Back to Multiple platform build/check report for BioC 3.11
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CHECK report for COHCAP on tokay2

This page was generated on 2020-10-17 11:56:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE COHCAP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 350/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.34.1
Charles Warden
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/COHCAP
Branch: RELEASE_3_11
Last Commit: 5882753
Last Changed Date: 2020-04-30 15:46:49 -0400 (Thu, 30 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: COHCAP
Version: 1.34.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COHCAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings COHCAP_1.34.1.tar.gz
StartedAt: 2020-10-17 02:49:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:51:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 107.9 seconds
RetCode: 0
Status:  OK  
CheckDir: COHCAP.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COHCAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings COHCAP_1.34.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/COHCAP.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.34.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/COHCAP/libs/i386/COHCAP.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/COHCAP.Rcheck/00check.log'
for details.

Installation output

COHCAP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/COHCAP_1.34.1.tar.gz && rm -rf COHCAP.buildbin-libdir && mkdir COHCAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=COHCAP.buildbin-libdir COHCAP_1.34.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL COHCAP_1.34.1.zip && rm COHCAP_1.34.1.tar.gz COHCAP_1.34.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 60852  100 60852    0     0  1010k      0 --:--:-- --:--:-- --:--:-- 1142k

install for i386

* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/fisher_f.hpp:12,
                 from Rcpp_BH_ANOVA.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_linear_regression.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_ttest.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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/mingw32/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/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/COHCAP.buildbin-libdir/00LOCK-COHCAP/00new/COHCAP/libs/i386
** 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

install for x64

* installing *source* package 'COHCAP' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/fisher_f.hpp:12,
                 from Rcpp_BH_ANOVA.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_linear_regression.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/beta.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/distributions/students_t.hpp:16,
                 from Rcpp_BH_ttest.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-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 -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/COHCAP.buildbin-libdir/COHCAP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COHCAP' as COHCAP_1.34.1.zip
* DONE (COHCAP)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'COHCAP' successfully unpacked and MD5 sums checked

Tests output

Example timings

COHCAP.Rcheck/examples_i386/COHCAP-Ex.timings

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.020.000.13
COHCAP.BSSeq_V2.methyl.table0.010.000.03
COHCAP.annotate1.760.041.89
COHCAP.avg.by.island2.520.032.89
COHCAP.avg.by.site2.480.052.68
COHCAP.denovo2.250.062.42
COHCAP.integrate.avg.by.island2.190.072.47
COHCAP.integrate.avg.by.site2.530.092.84
COHCAP.qc1.780.091.88
COHCAP.reformatFinalReport0.000.020.01
COHCAP.site2.290.062.45

COHCAP.Rcheck/examples_x64/COHCAP-Ex.timings

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.000.000.13
COHCAP.BSSeq_V2.methyl.table0.030.000.03
COHCAP.annotate1.590.101.68
COHCAP.avg.by.island1.920.112.16
COHCAP.avg.by.site1.710.071.89
COHCAP.denovo2.440.112.66
COHCAP.integrate.avg.by.island2.370.032.62
COHCAP.integrate.avg.by.site1.840.112.19
COHCAP.qc1.100.031.12
COHCAP.reformatFinalReport000
COHCAP.site1.550.041.69