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This page was generated on 2022-07-07 11:11:16 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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

BUILD results for HIBAG on kjohnson


To the developers/maintainers of the HIBAG package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HIBAG.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 880/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HIBAG 1.33.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/HIBAG
git_branch: master
git_last_commit: 26a89e5
git_last_commit_date: 2022-04-26 11:23:45 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  ERROR    ERROR  skippedskipped

Summary

Package: HIBAG
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HIBAG
StartedAt: 2022-07-06 22:31:26 -0400 (Wed, 06 Jul 2022)
EndedAt: 2022-07-06 22:31:37 -0400 (Wed, 06 Jul 2022)
EllapsedTime: 10.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HIBAG
###
##############################################################################
##############################################################################


* checking for file ‘HIBAG/DESCRIPTION’ ... OK
* preparing ‘HIBAG’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘HIBAG’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c HIBAG.cpp -o HIBAG.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA.cpp -o LibHLA.o
LibHLA.cpp:1240:7: warning: variable 'cpu_auto_avx2' set but not used [-Wunused-but-set-variable]
        bool cpu_auto_avx2, cpu_max;
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
LibHLA_ext_avx.cpp:529:6: error: out-of-line definition of '_PrepHaploMatch_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PrepHaploMatch_def'?
void SIMD_NAME(CAlg_Prediction::_PrepHaploMatch)(const TGenotype &Geno,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     _PrepHaploMatch_def
LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME'
#define SIMD_NAME(NAME)  NAME ## _avx
                         ^
<scratch space>:297:1: note: expanded from here
_PrepHaploMatch_avx
^
./LibHLA.h:416:15: note: '_PrepHaploMatch_def' declared here
                static void _PrepHaploMatch_def(const TGenotype &pG,
                            ^
LibHLA_ext_avx.cpp:536:10: error: out-of-line definition of '_BestGuess_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_BestGuess_def'?
THLAType SIMD_NAME(CAlg_Prediction::_BestGuess)(const CHaplotypeList &Haplo,
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         _BestGuess_def
LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME'
#define SIMD_NAME(NAME)  NAME ## _avx
                         ^
<scratch space>:298:1: note: expanded from here
_BestGuess_avx
^
./LibHLA.h:421:19: note: '_BestGuess_def' declared here
                static THLAType _BestGuess_def(const CHaplotypeList &Haplo, const TGenotype &Geno);
                                ^
LibHLA_ext_avx.cpp:542:8: error: out-of-line definition of '_PostProb_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PostProb_def'?
double SIMD_NAME(CAlg_Prediction::_PostProb)(const CHaplotypeList &Haplo,
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       _PostProb_def
LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME'
#define SIMD_NAME(NAME)  NAME ## _avx
                         ^
<scratch space>:299:1: note: expanded from here
_PostProb_avx
^
./LibHLA.h:424:17: note: '_PostProb_def' declared here
                static double _PostProb_def(const CHaplotypeList &Haplo, const TGenotype &Geno, const THLAType &HLA);
                              ^
LibHLA_ext_avx.cpp:548:8: error: out-of-line definition of '_PostProb2_avx' does not match any declaration in 'HLA_LIB::CAlg_Prediction'; did you mean '_PostProb2_def'?
double SIMD_NAME(CAlg_Prediction::_PostProb2)(const CHaplotypeList &Haplo,
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       _PostProb2_def
LibHLA_ext_avx.cpp:70:26: note: expanded from macro 'SIMD_NAME'
#define SIMD_NAME(NAME)  NAME ## _avx
                         ^
<scratch space>:300:1: note: expanded from here
_PostProb2_avx
^
./LibHLA.h:427:17: note: '_PostProb2_def' declared here
                static double _PostProb2_def(const CHaplotypeList &Haplo, const TGenotype &Geno, double Prob[]);
                              ^
4 errors generated.
make: *** [LibHLA_ext_avx.o] Error 1
ERROR: compilation failed for package ‘HIBAG’
* removing ‘/private/tmp/Rtmp9v0TIb/Rinstb977527b1269/HIBAG’
      -----------------------------------
ERROR: package installation failed