Xiuwen Zheng
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: devel |
| git_last_commit: 1457cda |
| git_last_commit_date: 2024-11-19 22:40:15 -0500 (Tue, 19 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1820/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.7.1 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 2.7.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SAIGEgds_2.7.1.tar.gz |
| StartedAt: 2024-12-24 01:46:33 -0500 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 01:49:09 -0500 (Tue, 24 Dec 2024) |
| EllapsedTime: 156.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SAIGEgds.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SAIGEgds.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SAIGEgds_2.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SAIGEgds’ version ‘2.7.1’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 4.4Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
seqAssocGLMM_ACAT_O.Rd: seqParallel, seqUnitFilterCond
seqAssocGLMM_ACAT_V.Rd: seqParallel, seqUnitFilterCond
seqAssocGLMM_Burden.Rd: seqParallel, seqUnitFilterCond
seqAssocGLMM_SKAT.Rd: seqParallel, seqUnitFilterCond
seqAssocGLMM_SPA.Rd: compression.gdsn, seqParallel
seqseqFitLDpruning.Rd: seqParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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_O 6.404 0.050 6.455
seqAssocGLMM_ACAT_V 6.056 0.020 6.076
seqAssocGLMM_Burden 5.919 0.024 5.947
SAIGEgds-package 5.679 0.023 5.704
seqAssocGLMM_SKAT 5.515 0.011 5.527
seqAssocGLMM_SPA 5.453 0.013 5.467
seqFitNullGLMM_SPA 5.062 0.008 5.070
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/SAIGEgds.Rcheck/00check.log’
for details.
SAIGEgds.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SAIGEgds ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SAIGEgds’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c SPATest.cpp -o SPATest.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c saige_fitnull.cpp -o saige_fitnull.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c saige_main.cpp -o saige_main.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c saige_misc.cpp -o saige_misc.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c vec_ext_avx2.cpp -o vec_ext_avx2.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c vec_ext_def.cpp -o vec_ext_def.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c vectorization.cpp -o vectorization.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/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 -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgcc -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/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) (2024-10-21 r87258) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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> # BiocGenerics:::testPackage("SAIGEgds")
>
> proc.time()
user system elapsed
0.142 0.033 0.164
SAIGEgds.Rcheck/SAIGEgds-Ex.timings
| name | user | system | elapsed | |
| SAIGEgds-package | 5.679 | 0.023 | 5.704 | |
| glmmHeritability | 4.945 | 0.010 | 4.954 | |
| pACAT | 0.003 | 0.000 | 0.003 | |
| seqAssocGLMM_ACAT_O | 6.404 | 0.050 | 6.455 | |
| seqAssocGLMM_ACAT_V | 6.056 | 0.020 | 6.076 | |
| seqAssocGLMM_Burden | 5.919 | 0.024 | 5.947 | |
| seqAssocGLMM_SKAT | 5.515 | 0.011 | 5.527 | |
| seqAssocGLMM_SPA | 5.453 | 0.013 | 5.467 | |
| seqFitNullGLMM_SPA | 5.062 | 0.008 | 5.070 | |
| seqFitSparseGRM | 0.199 | 0.004 | 0.202 | |
| seqSAIGE_LoadPval | 0.043 | 0.002 | 0.046 | |
| seqseqFitLDpruning | 1.638 | 0.081 | 1.720 | |