##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISoLDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ISoLDE_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/ISoLDE.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'ISoLDE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ISoLDE' version '1.33.0'
* package encoding: UTF-8
* 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 'ISoLDE' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package 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 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/ISoLDE/libs/x64/ISoLDE.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (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 files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'ISoLDE_result_on_example.pdf' 'vignette.Rnw' 'workflow.pdf'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/vignette.Rnw'
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testsIsolde.R'
 OK
* checking package vignettes ... NOTE
Package has 'vignettes' subdirectory but apparently no vignettes.
Perhaps the 'VignetteBuilder' information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/ISoLDE.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ISoLDE
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ISoLDE' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Isolde.c -o Isolde.o
gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ISoLDE/00new/ISoLDE/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 (ISoLDE)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ISoLDE)
> 
> targetfile <- system.file("extdata", "target_file.txt", package = "ISoLDE")
> rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE")
> normfile <- system.file("extdata", "normASRcounts_file.txt", package = "ISoLDE")
> 
> rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)
Reading raw input file...
Done
> normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
Reading normalized input file...
Done
> target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
Reading target file...
Done
> 
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
Filtering your data...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "parental", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000,pcore=1)
Warning: pcore is a percentage between 0 and 100, be sure you want to use 1% of your available cores.
ISoLDE is searching for allele-specific gene expression due to parental biases...
Done
According to the satisfying number of replicates the full method can be applied. See the vignette for more details
Testing...
This step can last for a few minutes. Please be patient :)
Note: the full method uses a bootstrap step which means some results might change from one test to another.
Open MP enabled 
Have Cores : 64 
UseCores : 1 
nu0= 0.100000 
Open MP enabled 
Have Cores : 64 
UseCores : 1 
lambda0 : 1.600000 
Open MP enabled 
Have Cores : 64 
UseCores : 1 
nu0= 0.100000 
Open MP enabled 
Have Cores : 64 
UseCores : 1 
lambda0 : 1.600000 
Open MP enabled 
Have Cores : 64 
UseCores : 1 
nu0= 0.200000 
Open MP enabled 
Have Cores : 64 
UseCores : 1 
lambda0 : 1.600000 
Done
46 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_07-16-2024_01-10-16.tsv.
6087 biallelic (BA) genes found and written in file ISoLDE_result_BA_07-16-2024_01-10-16.tsv.
44 Undetermined (UN) genes found and written in file ISoLDE_result_UN_07-16-2024_01-10-16.tsv.
Among these undetermined (UN) genes, 23 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="strain")
Filtering your data...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "strain", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000, method = "threshold")
ISoLDE is searching for allele-specific gene expression due to strain biases...
The predefined threshold method is about to proceed, but we strongly recommand the bootstrap method because ISoLDE detected more than 2 replicates in each cross.
Testing...
Done
308 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_07-16-2024_01-10-17.tsv.
4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_07-16-2024_01-10-17.tsv.
1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_07-16-2024_01-10-17.tsv.
Among these undetermined (UN) genes, 913 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
> 
> proc.time()
   user  system elapsed 
  45.70    0.78   46.51