Xiuwen Zheng
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1b9b0ae |
| git_last_commit_date: 2024-10-29 10:40:42 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 1835/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.6.0 (landing page) Xiuwen Zheng
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SAIGEgds |
| Version: 2.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SAIGEgds_2.6.0.tar.gz |
| StartedAt: 2024-11-20 11:59:32 -0000 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 12:02:24 -0000 (Wed, 20 Nov 2024) |
| EllapsedTime: 171.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SAIGEgds_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SAIGEgds.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.6.0’
* 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++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 9.5Mb
sub-directories of 1Mb or more:
libs 7.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘SeqArray:::.IsForking’ ‘SeqArray:::.McoreParallel’
‘SeqArray:::.NumParallel’ ‘SeqArray:::.seqProgForward’
‘SeqArray:::.seqProgress’ ‘SeqArray:::process_index’
‘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_Burden 5.188 0.020 5.218
seqAssocGLMM_ACAT_O 5.078 0.084 5.169
seqAssocGLMM_ACAT_V 5.069 0.036 5.114
* 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
‘/home/biocbuild/bbs-3.20-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.
SAIGEgds.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL SAIGEgds
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SPATest.cpp -o SPATest.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_fitnull.cpp -o saige_fitnull.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24,
from saige.h:37,
from saige_fitnull.cpp:29:
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_main.cpp -o saige_main.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24,
from saige.h:37,
from saige_main.cpp:30:
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c saige_misc.cpp -o saige_misc.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24,
from saige.h:37,
from saige_misc.cpp:25:
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vec_ext_def.cpp -o vec_ext_def.o
vec_ext_def.cpp: In function 'void vec_init_function()':
vec_ext_def.cpp:33:27: warning: unused variable 'VEC_ALGORITHM_AVX2' [-Wunused-variable]
33 | extern const bool VEC_ALGORITHM_AVX2;
| ^~~~~~~~~~~~~~~~~~
vec_ext_def.cpp:34:27: warning: unused variable 'VEC_ALGORITHM_AVX512BW' [-Wunused-variable]
34 | extern const bool VEC_ALGORITHM_AVX512BW;
| ^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -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 -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -lgcc -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.280 0.031 0.208
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
| name | user | system | elapsed | |
| SAIGEgds-package | 4.447 | 0.068 | 4.526 | |
| glmmHeritability | 3.560 | 0.012 | 3.577 | |
| pACAT | 0.003 | 0.000 | 0.003 | |
| seqAssocGLMM_ACAT_O | 5.078 | 0.084 | 5.169 | |
| seqAssocGLMM_ACAT_V | 5.069 | 0.036 | 5.114 | |
| seqAssocGLMM_Burden | 5.188 | 0.020 | 5.218 | |
| seqAssocGLMM_SKAT | 4.911 | 0.016 | 4.937 | |
| seqAssocGLMM_SPA | 4.741 | 0.044 | 4.794 | |
| seqFitNullGLMM_SPA | 4.353 | 0.008 | 4.369 | |
| seqFitSparseGRM | 0.220 | 0.012 | 0.233 | |
| seqSAIGE_LoadPval | 0.045 | 0.000 | 0.046 | |
| seqseqFitLDpruning | 1.755 | 0.048 | 1.826 | |