Multiple platform build/check report for BioC 3.21 - INSTALL results for XDE on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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 XDE on nebbiolo1

To the developers/maintainers of the XDE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XDE.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: XDE

Version: 2.53.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XDE

StartedAt: 2025-02-09 15:28:32 -0500 (Sun, 09 Feb 2025)

EndedAt: 2025-02-09 15:29:30 -0500 (Sun, 09 Feb 2025)

EllapsedTime: 58.4 seconds

RetCode: 0

Status: OK

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XDE
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘XDE’ ...
** this is package ‘XDE’ version ‘2.53.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Cholesky.cpp -o Cholesky.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Matrix_v2.cpp -o Matrix_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Potential_v2.cpp -o Potential_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Random_v2.cpp -o Random_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Rinterface_v2.cpp -o Rinterface_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Structure.cpp -o Structure.o
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(int*, int&, int, char**, std::vector<Potential*>&, std::vector<Update*>&, std::vector<Report*>&, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int)’:
Structure.cpp:1971:25: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 1971 |           filename.empty();
      |           ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/13/string:54,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:1983:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 1983 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:1990:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 1990 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:1996:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 1996 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2002:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2002 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2008:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2008 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2014:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2014 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2020:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2020 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2026:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2026 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2032:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2032 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2038:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2038 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2044:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2044 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2050:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2050 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2056:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2056 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2062:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2062 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2068:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2068 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2074:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2074 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2080:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2080 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2086:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2086 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2092:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2092 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2098:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2098 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2104:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2104 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
Structure.cpp:2110:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
 2110 |       filename.empty();
      |       ~~~~~~~~~~~~~~^~
/usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here
 1220 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Update_v2.cpp -o Update_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c Utility_v2.cpp -o Utility_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c diffExpressed_main.cpp -o diffExpressed_main.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘qqplot’ in package ‘XDE’
** 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 (XDE)