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This page was generated on 2023-06-06 11:00:45 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for XDE on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2185/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.47.0  (landing page)
Robert Scharpf
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/XDE
git_branch: devel
git_last_commit: 1304b47
git_last_commit_date: 2023-04-25 13:46:16 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

Summary

Package: XDE
Version: 2.47.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings XDE_2.47.0.tar.gz
StartedAt: 2023-06-06 09:30:59 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 09:35:17 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 258.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: XDE.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings XDE_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/XDE.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.47.0’
* 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 ‘XDE’ can be installed ... WARNING
Found the following significant warnings:
  Structure.cpp:1971:18: 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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
  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]
See ‘/home/biocbuild/bbs-3.18-bioc/meat/XDE.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.7Mb
* 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 R 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘XDE.Rnw’... OK
  ‘XdeParameterClass.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/XDE.Rcheck/00check.log’
for details.

Installation output

XDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL XDE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Cholesky.cpp -o Cholesky.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Matrix_v2.cpp -o Matrix_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Potential_v2.cpp -o Potential_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Random_v2.cpp -o Random_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8,
                 from Rinterface_v2.cpp:2:
Random.h:19: warning: "PI" redefined
   19 | #define PI         3.14159265
      | 
In file included from /home/biocbuild/R/R-4.3.0/include/R.h:72,
                 from Rinterface_v2.cpp:1:
/home/biocbuild/R/R-4.3.0/include/R_ext/Constants.h:39: note: this is the location of the previous definition
   39 | #define PI             M_PI
      | 
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -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:1971:18: 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++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       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();
      |       ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
                 from Structure.h:4,
                 from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
 1002 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Update_v2.cpp -o Update_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Utility_v2.cpp -o Utility_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
Random.h:19: warning: "PI" redefined
   19 | #define PI         3.14159265
      | 
In file included from /home/biocbuild/R/R-4.3.0/include/R.h:72,
                 from diffExpressed_main.cpp:4:
/home/biocbuild/R/R-4.3.0/include/R_ext/Constants.h:39: note: this is the location of the previous definition
   39 | #define PI             M_PI
      | 
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/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)

Tests output

XDE.Rcheck/tests/doRUnit.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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.

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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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "XDE"
+ 
+ 	if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ 		path <- file.path( getwd(), "..", "inst", "unitTests" )
+ 	} else {
+ 		path <- system.file( package=pkg, "unitTests" )
+ 	}
+ 
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 
+ 	##xmap.clear.cache()
+ 
+ 	##Fail on warnings
+ 	options( warn=2 )
+ 
+ 	## Get the pattern (if there is one?)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ 	if( is.null( patt ) || nchar( patt ) == 0 ) {
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     dirs=path,
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	} else {
+ 		##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 					     dirs=path )
+ 	}
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "XDE"

$getwd
[1] "/home/biocbuild/bbs-3.18-bioc/meat/XDE.Rcheck/tests"

$pathToUnitTests
[1] "/tmp/RtmpeXtEwP/RLIBS_19dbee340214a7/XDE/unitTests"

Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.47.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Jun  6 09:34:36 2023 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XDE unit testing - 0 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  7.592   0.255   7.845

Example timings

XDE.Rcheck/XDE-Ex.timings

nameusersystemelapsed
ExpressionSetList-class0.0150.0040.019
Parameters-class0.0010.0000.001
XdeMcmc-class000
XdeParameter-class0.0010.0000.001
burnin0.0010.0000.001
empiricalStart0.1750.0080.185
expressionSetList0.0150.0000.015
firstMcmc0.1550.0120.168
geneCenter0.0780.0000.078
hyperparameters0.0980.0000.098
lastMcmc000
output0.0740.0000.074
ssStatistic0.8270.0440.871
studyCenter0.0540.0040.057
symbolsInteresting0.1410.0040.146
xde0.0010.0000.000
xmcmc0.0820.0000.084
xsScores0.0580.0040.062