Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:39:58 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 1832/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SAIGEgds 2.3.2 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 2.3.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SAIGEgds_2.3.2.tar.gz |
StartedAt: 2024-03-27 23:49:10 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:52:07 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 177.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SAIGEgds.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SAIGEgds_2.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SAIGEgds.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SAIGEgds/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SAIGEgds’ version ‘2.3.2’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SAIGEgds’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 code 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 ... NOTE checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup? 44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup? 44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) seqFitSparseGRM.Rd:44: Lost braces; missing escapes or markup? 44 | $grm_{ij} = avg_l [(g_{il} - 2*p_l)*(g_{jl} - 2*p_l) / 2*p_l*(1 - p_l)]$ for | ^ checkRd: (-1) seqFitSparseGRM.Rd:45: Lost braces; missing escapes or markup? 45 | individuals i,j and locus l, where $g_{il}$ is 0, 1 or 2, and $p_l$ is the | ^ * 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 is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/SAIGEgds/libs/SAIGEgds.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) 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 6.362 0.188 6.623 seqAssocGLMM_ACAT_V 6.145 0.168 6.375 seqAssocGLMM_Burden 6.043 0.181 6.277 seqAssocGLMM_SKAT 6.018 0.112 6.178 SAIGEgds-package 5.623 0.089 5.764 seqAssocGLMM_SPA 5.385 0.069 5.497 glmmHeritability 5.325 0.058 5.419 seqFitNullGLMM_SPA 5.183 0.058 5.279 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/SAIGEgds.Rcheck/00check.log’ for details.
SAIGEgds.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SAIGEgds ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SAIGEgds’ ... ** 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 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPATest.cpp -o SPATest.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_fitnull.cpp -o saige_fitnull.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_main.cpp -o saige_main.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_misc.cpp -o saige_misc.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_avx2.cpp -o vec_ext_avx2.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_def.cpp -o vec_ext_def.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vectorization.cpp -o vectorization.o clang++ -arch x86_64 -std=gnu++11 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SAIGEgds.so 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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs ** 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 ** 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 (SAIGEgds)
SAIGEgds.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 0.219 0.089 0.296
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
name | user | system | elapsed | |
SAIGEgds-package | 5.623 | 0.089 | 5.764 | |
glmmHeritability | 5.325 | 0.058 | 5.419 | |
pACAT | 0.003 | 0.000 | 0.004 | |
seqAssocGLMM_ACAT_O | 6.362 | 0.188 | 6.623 | |
seqAssocGLMM_ACAT_V | 6.145 | 0.168 | 6.375 | |
seqAssocGLMM_Burden | 6.043 | 0.181 | 6.277 | |
seqAssocGLMM_SKAT | 6.018 | 0.112 | 6.178 | |
seqAssocGLMM_SPA | 5.385 | 0.069 | 5.497 | |
seqFitNullGLMM_SPA | 5.183 | 0.058 | 5.279 | |
seqFitSparseGRM | 0.107 | 0.006 | 0.114 | |
seqSAIGE_LoadPval | 0.047 | 0.005 | 0.052 | |
seqseqFitLDpruning | 2.780 | 0.236 | 3.060 | |