R Under development (unstable) (2025-02-10 r87710 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(testthat)
> library(flowr)
Loading required package: params
Loading required package: whisker
Flowr: streamlining workflows

Attaching package: 'flowr'

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

    check_args, get_opts, load_opts, set_opts

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

    setup

> 
> system("env")
!C:=C:\Windows\System32
!D:=d:\RCompile\CRANincoming\R-devel\flowr.Rcheck\tests
!ExitCode=00000000
ALLUSERSPROFILE=C:\ProgramData
APPDATA=C:\Users\CRAN\AppData\Roaming
BIBINPUTS=.;.;.;;D:/RCompile/recent/R/share/texmf/bibtex/bib;;D:/RCompile/recent/R/share/texmf/bibtex/bib;;D:/RCompile/recent/R/share/texmf/bibtex/bib;
BINDIR=bin/x64
BSTINPUTS=.;.;.;;D:/RCompile/recent/R/share/texmf/bibtex/bst;;D:/RCompile/recent/R/share/texmf/bibtex/bst;;D:/RCompile/recent/R/share/texmf/bibtex/bst;
COMMONPROGRAMFILES=C:\Program Files\Common Files
COMPUTERNAME=CRANWIN3
COMSPEC=C:\Windows\system32\cmd.exe
CURL_CA_BUNDLE=D:/RCompile/recent/R/etc/curl-ca-bundle.crt
CYGWIN=nodosfilewarning
CommonProgramFiles(x86)=C:\Program Files (x86)\Common Files
CommonProgramW6432=C:\Program Files\Common Files
DriverData=C:\Windows\System32\Drivers\DriverData
HOME=/c/Users/CRAN/Documents
HOMEDRIVE=C:
HOMEPATH=\Users\CRAN
JAGS_ROOT=C:/Program Files/JAGS/JAGS-4.3.1
JAVA_HOME=C:/Program Files/jdk-11.0.18.10-hotspot
LANGUAGE=C
LC_COLLATE=C
LC_MONETARY=C
LC_TIME=C
LOCALAPPDATA=C:\Users\CRAN\AppData\Local
LOGONSERVER=\\CRANWIN3
LS_HOME=D:\RCompile\CRANpkg\extralibs\localsolver_4_0
LS_LICENSE_PATH=D:\RCompile\CRANpkg\extralibs\localsolver_4_0\license.dat
MAKE=make
MAKEFLAGS=
MAKELEVEL=1
MFLAGS=-k
MSMPI_BENCHMARKS=C:\Program Files\Microsoft MPI\Benchmarks\
MSMPI_BIN=C:\Program Files\Microsoft MPI\Bin\
MSYS2_ENV_CONV_EXCL=R_ARCH
nextArg--timingsnextArg--install=check:flowr-install.outnextArg--library=d:/RCompile/CRANincoming/R-devel/libnextArgflowr_0.9.12.tar.gz
NUMBER_OF_PROCESSORS=48
OCL=d:/RCompile/CRANpkg/extralibs/OpenCL
OMP_THREAD_LIMIT=2
OS=Windows_NT
PATH=/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/d/RCompile/recent/R/bin/x64:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:.:/usr/bin:/x86_64-w64-mingw32.static.posix/bin:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files/gs/gs/bin:/d/compiler/qpdf/bin:/d/RCompile/CRANpkg/extralibs/localsolver_4_0/bin:/d/RCompile/CRANpkg/extralibs/MARK:/c/Program Files/7-Zip:/d/Compiler/gretl:/c/Program Files/Quarto/bin:/d/compiler/Ruby/bin:/c/Program Files/Microsoft MPI/Bin:/c/Program Files/Python/Scripts:/c/Program Files/Python:/c/Windows/system32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0:/c/Windows/System32/OpenSSH:/c/Program Files/PuTTY:/c/Program Files (x86)/WinSCP:/c/Program Files/Pandoc:/c/Program Files/MiKTeX/miktex/bin/x64:/c/Program Files (x86)/Windows Kits/10/Windows Performance Toolkit:/c/Program Files/gs/gs/bin:/c/Program Files/jdk-11.0.18.10-hotspot/bin:/d/compiler/perl/c/bin:/d/compiler/perl/perl/site/bin:/d/compiler/perl/perl/bin:/c/Users/CRAN/.cargo/bin:/c/Users/CRAN/AppData/Local/Microsoft/WindowsApps:/usr/bin:/c/Program Files/Julia/bin:/c/Users/CRAN/.cargo/bin:/d/compiler/LDC/bin:/d/RCompile/recent/R/bin/x64/
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC;.PY;.PYW;.RB;.RBW
PROCESSOR_ARCHITECTURE=AMD64
PROCESSOR_IDENTIFIER=AMD64 Family 25 Model 1 Stepping 1, AuthenticAMD
