Xiuwen Zheng
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8011316 |
| git_last_commit_date: 2023-05-01 20:07:45 -0400 (Mon, 01 May 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:36 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1800/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.0.1 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SAIGEgds package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SAIGEgds.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. |
| Package: SAIGEgds |
| Version: 2.0.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SAIGEgds.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SAIGEgds_2.0.1.tar.gz |
| StartedAt: 2023-10-16 06:21:26 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 06:24:16 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 169.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SAIGEgds.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SAIGEgds_2.0.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SAIGEgds/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SAIGEgds' version '2.0.1'
* 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 whether package 'SAIGEgds' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'SeqArray:::.IsForking' 'SeqArray:::.McoreParallel'
'SeqArray:::.NumParallel' 'SeqArray:::.seqProgForward'
'SeqArray:::.seqProgress' 'survey:::saddle'
See the note in ?`:::` about the use of this operator.
* 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/SAIGEgds/libs/x64/SAIGEgds.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqAssocGLMM_ACAT_O 6.11 0.04 6.16
seqAssocGLMM_ACAT_V 5.17 0.05 5.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck/00check.log'
for details.
SAIGEgds.Rcheck/00install.out
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c saige_misc.cpp -o saige_misc.o
saige_misc.cpp: In function 'SEXPREC* saige_grm_sp_calc_ijx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_misc.cpp:626:29: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
626 | if (SAIGE_NumThread > n_block) SAIGE_NumThread = n_block;
| ~~~~~~~~~~~~~~~~^~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vec_ext_def.cpp -o vec_ext_def.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vectorization.cpp -o vectorization.o
g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64
** R
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)
SAIGEgds.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
R is a collaborative project with many contributors.
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.
> # BiocGenerics:::testPackage("SAIGEgds")
>
> proc.time()
user system elapsed
0.17 0.09 0.25
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
| name | user | system | elapsed | |
| SAIGEgds-package | 4.80 | 0.07 | 5.00 | |
| glmmHeritability | 4.56 | 0.03 | 4.60 | |
| pACAT | 0 | 0 | 0 | |
| seqAssocGLMM_ACAT_O | 6.11 | 0.04 | 6.16 | |
| seqAssocGLMM_ACAT_V | 5.17 | 0.05 | 5.22 | |
| seqAssocGLMM_Burden | 4.90 | 0.06 | 4.97 | |
| seqAssocGLMM_SKAT | 4.86 | 0.05 | 4.91 | |
| seqAssocGLMM_SPA | 4.85 | 0.07 | 4.92 | |
| seqFitNullGLMM_SPA | 4.26 | 0.02 | 4.30 | |
| seqFitSparseGRM | 0.10 | 0.00 | 0.09 | |
| seqSAIGE_LoadPval | 0.03 | 0.00 | 0.20 | |
| seqseqFitLDpruning | 2.86 | 0.09 | 3.38 | |