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CHECK report for cydar on tokay1

This page was generated on 2018-04-12 13:29:35 -0400 (Thu, 12 Apr 2018).

Package 322/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cydar 1.2.1
Aaron Lun
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cydar
Branch: RELEASE_3_6
Last Commit: 47e594e
Last Changed Date: 2017-11-08 14:26:28 -0400 (Wed, 08 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cydar
Version: 1.2.1
Command: rm -rf cydar.buildbin-libdir cydar.Rcheck && mkdir cydar.buildbin-libdir cydar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cydar.buildbin-libdir cydar_1.2.1.tar.gz >cydar.Rcheck\00install.out 2>&1 && cp cydar.Rcheck\00install.out cydar-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cydar.buildbin-libdir --install="check:cydar-install.out" --force-multiarch --no-vignettes --timings cydar_1.2.1.tar.gz
StartedAt: 2018-04-11 23:19:47 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:29:53 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 605.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cydar.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cydar.buildbin-libdir cydar.Rcheck && mkdir cydar.buildbin-libdir cydar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cydar.buildbin-libdir cydar_1.2.1.tar.gz >cydar.Rcheck\00install.out 2>&1 && cp cydar.Rcheck\00install.out cydar-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=cydar.buildbin-libdir --install="check:cydar-install.out" --force-multiarch --no-vignettes --timings cydar_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cydar.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cydar/DESCRIPTION' ... OK
* this is package 'cydar' version '1.2.1'
* 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 'cydar' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/normalizeBatch.Rd:95: missing file link 'normalization'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:26: missing file link 'estimateLogicle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:36: missing file link 'flowFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:38: missing file link 'estimateLogicle'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/cydar.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::selectSome'
  'SummarizedExperiment:::.SummarizedExperiment.charbound'
  See the note in ?`:::` about the use of this operator.
* 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 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-3.6-bioc/meat/cydar.buildbin-libdir/cydar/libs/i386/cydar.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 installed files from 'inst/doc' ... OK
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/cydar.Rcheck/00check.log'
for details.

Installation output

cydar.Rcheck/00install.out


install for i386

* installing *source* package 'cydar' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_density.cpp -o compute_density.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (_sample_id.size()!=ncells) { 
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (_sample_id.size()!=ncells) { 
                          ^
compute_median_int.cpp:46:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex < 0 || curdex >= ncells) {
                                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c count_cells.cpp -o count_cells.o
In file included from count_cells.cpp:2:0:
packer.h: In instantiation of 'void pack_index_vector(std::deque<int>&, Iter, Iter) [with Iter = std::_Deque_iterator<unsigned int, unsigned int&, unsigned int*>]':
count_cells.cpp:38:73:   required from here
packer.h:28:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((*previous)+1!=sorted_ids.back()) {
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c drop_redundant.cpp -o drop_redundant.o
drop_redundant.cpp: In function 'SEXPREC* drop_redundant(SEXP, SEXP, SEXP, SEXP, SEXP)':
drop_redundant.cpp:15:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ordering.size()!=nhyper) {
                        ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c find_knn.cpp -o find_knn.o
find_knn.cpp: In function 'SEXPREC* find_knn(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
find_knn.cpp:20:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (_query.nrow()!=nmarkers) {
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c get_nndist.cpp -o get_nndist.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c objects.cpp -o objects.o
objects.cpp: In member function 'void naive_holder::find_neighbors(size_t, double, bool)':
objects.cpp:31:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
              ^
objects.cpp: In member function 'void naive_holder::find_nearest_neighbors(size_t, size_t, bool)':
objects.cpp:43:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
              ^
objects.cpp: In member function 'double naive_holder::compute_marker_sqdist(const double*, const double*) const':
objects.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t m=0; m<exprs.nrow(); ++m) {
                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pack_indices.cpp -o pack_indices.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c recount.cpp -o recount.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o find_knn.o get_nndist.o init.o objects.o pack_indices.o recount.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cydar.buildbin-libdir/cydar/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cydar'
    finding HTML links ... done
    countCells                              html  
    cyData-class                            html  
    cyData-getset                           html  
    cyData-subset                           html  
    diffIntDistr                            html  
    dnaGate                                 html  
    finding level-2 HTML links ... done

