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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Harman.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Harman_1.23.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Harman.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 'Harman/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Harman' version '1.23.1'
* 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 'Harman' 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 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 'D:/biocbuild/bbs-3.15-bioc/R/library/Harman/libs/x64/Harman.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 ... ERROR
Running examples in 'Harman-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterStats
> ### Title: Compute LVR and meandiff statistics for beta values after batch
> ###   correction
> ### Aliases: clusterStats
> 
> ### ** Examples
> 
> library(HarmanData)
> data(episcope)
Warning in data(episcope) : data set 'episcope' not found
> bad_batches <- c(1, 5, 9, 17, 25)
> is_bad_sample <- episcope$pd$array_num %in% bad_batches
Error in episcope$pd$array_num %in% bad_batches : 
  object 'episcope' not found
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test.cluster.math: Error in episcope$pd$array_num %in% bad_batches : 
    object 'episcope' not found
  
  Test files with failing tests
  
     test_clustering.R 
       test.cluster.math 
  
  
  Error in BiocGenerics:::testPackage("Harman") : 
    unit tests failed for package Harman
  In addition: Warning message:
  In kClusterMethylation(betas[1, , drop = FALSE], row_ks = ks[1]) :
    All rows have a cluster size of 1
  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: 2 ERRORs, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/Harman.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Harman
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Harman' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4  -D_USE_RCPP=1  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -I"D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include" -std=c++0x    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Harman.cpp -o Harman.o
Harman.cpp: In function 'SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
Harman.cpp:3008:3: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
   else
   ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
     std::vector<unsigned int>    tr_std_tmp     = Rcpp::as<std::vector<unsigned int> >(tr) ;
     ^~~
In file included from Harman.cpp:182:
CSelectRandom.h: In instantiation of 'std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long long unsigned int]':
Harman.cpp:1764:117:   required from here
CSelectRandom.h:943:20: warning: comparison of integer expressions of different signedness: 'long long int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     while (currval < howManyIN)
            ~~~~~~~~^~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Harman.dll tmp.def Harman.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Harman/00new/Harman/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Harman'
    finding HTML links ... done
    arrowPlot                               html  
    callHarman                              html  
    clusterStats                            html  
    detachHarman                            html  
    discoverClusteredMethylation            html  
    harman                                  html  
    harmanScores                            html  
    harmanresults                           html  
    kClusterMethylation                     html  
    pcaPlot                                 html  
    plot.harmanresults                      html  
    prcompPlot                              html  
    print.summary.harmanresults             html  
    reconstructData                         html  
    shiftBetas                              html  
    summary.harmanresults                   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 (Harman)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ModCon' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'rDGIdb' 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.

> BiocGenerics:::testPackage("Harman")
Timing stopped at: 0 0 0
Error in episcope$pd$array_num %in% bad_batches : 
  object 'episcope' not found
In addition: Warning message:
In data(episcope) : data set 'episcope' not found


RUNIT TEST PROTOCOL -- Tue Feb 15 19:22:14 2022 
*********************************************** 
Number of test functions: 14 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
Harman RUnit Tests - 14 test functions, 1 error, 0 failures
ERROR in test.cluster.math: Error in episcope$pd$array_num %in% bad_batches : 
  object 'episcope' not found

Test files with failing tests

   test_clustering.R 
     test.cluster.math 


Error in BiocGenerics:::testPackage("Harman") : 
  unit tests failed for package Harman
In addition: Warning message:
In kClusterMethylation(betas[1, , drop = FALSE], row_ks = ks[1]) :
  All rows have a cluster size of 1
Execution halted