| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:25 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
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To the developers/maintainers of the HIBAG package: - 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 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. |
| Package 916/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.35.3 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: HIBAG |
| Version: 1.35.3 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HIBAG |
| StartedAt: 2023-04-11 15:01:41 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 15:02:08 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 27.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HIBAG
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘HIBAG’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c HIBAG.cpp -o HIBAG.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA.cpp -o LibHLA.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_avx512bw.cpp -o LibHLA_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_avx512f.cpp -o LibHLA_ext_avx512f.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_avx512vpopcnt.cpp -o LibHLA_ext_avx512vpopcnt.o
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static HLA_LIB::THLAType HLA_LIB::CAlg_Prediction::_BestGuess_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
| ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:358:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
358 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
| ^
LibHLA_ext_avx512vpopcnt.cpp:358:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
358 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static double HLA_LIB::CAlg_Prediction::_PostProb_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&, const HLA_LIB::THLAType&)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
| ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:431:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
431 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
| ^
LibHLA_ext_avx512vpopcnt.cpp:431:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
431 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static double HLA_LIB::CAlg_Prediction::_PostProb2_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&, double*)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
239 | __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
| ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:500:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
500 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
237 | __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
| ^
LibHLA_ext_avx512vpopcnt.cpp:500:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
500 | const TGenoStruct_512vpopcnt GS(Haplo, Geno);
| ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o HIBAG.so HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_avx512vpopcnt.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o -lgcc -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-HIBAG/00new/HIBAG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (HIBAG)