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This page was generated on 2024-07-19 17:38 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1958/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SharedObject 1.18.0  (landing page)
Jiefei Wang
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/SharedObject
git_branch: RELEASE_3_19
git_last_commit: dff3b5c
git_last_commit_date: 2024-04-30 11:17:15 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    NA  


INSTALL results for SharedObject on nebbiolo1

To the developers/maintainers of the SharedObject package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SharedObject.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SharedObject
Version: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SharedObject
StartedAt: 2024-07-17 15:02:38 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 15:03:03 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 25.4 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SharedObject
###
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* installing to library ‘/home/biocbuild/bbs-3.19-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 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
mkdir -p ../inst/include&&\
 mkdir -p ../inst/include/SharedObject&&\
 mkdir -p ../inst/usrlib
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c C_interface.cpp -o C_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c altrepRegistration.cpp -o altrepRegistration.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c sharedMemory.cpp -o sharedMemory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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}
sharedObjectClass.cpp: In member function ‘void SharedObjectClass::openSharedMemoryHandle()’:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
sharedObjectClass.cpp: In member function ‘size_t SharedObjectClass::getSharedMemorySize()’:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
sharedObjectClass.cpp: In member function ‘void SharedObjectClass::allocateSharedMemory()’:
sharedObjectClass.cpp:29:12: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   29 |     return size;
      |            ^~~~
sharedObjectClass.cpp:27:14: note: ‘size’ was declared here
   27 |     offset_t size;
      |              ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c utils.cpp -o utils.o
utils.cpp: In function ‘void sharedMemoryPrint(const char*, ...)’:
utils.cpp:39:17: warning: format not a string literal and no format arguments [-Wformat-security]
   39 |         Rprintf(buffer);
      |                 ^~~~~~
utils.cpp: In function ‘void altrepPrint(const char*, ...)’:
utils.cpp:49:17: warning: format not a string literal and no format arguments [-Wformat-security]
   49 |         Rprintf(buffer);
      |                 ^~~~~~
utils.cpp: In function ‘void packagePrint(const char*, ...)’:
utils.cpp:59:17: warning: format not a string literal and no format arguments [-Wformat-security]
   59 |         Rprintf(buffer);
      |                 ^~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR
ar -crv SharedObject.a *.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-3.19-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)