This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves"
| 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves"
| 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
| 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life"
| 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life"
| 4493 |
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 |
INSTALL results for SharedObject on teran2
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
Command output
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SharedObject
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 13.2.0-23ubuntu4) 13.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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}
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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-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-3.20-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 /media/volume/teran2_disk/biocbuild/bbs-3.20-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)