Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -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 23:31:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 23:34:18 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 176.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LEA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/LEA.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * 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 15.0.0 (clang-1500.0.40.1)’ * 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 89.077 0.207 89.417 lfmm_pvalues 13.310 0.038 13.351 zscores 12.473 0.040 12.545 main_sNMF 9.434 1.436 11.772 readZscore 6.619 0.026 6.916 * 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-arm64/Resources/library’ * installing *source* package ‘LEA’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_LFMM.c -o R_LFMM.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_crossEntropy.c -o R_crossEntropy.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_createDataSet.c -o R_createDataSet.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_sNMF.c -o R_sNMF.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_geno2lfmm.c -o R_geno2lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_lfmm2geno.c -o R_lfmm2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_pca.c -o R_pca.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ped2geno.c -o R_ped2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_ped2lfmm.c -o R_ped2lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_vcf2geno.c -o R_vcf2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_tracyWidom.c -o R_tracyWidom.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_LEA.c -o R_init_LEA.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/bituint.c -o bituint/bituint.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/calc_bituint.c -o bituint/calc_bituint.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/slice_bituint.c -o bituint/slice_bituint.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bituint/thread_bituint.c -o bituint/thread_bituint.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/ancestrymap.c -o convert/ancestrymap.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/geno.c -o convert/geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/ped.c -o convert/ped.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/vcf2geno.c -o convert/vcf2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/geno2lfmm.c -o convert/geno2lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/lfmm2geno.c -o convert/lfmm2geno.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert/register_convert.c -o convert/register_convert.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/error_cds.c -o createDataSet/error_cds.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/print_cds.c -o createDataSet/print_cds.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c createDataSet/register_cds.c -o createDataSet/register_cds.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_double.c -o io/io_data_double.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_float.c -o io/io_data_float.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_data_int.c -o io/io_data_int.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_error.c -o io/io_error.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/io_tools.c -o io/io_tools.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io/print_bar.c -o io/print_bar.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/beta.c -o LFMM/beta.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/U.c -o LFMM/U.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/beta_k0.c -o LFMM/beta_k0.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/V.c -o LFMM/V.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/LFMM.c -o LFMM/LFMM.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LFMM/thread_var.c -o LFMM/thread_var.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/cholesky.c -o matrix/cholesky.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/error_matrix.c -o matrix/error_matrix.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/normalize.c -o matrix/normalize.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/slice_matrix.c -o matrix/slice_matrix.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/data.c -o matrix/data.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/inverse.c -o matrix/inverse.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/rand.c -o matrix/rand.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/sylvester.c -o matrix/sylvester.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/diagonalize.c -o matrix/diagonalize.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/matrix.c -o matrix/matrix.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/random_projection.c -o matrix/random_projection.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix/thread_matrix.c -o matrix/thread_matrix.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nnlsm/sort.c -o nnlsm/sort.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/calc_cov.c -o pca/calc_cov.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/error_pca.c -o pca/error_pca.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/pca.c -o pca/pca.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/print_pca.c -o pca/print_pca.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pca/register_pca.c -o pca/register_pca.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als.c -o sNMF/als.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_k1.c -o sNMF/als_k1.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/criteria.c -o sNMF/criteria.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/print_snmf.c -o sNMF/print_snmf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/sNMF.c -o sNMF/sNMF.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_Q.c -o sNMF/thread_Q.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_F.c -o sNMF/als_F.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/als_Q.c -o sNMF/als_Q.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/error_snmf.c -o sNMF/error_snmf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/register_snmf.c -o sNMF/register_snmf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_F.c -o sNMF/thread_F.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/beta_distribution.c -o stats/beta_distribution.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_density.c -o stats/gamma_density.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/ln_beta_function.c -o stats/ln_beta_function.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/beta_function.c -o stats/beta_function.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_distribution.c -o stats/gamma_distribution.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/student_t_distribution.c -o stats/student_t_distribution.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/factorial.c -o stats/factorial.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stats/gamma_function.c -o stats/gamma_function.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 | 0.176 | 0.014 | 0.190 | |
Q | 0.158 | 0.013 | 0.176 | |
ancestrymap2geno | 0.002 | 0.003 | 0.006 | |
ancestrymap2lfmm | 0.002 | 0.003 | 0.005 | |
barchart | 0.791 | 0.054 | 0.880 | |
crossEntropy | 0.140 | 0.017 | 0.157 | |
genetic_gap | 0.620 | 0.021 | 0.644 | |
genetic_offset | 0.598 | 0.024 | 0.625 | |
geno2lfmm | 0.027 | 0.004 | 0.030 | |
impute | 0.779 | 0.058 | 0.836 | |
lfmm2 | 0.436 | 0.015 | 0.451 | |
lfmm2_test | 0.328 | 0.015 | 0.345 | |
lfmm2geno | 0.028 | 0.003 | 0.031 | |
lfmm_pvalues | 13.310 | 0.038 | 13.351 | |
main_LFMM | 89.077 | 0.207 | 89.417 | |
main_createDataSet | 0.025 | 0.003 | 0.028 | |
main_crossEntropyEstimation | 0.083 | 0.009 | 0.093 | |
main_pca | 0.179 | 0.029 | 0.212 | |
main_sNMF | 9.434 | 1.436 | 11.772 | |
main_tracyWidom | 0.032 | 0.008 | 0.040 | |
ped2geno | 0.003 | 0.002 | 0.005 | |
ped2lfmm | 0.002 | 0.003 | 0.004 | |
readEnv | 0.001 | 0.000 | 0.001 | |
readGeno | 0.027 | 0.002 | 0.030 | |
readLfmm | 0.039 | 0.004 | 0.048 | |
readZscore | 6.619 | 0.026 | 6.916 | |
snmf_pvalues | 0.815 | 0.062 | 0.880 | |
struct2geno | 0.023 | 0.005 | 0.027 | |
vcf2geno | 0.003 | 0.003 | 0.006 | |
vcf2lfmm | 0.002 | 0.004 | 0.006 | |
writeEnv | 0.001 | 0.000 | 0.002 | |
writeGeno | 0.026 | 0.002 | 0.029 | |
writeLFMM | 0.038 | 0.004 | 0.042 | |
zscores | 12.473 | 0.040 | 12.545 | |