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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:plier.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings plier_1.76.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/plier.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 ‘plier/DESCRIPTION’ ... OK
* this is package ‘plier’ version ‘1.76.0’
* 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 ‘plier’ can be installed ... WARNING
Found the following significant warnings:
  rwrapper.cpp:192:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  rwrapper.cpp:193:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  rwrapper.cpp:194:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/plier.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
prepare_Rd: justPlier.Rd:50-52: Dropping empty section \examples
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/plier/libs/plier.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

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. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/plier.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL plier
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘plier’ ...
** using staged installation
** libs
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 affyplier.cpp -o affyplier.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c plier_impl.cpp -o plier_impl.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’:
plieralg.cpp:905:21: warning: variable ‘icount’ set but not used [-Wunused-but-set-variable]
  905 |         long count, icount;
      |                     ^~~~~~
plieralg.cpp: At global scope:
plieralg.cpp:49:12: warning: ‘g_ErrorCode’ defined but not used [-Wunused-variable]
   49 | static int g_ErrorCode=NoError;
      |            ^~~~~~~~~~~
plieralg.cpp: In function ‘long int NewtonPlier(plier_data*, double&)’:
plieralg.cpp:1257:31: warning: ‘LogLikelihood’ may be used uninitialized [-Wmaybe-uninitialized]
 1257 |         output = LogLikelihood/nSize;
      |                  ~~~~~~~~~~~~~^~~~~~
plieralg.cpp:910:16: note: ‘LogLikelihood’ was declared here
  910 |         double LogLikelihood;
      |                ^~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp: In function ‘void one_probeset(bool*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, bool*, bool*, bool*, double*, double*, int*, int*, int*, long int*, double*, double*, double*, double*, int*)’:
rwrapper.cpp:192:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  192 |     delete pm_ptr;
      |            ^~~~~~
rwrapper.cpp:151:44: note: returned from ‘void* operator new [](std::size_t)’
  151 |     double **pm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:193:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  193 |     delete mm_ptr;
      |            ^~~~~~
rwrapper.cpp:152:44: note: returned from ‘void* operator new [](std::size_t)’
  152 |     double **mm_ptr = new double *[*num_exp];
      |                                            ^
rwrapper.cpp:194:12: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  194 |     delete rpct;
      |            ^~~~
rwrapper.cpp:159:39: note: returned from ‘void* operator new [](std::size_t)’
  159 |     long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
      |                                       ^
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-plier/00new/plier/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (plier)