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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 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]
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.7Mb
* 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/casper.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL casper
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘casper’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c casper.cpp -o casper.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c dataframe.cpp -o dataframe.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c discretedf.cpp -o discretedf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c model.cpp -o model.o
In file included from /usr/include/stdio.h:980,
                 from model.cpp:1:
In function ‘int sprintf(char*, const char*, ...)’,
    inlined from ‘char* Model::toString()’ at model.cpp:147:10:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘<unknown>’ [-Wrestrict]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c model_cmp.cpp -o model_cmp.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c rcasper.cpp -o rcasper.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c variant.cpp -o variant.o
In file included from /usr/include/stdio.h:980,
                 from variant.cpp:1:
In function ‘int sprintf(char*, const char*, ...)’,
    inlined from ‘void Variant::toString(char*)’ at variant.cpp:164:45:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: ‘__builtin___sprintf_chk’ argument 5 overlaps destination object ‘str’ [-Wrestrict]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
variant.cpp: In member function ‘void Variant::toString(char*)’:
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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)