| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-10 10:04:40 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 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. 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 1769/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.1.1 (landing page) Xiuwen Zheng
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SAIGEgds |
| Version: 2.1.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SAIGEgds_2.1.1.tar.gz |
| StartedAt: 2023-05-10 03:17:15 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 03:20:25 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 190.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SAIGEgds_2.1.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SAIGEgds’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
libs 7.6Mb
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqAssocGLMM_ACAT_V 5.514 0.044 5.558
seqAssocGLMM_ACAT_O 5.067 0.028 5.096
* 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 ...
‘SAIGEgds.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.
SAIGEgds.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SAIGEgds ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘SAIGEgds’ ... ** 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-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c SPATest.cpp -o SPATest.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c saige_fitnull.cpp -o saige_fitnull.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c saige_main.cpp -o saige_main.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c saige_misc.cpp -o saige_misc.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c vec_ext_avx2.cpp -o vec_ext_avx2.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c vec_ext_def.cpp -o vec_ext_def.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -c vectorization.cpp -o vectorization.o g++ -std=gnu++11 -shared -L/usr/local/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 -llapack -L/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/lib -lRblas -lgfortran -lm -lgcc installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
0.195 0.029 0.205
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
| name | user | system | elapsed | |
| SAIGEgds-package | 4.215 | 0.045 | 4.273 | |
| glmmHeritability | 3.841 | 0.006 | 3.848 | |
| pACAT | 0.003 | 0.000 | 0.003 | |
| seqAssocGLMM_ACAT_O | 5.067 | 0.028 | 5.096 | |
| seqAssocGLMM_ACAT_V | 5.514 | 0.044 | 5.558 | |
| seqAssocGLMM_Burden | 4.832 | 0.008 | 4.840 | |
| seqAssocGLMM_SKAT | 4.284 | 0.044 | 4.331 | |
| seqAssocGLMM_SPA | 4.014 | 0.004 | 4.018 | |
| seqFitNullGLMM_SPA | 3.728 | 0.008 | 3.736 | |
| seqFitSparseGRM | 0.140 | 0.000 | 0.141 | |
| seqSAIGE_LoadPval | 0.046 | 0.000 | 0.047 | |
| seqseqFitLDpruning | 3.582 | 0.052 | 3.645 | |