##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IgGeneUsage.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IgGeneUsage_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/IgGeneUsage.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IgGeneUsage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IgGeneUsage' version '1.9.2'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'IgGeneUsage' 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   4.     | \-withr::with_path(rtools_path(), code)
   5.     |   \-base::force(code)
   6.     \-inline::cxxfunction(...)
   7.       \-inline:::compileCode(f, code, language = language, verbose = verbose)
  -- Error (test-model.R:8:3): stan model availability check ---------------------
  Error in `sink(type = "output")`: invalid connection
  Backtrace:
      x
   1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
   2.   \-rstan:::cxxfunctionplus(...)
   3.     \-base::sink(type = "output")
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/IgGeneUsage.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL IgGeneUsage
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'IgGeneUsage' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IgGeneUsage'
    finding HTML links ... done
    DGU                                     html  
    IGHV_Epitopes                           html  
    IGHV_HCV                                html  
    Ig                                      html  
    Ig_SE                                   html  
    LOO                                     html  
** 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 (IgGeneUsage)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'divergence' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(testthat)
> library(IgGeneUsage)
Loading required package: Rcpp
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: StanHeaders
> 
> test_check("IgGeneUsage")
Tests Frequentist methods 
Tests Summarized Experiment check 
Tests input rules 
Tests stan model 
make cmd is
  make -f "D:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf" -f "D:/biocbuild/bbs-3.15-bioc/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file49505054318.dll" WIN=64 TCLBIN=64 OBJECTS="file49505054318.o"

make would use
if test "zfile49505054318.o" != "z"; then \
  if test -e "file49505054318-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file49505054318.dll file49505054318-win.def file49505054318.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file49505054318.dll file49505054318-win.def file49505054318.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file49505054318.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file49505054318.dll tmp.def file49505054318.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file49505054318.dll tmp.def file49505054318.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]

== Failed tests ================================================================
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `compileCode(f, code, language = language, verbose = verbose)`: C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file49505054318.o:file49505054318.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1c): more undefined references to `tbb::internal::task_scheduler_observer_v3::observe(bool)' followcollect2.exe: error: ld returned 1 exit statusC:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.15-bioc/tmpdir/Rtmpkf4kGC/file49505054318.o: file format not recognizedWarning message:In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) :  running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "D:/biocbuild/bbs-3.15-bioc/tmpdir/Rtmpkf4kGC/file49505054318.o"' had status 1
Backtrace:
    x
 1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
 2.   \-rstan:::cxxfunctionplus(...)
 3.     +-pkgbuild::with_build_tools(...)
 4.     | \-withr::with_path(rtools_path(), code)
 5.     |   \-base::force(code)
 6.     \-inline::cxxfunction(...)
 7.       \-inline:::compileCode(f, code, language = language, verbose = verbose)
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `sink(type = "output")`: invalid connection
Backtrace:
    x
 1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
 2.   \-rstan:::cxxfunctionplus(...)
 3.     \-base::sink(type = "output")

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
Error: Test failures
Execution halted