std::set<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = Variant*; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_set.h:514:25,
    inlined from 'void DataFrame::path2Variants(std::set<Variant*, VariantCmp>*, std::set<Variant*, VariantCmp>*, std::set<std::__cxx11::basic_string<char> >*, bool*, std::set<Variant*, VariantCmp>*, Fragment*)' at dataframe.cpp:598:36:
/home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_tree.h:2114:42: warning: 'bestvar' may be used uninitialized [-Wmaybe-uninitialized]
 2114 |           __comp = _M_impl._M_key_compare(__k, _S_key(__x));
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
dataframe.cpp: In member function 'void DataFrame::path2Variants(std::set<Variant*, VariantCmp>*, std::set<Variant*, VariantCmp>*, std::set<std::__cxx11::basic_string<char> >*, bool*, std::set<Variant*, VariantCmp>*, Fragment*)':
dataframe.cpp:481:12: note: 'bestvar' was declared here
  481 |   Variant *bestvar;
      |            ^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c discretedf.cpp -o discretedf.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c model_cmp.cpp -o model_cmp.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rcasper.cpp -o rcasper.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall  -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o casper.so 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 -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-casper/00new/casper/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (casper)