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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SharedObject.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SharedObject_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SharedObject.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘SharedObject/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SharedObject’ version ‘1.21.0’
* package encoding: UTF-8
* 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 ‘SharedObject’ can be installed ... WARNING
Found the following significant warnings:
  altrep.cpp:146:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  altrep.cpp:241:98: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  numericAltrepOperations.cpp:13:27: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
  sharedObjectClass.cpp:93:62: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
  stringAltrepOperations.cpp:13:23: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/SharedObject.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs     2.2Mb
    usrlib   3.9Mb
* 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 whether startup messages can be suppressed ... 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 ... OK
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘SharedObject/libs/SharedObject.so’:
  Found non-API calls to R: ‘COMPLEX0’, ‘REAL0’, ‘SET_S4_OBJECT’,
    ‘UNSET_S4_OBJECT’
These entry points may be removed soon:
‘REAL0’, ‘COMPLEX0’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SharedObject.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SharedObject
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SharedObject’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c C_interface.cpp -o C_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c altrep.cpp -o altrep.o
altrep.cpp: In function ‘SEXPREC* createSharedStringFromSource(SEXP, bool, SEXP)’:
altrep.cpp:146:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  146 |                 Rf_error("Something is wrong with the unit size: %llu\n", unitSize);
      |                                                                  ~~~^     ~~~~~~~~
      |                                                                     |     |
      |                                                                     |     long unsigned int
      |                                                                     long long unsigned int
      |                                                                  %lu
altrep.cpp: In function ‘SEXPREC* unshareString(SEXP, SEXP)’:
altrep.cpp:241:98: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  241 |                         Rf_error("Unknown unit size in the unshareString function, unit size: %llu", (uint64_t)unitSize);
      |                                                                                               ~~~^   ~~~~~~~~~~~~~~~~~~
      |                                                                                                  |   |
      |                                                                                                  |   size_t {aka long unsigned int}
      |                                                                                                  long long unsigned int
      |                                                                                               %lu
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c altrepRegistration.cpp -o altrepRegistration.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c numericAltrepOperations.cpp -o numericAltrepOperations.o
numericAltrepOperations.cpp: In function ‘Rboolean sharedVector_Inspect(SEXP, int, int, int, void (*)(SEXP, int, int, int))’:
numericAltrepOperations.cpp:13:27: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
   13 |         Rprintf(" (len=%llu, type=%d, COW=%d, SC=%d, SS=%d) shared object ID:%s\n", Rf_xlength(x), TYPEOF(x),
      |                        ~~~^                                                         ~~~~~~~~~~~~~
      |                           |                                                                   |
      |                           long long unsigned int                                              R_xlen_t {aka long int}
      |                        %lu
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c sharedMemory.cpp -o sharedMemory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c sharedObjectClass.cpp -o sharedObjectClass.o
sharedObjectClass.cpp: In function ‘void validate_shared_memory(std::string, boost::interprocess::shared_memory_object*)’:
sharedObjectClass.cpp:73:14: warning: comparison of integer expressions of different signedness: ‘boost::interprocess::offset_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |     if (size > free_size)
      |         ~~~~~^~~~~~~~~~~
sharedObjectClass.cpp:93:62: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
   93 |             "Testing shared memory failed, key: %s, size: %lluB.\n"
      |                                                           ~~~^
      |                                                              |
      |                                                              long long unsigned int
      |                                                           %lu
......
   96 |             key.c_str(), (uint64_t)size);
      |                          ~~~~~~~~~~~~~~                       
      |                          |
      |                          uint64_t {aka long unsigned int}
In function ‘uint64_t get_size(boost::interprocess::shared_memory_object*)’,
    inlined from ‘void SharedObjectClass::openSharedMemoryHandle()’ at sharedObjectClass.cpp:121:20:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp: In member function ‘void SharedObjectClass::openSharedMemoryHandle()’:
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
In function ‘uint64_t get_size(boost::interprocess::shared_memory_object*)’,
    inlined from ‘size_t SharedObjectClass::getSharedMemorySize()’ at sharedObjectClass.cpp:148:28:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp: In member function ‘size_t SharedObjectClass::getSharedMemorySize()’:
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
In function ‘uint64_t get_size(boost::interprocess::shared_memory_object*)’,
    inlined from ‘size_t SharedObjectClass::getSharedMemorySize()’ at sharedObjectClass.cpp:141:24:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp: In member function ‘size_t SharedObjectClass::getSharedMemorySize()’:
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
In function ‘uint64_t get_size(boost::interprocess::shared_memory_object*)’,
    inlined from ‘void SharedObjectClass::allocateSharedMemory()’ at sharedObjectClass.cpp:228:20:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp: In member function ‘void SharedObjectClass::allocateSharedMemory()’:
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c stringAltrepOperations.cpp -o stringAltrepOperations.o
stringAltrepOperations.cpp: In function ‘Rboolean sharedString_Inspect(SEXP, int, int, int, void (*)(SEXP, int, int, int))’:
stringAltrepOperations.cpp:13:23: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘R_xlen_t’ {aka ‘long int’} [-Wformat=]
   13 |     Rprintf(" (len=%llu, COW=%d) shared string object\n", Rf_xlength(x),
      |                    ~~~^                                   ~~~~~~~~~~~~~
      |                       |                                             |
      |                       long long unsigned int                        R_xlen_t {aka long int}
      |                    %lu
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o SharedObject.so C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o -lrt -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
mkdir -p ../inst/include&&\
 mkdir -p ../inst/include/SharedObject&&\
 mkdir -p ../inst/usrlib
ar -crv SharedObject.a C_interface.o RcppExports.o altrep.o altrepRegistration.o numericAltrepOperations.o sharedMemory.o sharedObjectClass.o stringAltrepOperations.o utils.o
a - C_interface.o
a - RcppExports.o
a - altrep.o
a - altrepRegistration.o
a - numericAltrepOperations.o
a - sharedMemory.o
a - sharedObjectClass.o
a - stringAltrepOperations.o
a - utils.o
cp "sharedMemory.h" "../inst/include/SharedObject/"&&\
 cp SharedObject.a "../inst/usrlib/"
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-SharedObject/00new/SharedObject/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (SharedObject)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SharedObject)
> 
> test_check("SharedObject")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 403 ]
> 
> proc.time()
   user  system elapsed 
 23.373   2.767  50.885