Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1088/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LEA 3.19.1  (landing page)
Olivier Francois
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/LEA
git_branch: devel
git_last_commit: a37ac6c
git_last_commit_date: 2024-11-08 12:52:47 -0500 (Fri, 08 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for LEA on palomino7

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.

raw results


Summary

Package: LEA
Version: 3.19.1
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LEA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings LEA_3.19.1.tar.gz
StartedAt: 2024-12-24 02:01:27 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 02:04:36 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 188.6 seconds
RetCode: 0
Status:   OK  
CheckDir: LEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LEA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings LEA_3.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/LEA.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'LEA/DESCRIPTION' ... OK
* this is package 'LEA' version '3.19.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'LEA' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 ... 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/LEA/libs/x64/LEA.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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    82.53   0.09   82.72
zscores      13.47   0.03   13.58
lfmm_pvalues 13.31   0.03   13.43
main_sNMF     8.48   2.14   14.55
readZscore    6.72   0.00    6.75
* 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 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/LEA.Rcheck/00check.log'
for details.


Installation output

LEA.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL LEA
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'LEA' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_LFMM.c -o R_LFMM.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_crossEntropy.c -o R_crossEntropy.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_createDataSet.c -o R_createDataSet.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_sNMF.c -o R_sNMF.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_geno2lfmm.c -o R_geno2lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_lfmm2geno.c -o R_lfmm2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_pca.c -o R_pca.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_ped2geno.c -o R_ped2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_ped2lfmm.c -o R_ped2lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_vcf2geno.c -o R_vcf2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_tracyWidom.c -o R_tracyWidom.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_LEA.c -o R_init_LEA.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bituint/bituint.c -o bituint/bituint.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bituint/calc_bituint.c -o bituint/calc_bituint.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bituint/slice_bituint.c -o bituint/slice_bituint.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bituint/thread_bituint.c -o bituint/thread_bituint.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/ancestrymap.c -o convert/ancestrymap.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/geno.c -o convert/geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/ped.c -o convert/ped.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/vcf2geno.c -o convert/vcf2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/geno2lfmm.c -o convert/geno2lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/lfmm2geno.c -o convert/lfmm2geno.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert/register_convert.c -o convert/register_convert.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c createDataSet/error_cds.c -o createDataSet/error_cds.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c createDataSet/print_cds.c -o createDataSet/print_cds.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c createDataSet/register_cds.c -o createDataSet/register_cds.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/io_data_double.c -o io/io_data_double.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/io_data_float.c -o io/io_data_float.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/io_data_int.c -o io/io_data_int.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/io_error.c -o io/io_error.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/io_tools.c -o io/io_tools.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io/print_bar.c -o io/print_bar.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/beta.c -o LFMM/beta.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/U.c -o LFMM/U.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/beta_k0.c -o LFMM/beta_k0.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/V.c -o LFMM/V.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/LFMM.c -o LFMM/LFMM.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LFMM/thread_var.c -o LFMM/thread_var.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/cholesky.c -o matrix/cholesky.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/error_matrix.c -o matrix/error_matrix.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/normalize.c -o matrix/normalize.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/slice_matrix.c -o matrix/slice_matrix.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/data.c -o matrix/data.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/inverse.c -o matrix/inverse.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/rand.c -o matrix/rand.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/sylvester.c -o matrix/sylvester.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/diagonalize.c -o matrix/diagonalize.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/matrix.c -o matrix/matrix.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/random_projection.c -o matrix/random_projection.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrix/thread_matrix.c -o matrix/thread_matrix.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nnlsm/sort.c -o nnlsm/sort.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pca/calc_cov.c -o pca/calc_cov.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pca/error_pca.c -o pca/error_pca.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pca/pca.c -o pca/pca.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pca/print_pca.c -o pca/print_pca.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pca/register_pca.c -o pca/register_pca.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/als.c -o sNMF/als.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/als_k1.c -o sNMF/als_k1.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/criteria.c -o sNMF/criteria.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/print_snmf.c -o sNMF/print_snmf.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/sNMF.c -o sNMF/sNMF.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/thread_Q.c -o sNMF/thread_Q.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/als_F.c -o sNMF/als_F.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/als_Q.c -o sNMF/als_Q.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/error_snmf.c -o sNMF/error_snmf.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/register_snmf.c -o sNMF/register_snmf.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/thread_F.c -o sNMF/thread_F.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/beta_distribution.c -o stats/beta_distribution.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/gamma_density.c -o stats/gamma_density.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/ln_beta_function.c -o stats/ln_beta_function.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/beta_function.c -o stats/beta_function.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/gamma_distribution.c -o stats/gamma_distribution.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/student_t_distribution.c -o stats/student_t_distribution.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/factorial.c -o stats/factorial.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stats/gamma_function.c -o stats/gamma_function.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I.    -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
gcc -shared -s -static-libgcc -o LEA.dll tmp.def 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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-LEA/00new/LEA/libs/x64
** 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
** 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
G0.150.000.19
Q0.170.010.21
ancestrymap2geno0.000.000.03
ancestrymap2lfmm0.000.000.02
barchart0.640.081.37
crossEntropy0.170.020.29
genetic_gap0.480.000.48
genetic_offset0.460.060.52
geno2lfmm0.060.000.09
impute0.640.161.36
lfmm20.380.010.39
lfmm2_test0.260.020.28
lfmm2geno0.100.000.13
lfmm_pvalues13.31 0.0313.43
main_LFMM82.53 0.0982.72
main_createDataSet0.050.000.08
main_crossEntropyEstimation0.090.020.17
main_pca0.110.010.42
main_sNMF 8.48 2.1414.55
main_tracyWidom0.080.020.14
ped2geno0.000.000.02
ped2lfmm0.000.020.02
readEnv0.000.000.01
readGeno0.060.010.08
readLfmm0.110.000.12
readZscore6.720.006.75
snmf_pvalues0.640.161.42
struct2geno0.010.000.08
vcf2geno0.020.000.05
vcf2lfmm0.000.000.06
writeEnv0.000.000.02
writeGeno0.050.010.09
writeLFMM0.070.000.11
zscores13.47 0.0313.58