Olivier Francois
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/LEA |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7fc453b |
| git_last_commit_date: 2024-04-30 10:42:13 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 1103/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LEA 3.16.0 (landing page) Olivier Francois
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | 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: 3.16.0 |
| 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_3.16.0.tar.gz |
| StartedAt: 2024-06-10 20:02:02 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 20:05:29 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 207.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: LEA.Rcheck |
| Warnings: 1 |
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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_3.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/LEA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LEA/DESCRIPTION’ ... OK
* this is package ‘LEA’ version ‘3.16.0’
* 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 ... WARNING
Found the following significant warnings:
bituint/thread_bituint.c:83:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
LFMM/thread_lfmm.c:96:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
LFMM/thread_var.c:94:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
matrix/thread_matrix.c:82:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
sNMF/thread_snmf.c:81:5: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/LEA.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 63.304 0.407 87.438
lfmm_pvalues 9.382 0.091 13.848
zscores 9.322 0.090 13.345
main_sNMF 5.949 1.723 11.065
readZscore 4.594 0.029 5.474
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/LEA.Rcheck/00check.log’
for details.
LEA.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LEA
###
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##############################################################################
* 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-1500.1.0.2.5)’
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
bituint/thread_bituint.c:83:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
fct(Ma[0]);
^
1 warning generated.
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
LFMM/thread_lfmm.c:96:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
fct(Ma[0]);
^
1 warning generated.
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
LFMM/thread_var.c:94:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
fct(Ma[0]);
^
1 warning generated.
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
matrix/thread_matrix.c:82:12: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
fct(Ma[0]);
^
1 warning generated.
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
sNMF/thread_snmf.c:81:5: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
fct(Ma[0]);
^
1 warning generated.
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 | 0.111 | 0.019 | 0.181 | |
| Q | 0.096 | 0.020 | 0.185 | |
| ancestrymap2geno | 0.003 | 0.003 | 0.011 | |
| ancestrymap2lfmm | 0.002 | 0.003 | 0.006 | |
| barchart | 0.492 | 0.086 | 0.904 | |
| crossEntropy | 0.093 | 0.024 | 0.202 | |
| genetic_gap | 0.451 | 0.027 | 0.686 | |
| genetic_offset | 0.434 | 0.027 | 0.665 | |
| geno2lfmm | 0.022 | 0.006 | 0.049 | |
| impute | 0.527 | 0.099 | 0.977 | |
| lfmm2 | 0.473 | 0.019 | 0.729 | |
| lfmm2_test | 0.331 | 0.017 | 0.523 | |
| lfmm2geno | 0.022 | 0.005 | 0.038 | |
| lfmm_pvalues | 9.382 | 0.091 | 13.848 | |
| main_LFMM | 63.304 | 0.407 | 87.438 | |
| main_createDataSet | 0.020 | 0.003 | 0.023 | |
| main_crossEntropyEstimation | 0.053 | 0.010 | 0.062 | |
| main_pca | 0.112 | 0.038 | 0.263 | |
| main_sNMF | 5.949 | 1.723 | 11.065 | |
| main_tracyWidom | 0.024 | 0.010 | 0.034 | |
| ped2geno | 0.002 | 0.003 | 0.005 | |
| ped2lfmm | 0.002 | 0.003 | 0.005 | |
| readEnv | 0.000 | 0.001 | 0.001 | |
| readGeno | 0.020 | 0.003 | 0.023 | |
| readLfmm | 0.030 | 0.003 | 0.034 | |
| readZscore | 4.594 | 0.029 | 5.474 | |
| snmf_pvalues | 0.494 | 0.082 | 0.782 | |
| struct2geno | 0.019 | 0.006 | 0.035 | |
| vcf2geno | 0.003 | 0.008 | 0.027 | |
| vcf2lfmm | 0.003 | 0.004 | 0.011 | |
| writeEnv | 0.001 | 0.001 | 0.001 | |
| writeGeno | 0.021 | 0.003 | 0.038 | |
| writeLFMM | 0.031 | 0.004 | 0.045 | |
| zscores | 9.322 | 0.090 | 13.345 | |