Olivier Francois
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/LEA |
| git_branch: RELEASE_3_16 |
| git_last_commit: 3f79292 |
| git_last_commit_date: 2023-01-19 11:17:28 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:38 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1034/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| LEA 3.10.2 (landing page) Olivier Francois
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: LEA |
| Version: 3.10.2 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LEA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings LEA_3.10.2.tar.gz |
| StartedAt: 2023-04-11 02:45:50 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 02:48:38 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 168.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: LEA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LEA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings LEA_3.10.2.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/LEA.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'LEA/DESCRIPTION' ... OK
* this is package 'LEA' version '3.10.2'
* 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
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/LEA/libs/x64/LEA.dll':
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. 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 69.13 0.10 69.49
zscores 10.92 0.00 10.93
lfmm_pvalues 10.59 0.05 10.64
main_sNMF 7.86 2.12 12.10
readZscore 5.65 0.02 5.69
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/LEA.Rcheck/00check.log'
for details.
LEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL LEA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'LEA' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_LFMM.c -o R_LFMM.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_crossEntropy.c -o R_crossEntropy.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_createDataSet.c -o R_createDataSet.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_sNMF.c -o R_sNMF.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_geno2lfmm.c -o R_geno2lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_lfmm2geno.c -o R_lfmm2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_pca.c -o R_pca.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_ped2geno.c -o R_ped2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_ped2lfmm.c -o R_ped2lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_vcf2geno.c -o R_vcf2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_tracyWidom.c -o R_tracyWidom.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_LEA.c -o R_init_LEA.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bituint/bituint.c -o bituint/bituint.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bituint/calc_bituint.c -o bituint/calc_bituint.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bituint/slice_bituint.c -o bituint/slice_bituint.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bituint/thread_bituint.c -o bituint/thread_bituint.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/ancestrymap.c -o convert/ancestrymap.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/geno.c -o convert/geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/ped.c -o convert/ped.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/vcf2geno.c -o convert/vcf2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/geno2lfmm.c -o convert/geno2lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/lfmm2geno.c -o convert/lfmm2geno.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c convert/register_convert.c -o convert/register_convert.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c createDataSet/error_cds.c -o createDataSet/error_cds.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c createDataSet/print_cds.c -o createDataSet/print_cds.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c createDataSet/register_cds.c -o createDataSet/register_cds.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/io_data_double.c -o io/io_data_double.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/io_data_float.c -o io/io_data_float.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/io_data_int.c -o io/io_data_int.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/io_error.c -o io/io_error.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/io_tools.c -o io/io_tools.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io/print_bar.c -o io/print_bar.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/beta.c -o LFMM/beta.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/U.c -o LFMM/U.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/beta_k0.c -o LFMM/beta_k0.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/V.c -o LFMM/V.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/LFMM.c -o LFMM/LFMM.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LFMM/thread_var.c -o LFMM/thread_var.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/cholesky.c -o matrix/cholesky.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/error_matrix.c -o matrix/error_matrix.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/normalize.c -o matrix/normalize.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/slice_matrix.c -o matrix/slice_matrix.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/data.c -o matrix/data.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/inverse.c -o matrix/inverse.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/rand.c -o matrix/rand.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/sylvester.c -o matrix/sylvester.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/diagonalize.c -o matrix/diagonalize.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/matrix.c -o matrix/matrix.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/random_projection.c -o matrix/random_projection.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix/thread_matrix.c -o matrix/thread_matrix.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c nnlsm/sort.c -o nnlsm/sort.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pca/calc_cov.c -o pca/calc_cov.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pca/error_pca.c -o pca/error_pca.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pca/pca.c -o pca/pca.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pca/print_pca.c -o pca/print_pca.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pca/register_pca.c -o pca/register_pca.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/als.c -o sNMF/als.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/als_k1.c -o sNMF/als_k1.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/criteria.c -o sNMF/criteria.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/print_snmf.c -o sNMF/print_snmf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/sNMF.c -o sNMF/sNMF.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/thread_Q.c -o sNMF/thread_Q.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/als_F.c -o sNMF/als_F.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/als_Q.c -o sNMF/als_Q.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/error_snmf.c -o sNMF/error_snmf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/register_snmf.c -o sNMF/register_snmf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/thread_F.c -o sNMF/thread_F.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/beta_distribution.c -o stats/beta_distribution.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/gamma_density.c -o stats/gamma_density.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/ln_beta_function.c -o stats/ln_beta_function.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/beta_function.c -o stats/beta_function.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/gamma_distribution.c -o stats/gamma_distribution.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/student_t_distribution.c -o stats/student_t_distribution.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/factorial.c -o stats/factorial.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c stats/gamma_function.c -o stats/gamma_function.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I. -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -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 -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-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)
LEA.Rcheck/LEA-Ex.timings
| name | user | system | elapsed | |
| G | 0.14 | 0.01 | 0.18 | |
| Q | 0.14 | 0.00 | 0.14 | |
| ancestrymap2geno | 0.00 | 0.00 | 0.02 | |
| ancestrymap2lfmm | 0.00 | 0.02 | 0.01 | |
| barchart | 0.59 | 0.08 | 0.91 | |
| crossEntropy | 0.11 | 0.01 | 0.19 | |
| genetic_gap | 0.41 | 0.02 | 0.42 | |
| genetic_offset | 2.70 | 0.36 | 3.06 | |
| geno2lfmm | 0.03 | 0.00 | 0.05 | |
| impute | 0.64 | 0.09 | 0.98 | |
| lfmm2 | 0.3 | 0.0 | 0.3 | |
| lfmm2_test | 0.26 | 0.02 | 0.28 | |
| lfmm2geno | 0.05 | 0.00 | 0.06 | |
| lfmm_pvalues | 10.59 | 0.05 | 10.64 | |
| main_LFMM | 69.13 | 0.10 | 69.49 | |
| main_createDataSet | 0.03 | 0.00 | 0.05 | |
| main_crossEntropyEstimation | 0.09 | 0.02 | 0.12 | |
| main_pca | 0.08 | 0.02 | 0.31 | |
| main_sNMF | 7.86 | 2.12 | 12.10 | |
| main_tracyWidom | 0.03 | 0.03 | 0.09 | |
| ped2geno | 0.00 | 0.00 | 0.02 | |
| ped2lfmm | 0.02 | 0.00 | 0.01 | |
| readEnv | 0.00 | 0.00 | 0.02 | |
| readGeno | 0.05 | 0.00 | 0.06 | |
| readLfmm | 0.06 | 0.00 | 0.08 | |
| readZscore | 5.65 | 0.02 | 5.69 | |
| snmf_pvalues | 0.52 | 0.08 | 0.87 | |
| struct2geno | 0.04 | 0.00 | 0.06 | |
| vcf2geno | 0.00 | 0.03 | 0.03 | |
| vcf2lfmm | 0.00 | 0.01 | 0.02 | |
| writeEnv | 0 | 0 | 0 | |
| writeGeno | 0.05 | 0.02 | 0.06 | |
| writeLFMM | 0.03 | 0.01 | 0.06 | |
| zscores | 10.92 | 0.00 | 10.93 | |