    expandRadius                            html  
    findFirstSphere                         html  
    intensityRanges                         html  
    interpretSpheres                        html  
    labelSpheres                            html  
    medIntensities                          html  
    multiIntHist                            html  
    neighborDistances                       html  
    normalizeBatch                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/normalizeBatch.Rd:95: missing file link 'normalization'
    outlierGate                             html  
    packIndices                             html  
    pickBestMarkers                         html  
    plotCells                               html  
    poolCells                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:26: missing file link 'estimateLogicle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:36: missing file link 'flowFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpimqi2a/R.INSTALL51068b55f96/cydar/man/poolCells.Rd:38: missing file link 'estimateLogicle'
    prepareCellData                         html  
    recountCells                            html  
    spatialFDR                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cydar' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_density.cpp -o compute_density.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function 'SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP)':
compute_hyperstats.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (_sample_id.size()!=ncells) { 
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function 'SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP)':
compute_median_int.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (_sample_id.size()!=ncells) { 
                          ^
compute_median_int.cpp:46:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (curdex < 0 || curdex >= ncells) {
                                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c count_cells.cpp -o count_cells.o
In file included from count_cells.cpp:2:0:
packer.h: In instantiation of 'void pack_index_vector(std::deque<int>&, Iter, Iter) [with Iter = std::_Deque_iterator<long long unsigned int, long long unsigned int&, long long unsigned int*>]':
count_cells.cpp:38:73:   required from here
packer.h:28:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((*previous)+1!=sorted_ids.back()) {
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c drop_redundant.cpp -o drop_redundant.o
drop_redundant.cpp: In function 'SEXPREC* drop_redundant(SEXP, SEXP, SEXP, SEXP, SEXP)':
drop_redundant.cpp:15:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (ordering.size()!=nhyper) {
                        ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c find_knn.cpp -o find_knn.o
find_knn.cpp: In function 'SEXPREC* find_knn(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
find_knn.cpp:20:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (_query.nrow()!=nmarkers) {
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c get_nndist.cpp -o get_nndist.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c objects.cpp -o objects.o
objects.cpp: In member function 'void naive_holder::find_neighbors(size_t, double, bool)':
objects.cpp:31:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
              ^
objects.cpp: In member function 'void naive_holder::find_nearest_neighbors(size_t, size_t, bool)':
objects.cpp:43:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (cell >= exprs.ncol()) { throw std::runtime_error("cell index out of range"); }
              ^
objects.cpp: In member function 'double naive_holder::compute_marker_sqdist(const double*, const double*) const':
objects.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t m=0; m<exprs.nrow(); ++m) {
                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pack_indices.cpp -o pack_indices.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c recount.cpp -o recount.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cydar.dll tmp.def compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o find_knn.o get_nndist.o init.o objects.o pack_indices.o recount.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/cydar.buildbin-libdir/cydar/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cydar' as cydar_1.2.1.zip
* DONE (cydar)
In R CMD INSTALL
In R CMD INSTALL

Tests output

cydar.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(cydar)
Loading required package: BiocParallel
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

> test_check("cydar")

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...
== testthat results  ===========================================================
OK: 8229 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 108.00    0.96  110.15

cydar.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(cydar)
Loading required package: BiocParallel
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

> test_check("cydar")

Estimating landmarks for channel X1 ...
Registering curves for parameter X1 ...

Estimating landmarks for channel X2 ...
Registering curves for parameter X2 ...
== testthat results  ===========================================================
OK: 8229 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 106.03    0.59  106.60

Example timings

cydar.Rcheck/examples_i386/cydar-Ex.timings

nameusersystemelapsed
countCells2.320.052.36
cyData-class0.120.000.12
cyData-getset0.070.030.11
cyData-subset0.210.050.25
diffIntDistr0.860.000.85
dnaGate0.870.000.88
expandRadius1.170.001.17
findFirstSphere0.110.000.11
intensityRanges1.280.001.28
interpretSpheres2.420.002.42
labelSpheres0.030.000.03
medIntensities1.50.01.5
multiIntHist0.010.000.01
neighborDistances1.880.031.91
normalizeBatch0.530.000.53
outlierGate1.700.031.73
packIndices000
pickBestMarkers1.360.021.38
plotCells0.220.000.22
poolCells1.140.001.14
prepareCellData2.000.012.01
recountCells1.900.001.91
spatialFDR0.150.000.14

cydar.Rcheck/examples_x64/cydar-Ex.timings

nameusersystemelapsed
countCells2.150.032.18
cyData-class0.130.000.12
cyData-getset0.090.020.11
cyData-subset0.250.030.28
diffIntDistr0.630.000.63
dnaGate0.840.000.84
expandRadius1.170.001.18
findFirstSphere0.110.000.11
intensityRanges1.130.041.17
interpretSpheres2.460.002.47
labelSpheres0.020.000.01
medIntensities1.220.001.22
multiIntHist000
neighborDistances1.290.021.29
normalizeBatch0.290.000.30
outlierGate1.340.001.34
packIndices000
pickBestMarkers1.050.001.05
plotCells0.140.000.14
poolCells0.920.000.92
prepareCellData1.520.001.51
recountCells1.430.001.44
spatialFDR0.070.000.06