PROCESSOR_LEVEL=25
PROCESSOR_REVISION=0101
PROGRAMFILES=C:\Program Files
PROMPT=$P$G
PSModulePath=%ProgramFiles%\WindowsPowerShell\Modules;C:\Windows\system32\WindowsPowerShell\v1.0\Modules
PUBLIC=C:\Users\Public
PWD=D:/RCompile/CRANincoming/R-devel
ProgramData=C:\ProgramData
ProgramFiles(x86)=C:\Program Files (x86)
ProgramW6432=C:\Program Files
RTOOLS44_HOME=D:\rtools44
R_ARCH=/x64
R_BROWSER=false
R_BZIPCMD=bzip2
R_CMD=R CMD
R_COMPILED_BY=gcc 13.3.0
R_CRAN_WEB=https://cran.wu.ac.at
R_CUSTOM_TOOLS_PATH=d:/rtools44/usr/bin;d:/rtools44/x86_64-w64-mingw32.static.posix/bin
R_CUSTOM_TOOLS_SOFT=d:/rtools44/x86_64-w64-mingw32.static.posix
R_DOC_DIR=D:/RCompile/recent/R/doc
R_ENVIRON_USER='no_such_file'
R_GSCMD=C:\Progra~1\gs\gs\bin\gswin64c.exe
R_GZIPCMD=gzip
R_HOME=D:/RCompile/recent/R
R_INCLUDE_DIR=D:/RCompile/recent/R/include
R_INSTALL_TAR=d:/rtools44/usr/bin/tar
R_LIBS=D:\temp\2025_02_11_17_35_17_19189\Rtmp2P3Jby\RLIBS_14c3877e47d14
R_LIBS_SITE='NULL'
R_LIBS_USER='NULL'
R_MAX_NUM_DLLS=153
R_OSTYPE=windows
R_PAPERSIZE=a4
R_PAPERSIZE_USER=a4
R_PARALLEL_PORT=random
R_RD4PDF=times,inconsolata,hyper
R_RTOOLS44_PATH=D:\rtools44/x86_64-w64-mingw32.static.posix/bin;D:\rtools44/usr/bin
R_SCRIPT_LEGACY=yes
R_SHARE_DIR=D:/RCompile/recent/R/share
R_TESTS=startup.Rs
R_UNZIPCMD=unzip
R_USER=C:\Users\CRAN\Documents
R_VERSION=4.5.0
R_ZIPCMD=zip
SED=sed
SHLVL=0
SYSTEMDRIVE=C:
SYSTEMROOT=C:\Windows
TAR=d:/rtools44/usr/bin/tar
TAR_OPTIONS=--force-local --no-same-owner --no-same-permissions
TEMP=/d/temp/2025_02_11_17_35_17_19189
TERM=xterm-256color
TEXINPUTS=.;.;.;;D:/RCompile/recent/R/share/texmf/tex/latex;;D:/RCompile/recent/R/share/texmf/tex/latex;;D:/RCompile/recent/R/share/texmf/tex/latex;
TMP=/d/temp/2025_02_11_17_35_17_19189
TMPDIR=/d/temp/2025_02_11_17_35_17_19189
USERDOMAIN=CRANWIN3
USERDOMAIN_ROAMINGPROFILE=CRANWIN3
USERNAME=CRAN
USERPROFILE=C:\Users\CRAN
WINDIR=C:\Windows
_=D:/RCompile/recent/R/bin/x64/R
_R_CHECK_AUTOCONF_=true
_R_CHECK_BOGUS_RETURN_=true
_R_CHECK_BROWSER_NONINTERACTIVE_=true
_R_CHECK_BUILD_VIGNETTES_SEPARATELY_=false
_R_CHECK_CODETOOLS_PROFILE_=suppressPartialMatchArgs=false
_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
_R_CHECK_CODE_ATTACH_=TRUE
_R_CHECK_CODE_CLASS_IS_STRING_=true
_R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
_R_CHECK_CODE_USAGE_WITHOUT_LOADING_=TRUE
_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_=true
_R_CHECK_CODOC_VARIABLES_IN_USAGES_=true
_R_CHECK_COMPACT_DATA2_=TRUE
_R_CHECK_COMPILATION_FLAGS_=TRUE
_R_CHECK_CONNECTIONS_LEFT_OPEN_=TRUE
_R_CHECK_CRAN_INCOMING_=TRUE
_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_=true
_R_CHECK_CRAN_INCOMING_CHECK_URLS_IN_PARALLEL_=true
_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=TRUE
_R_CHECK_CRAN_INCOMING_REMOTE_=TRUE
_R_CHECK_CRAN_INCOMING_USE_ASPELL_=TRUE
_R_CHECK_DATALIST_=true
_R_CHECK_DEPRECATED_DEFUNCT_=TRUE
_R_CHECK_DOC_SIZES2_=TRUE
_R_CHECK_DOT_FIRSTLIB_=TRUE
_R_CHECK_DOT_INTERNAL_=TRUE
_R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10
_R_CHECK_EXECUTABLES_=FALSE
_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
_R_CHECK_FF_CALLS_=registration
_R_CHECK_FF_DUP_=TRUE
_R_CHECK_FORCE_SUGGESTS_=FALSE
_R_CHECK_FUTURE_FILE_TIMESTAMPS_=true
_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_=6h
_R_CHECK_HAVE_MYSQL_=TRUE
_R_CHECK_HAVE_ODBC_=TRUE
_R_CHECK_HAVE_PERL_=TRUE
_R_CHECK_HAVE_POSTGRES_=TRUE
_R_CHECK_INSTALL_DEPENDS_=TRUE
_R_CHECK_INTERNALS2_=1
