Olivier Francois
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/LEA |
| git_branch: RELEASE_3_20 |
| git_last_commit: 54d047e |
| git_last_commit_date: 2024-10-29 09:59:13 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1095/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LEA 3.18.0 (landing page) Olivier Francois
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the LEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LEA.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: LEA |
| Version: 3.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LEA_3.18.0.tar.gz |
| StartedAt: 2024-12-20 05:14:51 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 05:19:00 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 249.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LEA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LEA_3.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LEA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘3.18.0’
* 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 ‘LEA’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... OK
* 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) main_sNMF.Rd:113: Lost braces; missing escapes or markup?
113 | The following methods can be applied to the object of class {snmfProject}:
| ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
main_LFMM 101.369 0.476 111.829
lfmm_pvalues 16.124 0.091 17.091
zscores 15.931 0.095 16.991
main_sNMF 11.495 2.911 16.762
readZscore 7.987 0.039 8.417
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/LEA.Rcheck/00check.log’
for details.
LEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LEA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘LEA’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_LFMM.c -o R_LFMM.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_crossEntropy.c -o R_crossEntropy.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_createDataSet.c -o R_createDataSet.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_sNMF.c -o R_sNMF.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_geno2lfmm.c -o R_geno2lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_lfmm2geno.c -o R_lfmm2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_pca.c -o R_pca.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ped2geno.c -o R_ped2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ped2lfmm.c -o R_ped2lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_vcf2geno.c -o R_vcf2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_tracyWidom.c -o R_tracyWidom.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_LEA.c -o R_init_LEA.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/bituint.c -o bituint/bituint.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/ancestrymap.c -o convert/ancestrymap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/geno.c -o convert/geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/ped.c -o convert/ped.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/vcf2geno.c -o convert/vcf2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/geno2lfmm.c -o convert/geno2lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/lfmm2geno.c -o convert/lfmm2geno.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/register_convert.c -o convert/register_convert.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/error_cds.c -o createDataSet/error_cds.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/print_cds.c -o createDataSet/print_cds.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/register_cds.c -o createDataSet/register_cds.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_double.c -o io/io_data_double.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_float.c -o io/io_data_float.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_int.c -o io/io_data_int.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_error.c -o io/io_error.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_tools.c -o io/io_tools.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/print_bar.c -o io/print_bar.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/beta.c -o LFMM/beta.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/U.c -o LFMM/U.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/beta_k0.c -o LFMM/beta_k0.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/V.c -o LFMM/V.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/LFMM.c -o LFMM/LFMM.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/thread_var.c -o LFMM/thread_var.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/cholesky.c -o matrix/cholesky.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/error_matrix.c -o matrix/error_matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/normalize.c -o matrix/normalize.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/slice_matrix.c -o matrix/slice_matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/data.c -o matrix/data.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/inverse.c -o matrix/inverse.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/rand.c -o matrix/rand.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/sylvester.c -o matrix/sylvester.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/diagonalize.c -o matrix/diagonalize.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/matrix.c -o matrix/matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/random_projection.c -o matrix/random_projection.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/thread_matrix.c -o matrix/thread_matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/sort.c -o nnlsm/sort.