Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:52 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for LEA on machv2


To the developers/maintainers of the LEA package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 991/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LEA 3.6.0  (landing page)
Olivier Francois
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/LEA
git_branch: RELEASE_3_14
git_last_commit: d44b9c2
git_last_commit_date: 2021-10-26 12:19:12 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: LEA
Version: 3.6.0
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_3.6.0.tar.gz
StartedAt: 2022-01-16 14:29:48 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 14:33:13 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 204.7 seconds
RetCode: 0
Status:   OK  
CheckDir: LEA.Rcheck
Warnings: 0

Command output

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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_3.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/LEA.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘3.6.0’
* 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 ‘LEA’ can be installed ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 ... 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 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    90.685  0.231  91.556
main_sNMF    15.379  3.195  18.907
zscores      14.418  0.046  14.480
lfmm_pvalues 14.393  0.046  14.459
readZscore    7.412  0.019   7.435
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/LEA.Rcheck/00check.log’
for details.



Installation output

LEA.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LEA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘LEA’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_LFMM.c -o R_LFMM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_crossEntropy.c -o R_crossEntropy.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_createDataSet.c -o R_createDataSet.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_sNMF.c -o R_sNMF.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_geno2lfmm.c -o R_geno2lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_lfmm2geno.c -o R_lfmm2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_pca.c -o R_pca.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ped2geno.c -o R_ped2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_ped2lfmm.c -o R_ped2lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_vcf2geno.c -o R_vcf2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_tracyWidom.c -o R_tracyWidom.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_LEA.c -o R_init_LEA.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/bituint.c -o bituint/bituint.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/calc_bituint.c -o bituint/calc_bituint.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/slice_bituint.c -o bituint/slice_bituint.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c bituint/thread_bituint.c -o bituint/thread_bituint.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/ancestrymap.c -o convert/ancestrymap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/geno.c -o convert/geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/ped.c -o convert/ped.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/vcf2geno.c -o convert/vcf2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/geno2lfmm.c -o convert/geno2lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/lfmm2geno.c -o convert/lfmm2geno.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert/register_convert.c -o convert/register_convert.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/error_cds.c -o createDataSet/error_cds.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/print_cds.c -o createDataSet/print_cds.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c createDataSet/register_cds.c -o createDataSet/register_cds.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_double.c -o io/io_data_double.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_float.c -o io/io_data_float.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_data_int.c -o io/io_data_int.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_error.c -o io/io_error.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/io_tools.c -o io/io_tools.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c io/print_bar.c -o io/print_bar.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/beta.c -o LFMM/beta.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/U.c -o LFMM/U.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/beta_k0.c -o LFMM/beta_k0.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/V.c -o LFMM/V.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/LFMM.c -o LFMM/LFMM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LFMM/thread_var.c -o LFMM/thread_var.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/cholesky.c -o matrix/cholesky.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/error_matrix.c -o matrix/error_matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/normalize.c -o matrix/normalize.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/slice_matrix.c -o matrix/slice_matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/data.c -o matrix/data.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/inverse.c -o matrix/inverse.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/rand.c -o matrix/rand.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/sylvester.c -o matrix/sylvester.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/diagonalize.c -o matrix/diagonalize.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/matrix.c -o matrix/matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/random_projection.c -o matrix/random_projection.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix/thread_matrix.c -o matrix/thread_matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c nnlsm/sort.c -o nnlsm/sort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/calc_cov.c -o pca/calc_cov.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/error_pca.c -o pca/error_pca.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/pca.c -o pca/pca.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/print_pca.c -o pca/print_pca.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c pca/register_pca.c -o pca/register_pca.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als.c -o sNMF/als.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_k1.c -o sNMF/als_k1.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/criteria.c -o sNMF/criteria.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/print_snmf.c -o sNMF/print_snmf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/sNMF.c -o sNMF/sNMF.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_Q.c -o sNMF/thread_Q.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_F.c -o sNMF/als_F.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/als_Q.c -o sNMF/als_Q.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/error_snmf.c -o sNMF/error_snmf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/register_snmf.c -o sNMF/register_snmf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_F.c -o sNMF/thread_F.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/beta_distribution.c -o stats/beta_distribution.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_density.c -o stats/gamma_density.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/ln_beta_function.c -o stats/ln_beta_function.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/beta_function.c -o stats/beta_function.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_distribution.c -o stats/gamma_distribution.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/student_t_distribution.c -o stats/student_t_distribution.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/factorial.c -o stats/factorial.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c stats/gamma_function.c -o stats/gamma_function.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I.  -I/usr/local/include   -fPIC  -Wall -g -O2  -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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)

Tests output


Example timings

LEA.Rcheck/LEA-Ex.timings

nameusersystemelapsed
G0.1820.0180.202
Q0.1620.0160.178
ancestrymap2geno0.0050.0030.009
ancestrymap2lfmm0.0030.0030.006
barchart0.8040.0750.925
crossEntropy0.1590.0220.182
genetic_offset2.8060.1022.910
geno2lfmm0.0400.0040.044
impute0.8860.0760.964
lfmm20.6380.0240.662
lfmm2_test0.6140.0130.629
lfmm2geno0.0430.0060.049
lfmm_pvalues14.393 0.04614.459
main_LFMM90.685 0.23191.556
main_createDataSet0.0370.0050.042
main_crossEntropyEstimation0.1020.0120.115
main_pca0.1700.0300.201
main_sNMF15.379 3.19518.907
main_tracyWidom0.0490.0090.059
ped2geno0.0050.0040.009
ped2lfmm0.0050.0030.007
readEnv0.0020.0000.002
readGeno0.0380.0020.041
readLfmm0.0680.0040.073
readZscore7.4120.0197.435
snmf_pvalues0.8660.0811.018
struct2geno0.0310.0070.038
vcf2geno0.0060.0040.009
vcf2lfmm0.0060.0060.012
writeEnv0.0020.0010.003
writeGeno0.0460.0030.049
writeLFMM0.0760.0040.079
zscores14.418 0.04614.480