| Back to Multiple platform build/check report for BioC 3.16 |
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This page was generated on 2022-07-11 11:06:48 -0400 (Mon, 11 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4168 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 3545 |
| 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 | ||||
|
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. |
| Package 882/2130 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.33.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | ERROR | NA | NA | NA | |||||||||
| Package: HIBAG |
| Version: 1.33.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HIBAG |
| StartedAt: 2022-07-10 15:08:57 -0400 (Sun, 10 Jul 2022) |
| EndedAt: 2022-07-10 15:09:13 -0400 (Sun, 10 Jul 2022) |
| EllapsedTime: 15.5 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HIBAG
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* 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 ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/HIBAG’