##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings QuasR_1.45.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'QuasR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuasR' version '1.45.1'
* 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 'QuasR' can be installed ... WARNING
Found the following significant warnings:
  quantify_methylation.cpp:1077:57: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  quantify_methylation.cpp:1077:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  quantify_methylation.cpp:1077:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs     10.9Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  'ShortRead:::.ShortReadQQA' 'ShortRead:::.qa_adapterContamination'
  'ShortRead:::.set_omp_threads'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 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 ... NOTE
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-3.20-bioc/R/library/QuasR/libs/x64/QuasR.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
qCount         21.53   1.89   84.53
qMeth           0.47   0.31   33.74
qExportWig      0.17   0.10   28.83
qProject-class  0.08   0.16   30.09
* 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: 1 WARNING, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL QuasR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'QuasR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_cat.c -o bam_cat.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cat_bam.c -o cat_bam.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_alignments.c -o count_alignments.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_junctions.cpp -o count_junctions.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c export_wig.c -o export_wig.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filter_hisat2.c -o filter_hisat2.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c idxstats_bam.c -o idxstats_bam.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profile_alignments.c -o profile_alignments.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c quantify_methylation.cpp -o quantify_methylation.o
quantify_methylation.cpp: In function 'SEXPREC* quantify_methylation_singleAlignments(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
quantify_methylation.cpp:1077:57: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                       ~~^
      |                                                         |
      |                                                         long int
      |                                                       %lld
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                  ~~~~~~~~~                               
      |                  |
      |                  R_xlen_t {aka long long int}
quantify_methylation.cpp:1077:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                           ~~^
      |                                                             |
      |                                                             long unsigned int
      |                                                           %llu
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                             ~~~~~~~~~~~~~~~                  
      |                                          |
      |                                          std::vector<unsigned int>::size_type {aka long long unsigned int}
quantify_methylation.cpp:1077:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                               ~~^
      |                                                                 |
      |                                                                 long unsigned int
      |                                                               %llu
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                                              ~~~~~~~~~~~~~~~~    
      |                                                            |
      |                                                            std::vector<int>::size_type {aka long long unsigned int}
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam_opts.c -o sam_opts.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam_utils.c -o sam_utils.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c split_sam_chr.c -o split_sam_chr.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
g++ -std=gnu++17 -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o bam_cat.o bam_plbuf.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam_opts.o sam_utils.o split_sam_chr.o utilities.o F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-QuasR/00new/QuasR/libs/x64
** R
** 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 (QuasR)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(QuasR)
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Rbowtie
> 
> test_check("QuasR")
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
* DONE (BSgenome.HSapiens.QuasR.hg19sub)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpA31sYk/RtmpA31sYk\file13ed0e8c1729.fa
Finished creating index
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub.Rbowtie' ...
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** 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 (BSgenome.HSapiens.QuasR.hg19sub.Rbowtie)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed060429d7.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed057912e86.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Creating an RbowtieCtoT index for F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpA31sYk\file13ed071dd2572.fa
Finished creating index
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT' ...
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** 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 (BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed0699d461.txt
Genomic alignments have been created successfully

Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
    create 2 auxiliary alignment(s)
Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed04d115dba.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/NC_001422.1.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
nodeNames
PALOMINO4 
        2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed0478f6e98.txt
Auxiliary alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Reading and processing the SNP file: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed02eb039a5.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed0568a1a83.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 4 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed01ee26003.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed063bc29ab.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 4 genomic alignment(s)
Creating an Rhisat2 index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed027b34228.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed06c7db62.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create splice site file for gene annotation
    create 2 genomic alignment(s)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed01ab2c1b.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create splice site file for gene annotation
    create 2 genomic alignment(s)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed01fcb47ce.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Creating an RbowtieCtoT index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed031272082.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed050105405.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Creating an RbowtieCtoT index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_13ed0524d285d.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13ed07ccf2a57.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13ed0397a37f7.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13ed0537529f2.fa
all necessary alignment files found
[E::hts_open_format] Failed to open file "no-file" : No such file or directory
[samopen] no @SQ lines in the header.
samtools cat: fail to open output file 'not-there/bfile': No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for 'F:/biocbuild/bbs-3.20-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file13ed043b9469a.sam'
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::hts_open_format] Failed to open file "err/err" : No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  2 nodes produced errors; first error: there is no package called 'does_not_exist'
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ]
Warning messages:
1: In for (i in seq_len(n)) { :
  closing unused connection 8 (<-palomino4:11559)
2: In for (i in seq_len(n)) { :
  closing unused connection 7 (<-palomino4:11559)
> 
> proc.time()
   user  system elapsed 
  52.81   23.06  371.90