Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 628/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 2.4.0  (landing page)
Xiuyu Ma
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/EBSeq
git_branch: RELEASE_3_20
git_last_commit: 6f13304
git_last_commit_date: 2024-10-29 09:46:06 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR    OK    ERROR    ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR    OK    ERROR    ERROR  
kjohnson1macOS 13.6.6 Ventura / arm64  ERROR    OK    ERROR    ERROR  

BUILD BIN results for EBSeq on merida1

To the developers/maintainers of the EBSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBSeq.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: EBSeq
Version: 2.4.0
Command: rm -rf EBSeq.buildbin-libdir && mkdir EBSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh EBSeq_2.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R EBSeq.buildbin-libdir
StartedAt: 2024-12-20 12:18:53 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 12:19:04 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 11.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBSeq.buildbin-libdir && mkdir EBSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh EBSeq_2.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R EBSeq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=EBSeq.buildbin-libdir EBSeq_2.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘EBSeq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Rexport.cpp -o Rexport.o
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:28:6: warning: "Boost.Math requires C++14" [-W#warnings]
#    warning "Boost.Math requires C++14"
     ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:176:12: error: no member named 'is_null_pointer' in namespace 'std'; did you mean 'is_pointer'?
using std::is_null_pointer;
      ~~~~~^~~~~~~~~~~~~~~
           is_pointer
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:924:50: note: 'is_pointer' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS is_pointer
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:208:12: error: no member named 'is_final' in namespace 'std'
using std::is_final;
      ~~~~~^
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:259:12: error: no member named 'remove_cv_t' in namespace 'std'; did you mean 'remove_cv'?
using std::remove_cv_t;
      ~~~~~^~~~~~~~~~~
           remove_cv
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:776:50: note: 'remove_cv' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_cv
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:261:12: error: no member named 'remove_const_t' in namespace 'std'; did you mean 'remove_const'?
using std::remove_const_t;
      ~~~~~^~~~~~~~~~~~~~
           remove_const
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:734:50: note: 'remove_const' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_const            {typedef _Tp type;};
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:263:12: error: no member named 'remove_volatile_t' in namespace 'std'; did you mean 'remove_volatile'?
using std::remove_volatile_t;
      ~~~~~^~~~~~~~~~~~~~~~~
           remove_volatile
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:755:50: note: 'remove_volatile' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_volatile               {typedef _Tp type;};
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:265:12: error: no member named 'add_cv_t' in namespace 'std'; did you mean 'add_cv'?
using std::add_cv_t;
      ~~~~~^~~~~~~~
           add_cv
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1347:50: note: 'add_cv' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_cv {
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:267:12: error: no member named 'add_const_t' in namespace 'std'; did you mean 'add_const'?
using std::add_const_t;
      ~~~~~^~~~~~~~~~~
           add_const
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1328:50: note: 'add_const' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_const {
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:269:12: error: no member named 'add_volatile_t' in namespace 'std'; did you mean 'add_volatile'?
using std::add_volatile_t;
      ~~~~~^~~~~~~~~~~~~~
           add_volatile
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1338:50: note: 'add_volatile' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_volatile {
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:273:12: error: no member named 'remove_reference_t' in namespace 'std'; did you mean 'remove_reference'?
using std::remove_reference_t;
      ~~~~~^~~~~~~~~~~~~~~~~~
           remove_reference
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1364:50: note: 'remove_reference' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_reference        {typedef _LIBCPP_NODEBUG_TYPE _Tp type;};
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:275:12: error: no member named 'add_lvalue_reference_t' in namespace 'std'; did you mean 'add_lvalue_reference'?
using std::add_lvalue_reference_t;
      ~~~~~^~~~~~~~~~~~~~~~~~~~~~
           add_lvalue_reference
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1379:50: note: 'add_lvalue_reference' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_lvalue_reference
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:277:12: error: no member named 'add_rvalue_reference_t' in namespace 'std'; did you mean 'add_rvalue_reference'?
using std::add_rvalue_reference_t;
      ~~~~~^~~~~~~~~~~~~~~~~~~~~~
           add_rvalue_reference
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1389:50: note: 'add_rvalue_reference' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_rvalue_reference
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:281:12: error: no member named 'remove_pointer_t' in namespace 'std'; did you mean 'remove_pointer'?
using std::remove_pointer_t;
      ~~~~~^~~~~~~~~~~~~~~~
           remove_pointer
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1446:50: note: 'remove_pointer' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_pointer                      {typedef _LIBCPP_NODEBUG_TYPE _Tp type;};
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:283:12: error: no member named 'add_pointer_t' in namespace 'std'; did you mean 'add_pointer'?
using std::add_pointer_t;
      ~~~~~^~~~~~~~~~~~~
           add_pointer
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1466:50: note: 'add_pointer' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS add_pointer
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:287:12: error: no member named 'make_signed_t' in namespace 'std'; did you mean 'make_signed'?
using std::make_signed_t;
      ~~~~~^~~~~~~~~~~~~
           make_signed
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:2309:29: note: 'make_signed' declared here
struct _LIBCPP_TEMPLATE_VIS make_signed
                            ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:289:12: error: no member named 'make_unsigned_t' in namespace 'std'; did you mean 'make_unsigned'?
using std::make_unsigned_t;
      ~~~~~^~~~~~~~~~~~~~~
           make_unsigned
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:2342:29: note: 'make_unsigned' declared here
struct _LIBCPP_TEMPLATE_VIS make_unsigned
                            ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:293:12: error: no member named 'remove_extent_t' in namespace 'std'; did you mean 'remove_extent'?
using std::remove_extent_t;
      ~~~~~^~~~~~~~~~~~~~~
           remove_extent
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1601:50: note: 'remove_extent' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_extent
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:295:12: error: no member named 'remove_all_extents_t' in namespace 'std'; did you mean 'remove_all_extents'?
using std::remove_all_extents_t;
      ~~~~~^~~~~~~~~~~~~~~~~~~~
           remove_all_extents
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1614:50: note: 'remove_all_extents' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_all_extents
                                                 ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:299:12: error: no member named 'decay_t' in namespace 'std'; did you mean 'decay'?
using std::decay_t;
      ~~~~~^~~~~~~
           decay
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:1669:29: note: 'decay' declared here
struct _LIBCPP_TEMPLATE_VIS decay
                            ^
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:17:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/tools/type_traits.hpp:301:12: error: no member named 'enable_if_t' in namespace 'std'; did you mean 'enable_if'?
using std::enable_if_t;
      ~~~~~^~~~~~~~~~~
           enable_if
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/type_traits:538:63: note: 'enable_if' declared here
template <bool, class _Tp = void> struct _LIBCPP_TEMPLATE_VIS enable_if {};
                                                              ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
make: *** [Rexport.o] Error 1
ERROR: compilation failed for package ‘EBSeq’
* removing ‘/Users/biocbuild/bbs-3.20-bioc/meat/EBSeq.buildbin-libdir/EBSeq’