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/calc_cov.c -o pca/calc_cov.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/error_pca.c -o pca/error_pca.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/pca.c -o pca/pca.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/print_pca.c -o pca/print_pca.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/register_pca.c -o pca/register_pca.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als.c -o sNMF/als.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_k1.c -o sNMF/als_k1.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/criteria.c -o sNMF/criteria.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/print_snmf.c -o sNMF/print_snmf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/sNMF.c -o sNMF/sNMF.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_Q.c -o sNMF/thread_Q.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_F.c -o sNMF/als_F.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_Q.c -o sNMF/als_Q.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/error_snmf.c -o sNMF/error_snmf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/register_snmf.c -o sNMF/register_snmf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_F.c -o sNMF/thread_F.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/beta_distribution.c -o stats/beta_distribution.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_density.c -o stats/gamma_density.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/ln_beta_function.c -o stats/ln_beta_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/beta_function.c -o stats/beta_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_distribution.c -o stats/gamma_distribution.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/student_t_distribution.c -o stats/student_t_distribution.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/factorial.c -o stats/factorial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_function.c -o stats/gamma_function.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o LEA.so R_LFMM.o R_crossEntropy.o R_createDataSet.o R_sNMF.o R_ancestrymap2geno.o R_ancestrymap2lfmm.o R_geno2lfmm.o R_lfmm2geno.o R_pca.o R_ped2geno.o R_ped2lfmm.o R_vcf2geno.o R_tracyWidom.o R_init_LEA.o bituint/bituint.o bituint/calc_bituint.o bituint/io_geno_bituint.o bituint/slice_bituint.o bituint/thread_bituint.o convert/ancestrymap.o convert/geno.o convert/ped.o convert/vcf2geno.o convert/geno2lfmm.o convert/lfmm2geno.o convert/register_convert.o createDataSet/createDataSet.o createDataSet/error_cds.o createDataSet/print_cds.o createDataSet/register_cds.o crossEntropy/crossEntropy.o crossEntropy/error_ce.o crossEntropy/print_ce.o crossEntropy/register_ce.o io/io_data_double.o io/io_data_float.o io/io_data_int.o io/io_error.o io/io_tools.o io/print_bar.o LFMM/beta.o LFMM/error_lfmm.o LFMM/lfmm_k0.o LFMM/slice_lfmm.o LFMM/U.o LFMM/beta_k0.o LFMM/lfmm_algo.o LFMM/print_lfmm.o LFMM/thread_lfmm.o LFMM/V.o LFMM/data_lfmm.o LFMM/LFMM.o LFMM/register_lfmm.o LFMM/thread_var.o matrix/cholesky.o matrix/error_matrix.o matrix/normalize.o matrix/slice_matrix.o matrix/data.o matrix/inverse.o matrix/rand.o matrix/sylvester.o matrix/diagonalize.o matrix/matrix.o matrix/random_projection.o matrix/thread_matrix.o nnlsm/blockpivot.o nnlsm/nnlsm.o nnlsm/solvenormaleqcomb.o nnlsm/sort.o pca/calc_cov.o pca/error_pca.o pca/pca.o pca/print_pca.o pca/register_pca.o sNMF/als.o sNMF/als_k1.o sNMF/criteria.o sNMF/print_snmf.o sNMF/sNMF.o sNMF/thread_Q.o sNMF/als_F.o sNMF/als_Q.o sNMF/error_snmf.o sNMF/register_snmf.o sNMF/thread_F.o sNMF/thread_snmf.o stats/beta_distribution.o stats/gamma_density.o stats/ln_beta_function.o stats/beta_function.o stats/gamma_distribution.o stats/ln_gamma_function.o stats/entire_incomplete_gamma_function.o stats/gamma_dist_tables.o stats/student_t_distribution.o stats/factorial.o stats/gamma_function.o tracyWidom/error_tracyWidom.o tracyWidom/register_tracyWidom.o tracyWidom/print_tracyWidom.o tracyWidom/tracyWidom.o -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-LEA/00new/LEA/libs ** R ** data ** 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 (LEA)
LEA.Rcheck/LEA-Ex.timings
| name | user | system | elapsed | |
| G | 0.217 | 0.027 | 0.253 | |
| Q | 0.180 | 0.023 | 0.223 | |
| ancestrymap2geno | 0.004 | 0.004 | 0.010 | |
| ancestrymap2lfmm | 0.005 | 0.004 | 0.011 | |
| barchart | 0.882 | 0.115 | 1.087 | |
| crossEntropy | 0.178 | 0.035 | 0.230 | |
| genetic_gap | 0.829 | 0.046 | 0.924 | |
| genetic_offset | 0.793 | 0.041 | 0.883 | |
| geno2lfmm | 0.053 | 0.006 | 0.089 | |
| impute | 1.036 | 0.127 | 1.315 | |
| lfmm2 | 0.837 | 0.040 | 1.008 | |
| lfmm2_test | 0.715 | 0.041 | 0.874 | |
| lfmm2geno | 0.053 | 0.007 | 0.064 | |
| lfmm_pvalues | 16.124 | 0.091 | 17.091 | |
| main_LFMM | 101.369 | 0.476 | 111.829 | |
| main_createDataSet | 0.047 | 0.005 | 0.056 | |
| main_crossEntropyEstimation | 0.111 | 0.019 | 0.143 | |
| main_pca | 0.182 | 0.043 | 0.268 | |
| main_sNMF | 11.495 | 2.911 | 16.762 | |
| main_tracyWidom | 0.056 | 0.013 | 0.071 | |
| ped2geno | 0.004 | 0.004 | 0.009 | |
| ped2lfmm | 0.005 | 0.005 | 0.009 | |
| readEnv | 0.002 | 0.001 | 0.003 | |
| readGeno | 0.051 | 0.003 | 0.062 | |
| readLfmm | 0.086 | 0.006 | 0.097 | |
| readZscore | 7.987 | 0.039 | 8.417 | |
| snmf_pvalues | 0.899 | 0.110 | 1.148 | |
| struct2geno | 0.036 | 0.011 | 0.059 | |
| vcf2geno | 0.006 | 0.006 | 0.014 | |
| vcf2lfmm | 0.007 | 0.008 | 0.023 | |
| writeEnv | 0.001 | 0.001 | 0.003 | |
| writeGeno | 0.052 | 0.004 | 0.057 | |
| writeLFMM | 0.085 | 0.006 | 0.097 | |
| zscores | 15.931 | 0.095 | 16.991 | |