Multiple platform build/check report for BioC 3.10 - CHECK report for DepecheR on tokay1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DepecheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DepecheR_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DepecheR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DepecheR/DESCRIPTION' ... OK
* this is package 'DepecheR' version '1.2.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'DepecheR' 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
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'microClust'
* 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 data for ASCII and uncompressed saves ... 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 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-3.10-bioc/R/library/DepecheR/libs/i386/DepecheR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/DepecheR/libs/x64/DepecheR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/DepecheR.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DepecheR_1.2.2.tar.gz && rm -rf DepecheR.buildbin-libdir && mkdir DepecheR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DepecheR.buildbin-libdir DepecheR_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DepecheR_1.2.2.zip && rm DepecheR_1.2.2.tar.gz DepecheR_1.2.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0 1073k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1073k  100 1073k    0     0  3386k      0 --:--:-- --:--:-- --:--:-- 3418k

install for i386

* installing *source* package 'DepecheR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Clusterer.cpp -o Clusterer.o
Clusterer.cpp: In member function 'double Clusterer::cluster_norm(const RowMatrixXd&, const RowMatrixXd&, Eigen::VectorXi, double)':
Clusterer.cpp:204:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned int i = 0; i<centers.cols(); i++){
                              ^
Clusterer.cpp:205:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(unsigned int j = 0; j<centers.rows(); j++){
                                  ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c InterfaceUtils.cpp -o InterfaceUtils.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DepecheR.dll tmp.def Clusterer.o InterfaceUtils.o RcppExports.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
if test -e "/usr/bin/strip" && test -e "/bin/uname" && [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.dll; fi
rm *.o
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/DepecheR.buildbin-libdir/00LOCK-DepecheR/00new/DepecheR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DepecheR'
    finding HTML links ... done
    DepecheR-package                        html  
    dAllocate                               html  
    dColorPlot                              html  
    dColorVector                            html  
    dContours                               html  
    dDensityPlot                            html  
    dResidualPlot                           html  
    dScale                                  html  
    dSplsda                                 html  
    dViolins                                html  
    dWilcox                                 html  
    depeche                                 html  
    groupProbPlot                           html  
    microClust                              html  
    testData                                html  
    testDataDepeche                         html  
    testDataSNE                             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 'DepecheR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Clusterer.cpp -o Clusterer.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c InterfaceUtils.cpp -o InterfaceUtils.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -pthread -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DepecheR.dll tmp.def Clusterer.o InterfaceUtils.o RcppExports.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
if test -e "/usr/bin/strip" && test -e "/bin/uname" && [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug DepecheR.dll; fi
rm *.o
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/DepecheR.buildbin-libdir/DepecheR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DepecheR' as DepecheR_1.2.2.zip
* DONE (DepecheR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DepecheR' successfully unpacked and MD5 sums checked

CHECK report for DepecheR on tokay1

Summary

Command output

Installation output

Tests output

Example timings