##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COHCAP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings COHCAP_1.41.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/COHCAP.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 'COHCAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COHCAP' version '1.41.0'
* 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 'COHCAP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.UCSC'
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.HMM'
COHCAP.annotate: no visible binding for global variable 'COHCAP.27k'
COHCAP.integrate.avg.by.island: no visible binding for global variable
  'na.rm'
cor.test.est: no visible binding for global variable 'na.rm'
cor.test.pvalue: no visible binding for global variable 'na.rm'
Undefined global functions or variables:
  COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/COHCAP/libs/x64/COHCAP.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 ... OK
* 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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/COHCAP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL COHCAP
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/gamma.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/fisher_f.hpp:12,
                 from Rcpp_BH_ANOVA.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/gamma.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_linear_regression.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/gamma.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:15,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_ttest.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o COHCAP.dll tmp.def RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_linear_regression.o Rcpp_BH_ttest.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-COHCAP/00new/COHCAP/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'COHCAP'
    finding HTML links ... done
    COHCAP.BSSeq.preprocess                 html  
    COHCAP.BSSeq_V2.methyl.table            html  
    COHCAP.annotate                         html  
    COHCAP.avg.by.island                    html  
    COHCAP.avg.by.site                      html  
    COHCAP.denovo                           html  
    COHCAP.integrate.avg.by.island          html  
    COHCAP.integrate.avg.by.site            html  
    COHCAP.qc                               html  
    COHCAP.reformatFinalReport              html  
    COHCAP.site                             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 (COHCAP)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OSAT' is missing or broken
 done