##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:raer.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings raer_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/raer.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'raer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'raer' version '1.7.2'
* 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 'raer' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* checking installed package size ... INFO
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annot_snps.Rd: GRanges, SummarizedExperiment
  calc_AEI.Rd: GRanges, TxDb, SNPlocs, GPos, BiocParallelParam
  calc_edit_frequency.Rd: RangedSummarizedExperiment
  find_de_sites.Rd: RangedSummarizedExperiment
  find_scde_sites.Rd: SingleCellExperiment, rowData, DataFrame
  make_de_object.Rd: RangedSummarizedExperiment
  pileup_cells.Rd: GRanges, BamFile, BamFileList, SingleCellExperiment,
    rowRanges
  pileup_sites.Rd: RangedSummarizedExperiment, BamFile, BamFileList,
    colData, GRanges, BiocParallel, rowRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 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 ... INFO
GNU make is a SystemRequirements.
* 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-3.22-bioc/R/library/raer/libs/x64/raer.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' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
annot_snps       37.06   1.08   44.56
get_splice_sites 12.39   0.80   13.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/raer.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL raer
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'raer' ...
** this is package 'raer' version '1.7.2'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c plp.c -o plp.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c plp_data.c -o plp_data.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c plp_utils.c -o plp_utils.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c regfile.c -o regfile.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c sc-plp.c -o sc-plp.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c utils.c -o utils.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.o
gcc -shared -s -static-libgcc -o raer.dll tmp.def init.o plp.o plp_data.o plp_utils.o regfile.o sc-plp.o utils.o ext/bcftools/bcftools-ext.o ext/htsbox/htsbox-ext.o ext/samtools/samtools-ext.o F:/biocbuild/bbs-3.22-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lnghttp2 -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-raer/00new/raer/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (raer)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(raer)
> 
> test_check("raer")
Using classic mode.
[raer internal] fail to parse region 'chr1' with F:/biocbuild/bbs-3.22-bioc/R/library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
[raer internal] fail to parse region 'chrHello' with F:/biocbuild/bbs-3.22-bioc/R/library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh38
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: BSgenome.Hsapiens.NCBI.GRCh38
i `filter_clustered_variants()`:  removed 70 sites from 72 (2 remain)
i `filter_clustered_variants()`:  removed 3 sites from 9 (6 remain)
i `filter_clustered_variants()`:  removed 6 sites from 9 (3 remain)
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 261 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 261 ]
> 
> proc.time()
   user  system elapsed 
 129.98    6.12  165.04