_R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose
_R_CHECK_LICENSE_=TRUE
_R_CHECK_LIMIT_CORES_=true
_R_CHECK_LOG_USE_INFO_=true
_R_CHECK_MATRIX_DATA_=TRUE
_R_CHECK_MBCS_CONVERSION_FAILURE_=true
_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=false
_R_CHECK_NEWS_IN_PLAIN_TEXT_=true
_R_CHECK_NO_RECOMMENDED_=TRUE
_R_CHECK_NO_STOP_ON_TEST_ERROR_=true
_R_CHECK_ORPHANED_=true
_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=TRUE
_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=true
_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_=TRUE
_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_=true
_R_CHECK_PACKAGE_NAME_=flowr
_R_CHECK_PKG_SIZES_=TRUE
_R_CHECK_PKG_SIZES_THRESHOLD_=50
_R_CHECK_PRAGMAS_=TRUE
_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
_R_CHECK_RD_LINE_WIDTHS_=TRUE
_R_CHECK_RD_MATH_RENDERING_=true
_R_CHECK_RD_NOTE_LOST_BRACES_=true
_R_CHECK_RD_VALIDATE_RD2HTML_=true
_R_CHECK_REPLACING_IMPORTS_=TRUE
_R_CHECK_R_DEPENDS_=warn
_R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_=true
_R_CHECK_SCREEN_DEVICE_=stop
_R_CHECK_SERIALIZATION_=true
_R_CHECK_SHLIB_OPENMP_FLAGS_=TRUE
_R_CHECK_SRC_MINUS_W_IMPLICIT_=TRUE
_R_CHECK_SUBDIRS_NOCASE_=TRUE
_R_CHECK_SUGGESTS_ONLY_=TRUE
_R_CHECK_SYSTEM_CLOCK_=false
_R_CHECK_TESTS_NLINES_=0 
_R_CHECK_TEST_TIMING_=yes
_R_CHECK_TIMINGS_=10
_R_CHECK_TOPLEVEL_FILES_=TRUE
_R_CHECK_UNDOC_USE_ALL_NAMES_=TRUE
_R_CHECK_UNSAFE_CALLS_=TRUE
_R_CHECK_URLS_SHOW_301_STATUS_=true
_R_CHECK_VC_DIRS_=TRUE
_R_CHECK_VIGNETTES_NLINES_=0
_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true
_R_CHECK_VIGNETTE_TIMING_=yes
_R_CHECK_VIGNETTE_TITLES_=true
_R_CHECK_WINDOWS_DEVICE_=TRUE
_R_CHECK_XREFS_NOTE_MISSING_PACKAGE_ANCHORS_=true
_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_=true
_R_CLASS_MATRIX_ARRAY_=true
_R_DEPRECATED_IS_R_=self
_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=true
_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_=TRUE
_R_USE_STRICT_R_HEADERS_=true
maj.version=4.5
tempdirname=d:\temp\2025_02_11_17_35_17_19189
__R_CHECK_DOC_FILES_NOTE_IF_ALL_SPECIAL__=TRUE
[1] 0
> system.file(package = "flowr")
[1] "D:/RCompile/CRANincoming/R-devel/lib/flowr"
> 
> #set_opts("verbose")
> opts_flow$get()


|name              |value                    |
|:-----------------|:------------------------|
|flow_base_path    |~/flowr                  |
|flow_conf_path    |{{flow_base_path}}/conf  |
|flow_parse_lsf    |.*(\<[0-9]*\>).*         |
|flow_parse_moab   |(.*)                     |
|flow_parse_sge    |(.*)                     |
|flow_parse_slurm  |.* ([0-9]+)              |
|flow_parse_torque |(.?)\..*                 |
|flow_pipe_paths   |~/flowr/pipelines        |
|flow_pipe_urls    |~/flowr/pipelines        |
|flow_platform     |local                    |
|flow_run_path     |~/flowr/runs             |
|local_cores       |4                        |
|module_cmds       |                         |
|time_format       |%a %b %e %H:%M:%S CDT %Y |
|verbose           |1                        |
> 
> test_check("flowr")



[ FAIL 0 | WARN 0 | SKIP 4 | PASS 43 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• case 1 (1): 'test-cases.R:15:3'
• rerunning (3): 'test-toflow.R:137:5', 'test-toflow.R:137:5',
  'test-toflow.R:137:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 43 ]
> 
> 
> #test_package("flowr")
> 
> proc.time()
   user  system elapsed 
   2.21    0.31    2.68