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This page was generated on 2022-01-19 13:07:01 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ncdfFlow on tokay2


To the developers/maintainers of the ncdfFlow package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ncdfFlow.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1272/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.40.0  (landing page)
Mike Jiang , Jake Wagner
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/ncdfFlow
git_branch: RELEASE_3_14
git_last_commit: 631576d
git_last_commit_date: 2021-10-26 12:01:16 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ncdfFlow
Version: 2.40.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ncdfFlow.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ncdfFlow_2.40.0.tar.gz
StartedAt: 2022-01-18 23:23:47 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 23:27:00 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 192.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ncdfFlow.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ncdfFlow.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ncdfFlow_2.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ncdfFlow/DESCRIPTION' ... OK
* this is package 'ncdfFlow' version '2.40.0'
* 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 'ncdfFlow' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Invalid license file pointers: LICENSE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'BH' 'RcppArmadillo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'flowCore:::check_channel_alias' 'flowCore:::guid'
  'flowCore:::makeFCSparameters' 'flowCore:::readFCSgetPar'
  'flowCore:::update_channel_by_alias'
  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 ... NOTE
ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs =
  matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]),
  keyword(x[[guid]])), env = e1): partial argument match of 'env' to
  'envir'
rbind2,ncdfFlowList-ANY : <anonymous> : <anonymous>: warning in
  assign(curSample, NA, env = indiceEnv): partial argument match of
  'env' to 'envir'
read.ncdfFlowSet: no visible global function definition for 'mclapply'
Undefined global functions or variables:
  mclapply
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ncdfFlow/libs/i386/ncdfFlow.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-3.14-bioc/R/library/ncdfFlow/libs/x64/ncdfFlow.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 '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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.Rcheck/00check.log'
for details.



Installation output

ncdfFlow.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ncdfFlow_2.40.0.tar.gz && rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ncdfFlow.buildbin-libdir ncdfFlow_2.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ncdfFlow_2.40.0.zip && rm ncdfFlow_2.40.0.tar.gz ncdfFlow_2.40.0.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 56288  100 56288    0     0   503k      0 --:--:-- --:--:-- --:--:--  508k

install for i386

* installing *source* package 'ncdfFlow' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bitOps.cpp -o bitOps.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hdfFlow.cpp -o hdfFlow.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from hdfFlow.cpp:2:
C:/Users/biocbuild/bbs-3.14-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-3.14-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>::************
                     ^
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int>, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readFrame.cpp -o readFrame.o
readFrame.cpp: In function 'Rcpp::S4 readFrame(Rcpp::S4, Rcpp::RObject, Rcpp::RObject, bool)':
readFrame.cpp:98:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
    for(unsigned i = 0; i < j_val.size(); i++){
                        ~~^~~~~~~~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386"
"C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/lib/i386/libncdfFlow.a
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ncdfFlow'
    finding HTML links ... done
    Indices                                 html  
    as.flowSet                              html  
    clone.ncdfFlowSet                       html  
    extractFlowFrame                        html  
    finding level-2 HTML links ... done

    flowSet-accessor                        html  
    getFileName                             html  
    lapply-methods                          html  
    ncdfFlow                                html  
    ncdfFlowList-class                      html  
    ncdfFlowSet-Subset                      html  
    ncdfFlowSet-class                       html  
    ncdfFlowSet-constructor                 html  
    ncdfFlowSet-split                       html  
    ncfsApply-ncdfFlowSet-method            html  
    rbind2-method                           html  
    read.ncdfFlowSet                        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/00LOCK-ncdfFlow/00new/ncdfFlow/help/read.ncdfFlowset.html
    replacement-method-for-ncdfFlowSet      html  
    save_ncfs                               html  
    subset-functions                        html  
    subset-methods                          html  
    unlink-ncdfFlowSet-method               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 'ncdfFlow' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bitOps.cpp -o bitOps.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hdfFlow.cpp -o hdfFlow.o
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from hdfFlow.cpp:2:
C:/Users/biocbuild/bbs-3.14-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-3.14-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>::************
                     ^
hdfFlow.cpp: In function 'void readSlice_cpp(hid_t, hid_t, hid_t, std::vector<unsigned int>, unsigned int, unsigned int, double*, bool)':
hdfFlow.cpp:486:14: warning: variable 'status' set but not used [-Wunused-but-set-variable]
  herr_t      status;
              ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readFrame.cpp -o readFrame.o
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a" RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/lib/x64/libncdfFlow.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o ncdfFlow.dll tmp.def RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ncdfFlow' as ncdfFlow_2.40.0.zip
* DONE (ncdfFlow)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ncdfFlow' successfully unpacked and MD5 sums checked

Tests output

ncdfFlow.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(ncdfFlow)
Loading required package: flowCore
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("ncdfFlow")
== Skipped tests ===============================================================
* ###this will cause crashing error see #50 (2)
* file.exists(filename) is not TRUE (1)

[ FAIL 0 | WARN 42 | SKIP 3 | PASS 338 ]
There were 37 warnings (use warnings() to see them)
> #devtools::test("~/rglab/workspace/ncdfFlow")
> #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowSet_accessor.R")
> #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowList.R")
> 
> 
> proc.time()
   user  system elapsed 
  11.10    0.93   12.03 

ncdfFlow.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> library(testthat)
> library(ncdfFlow)
Loading required package: flowCore
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("ncdfFlow")
== Skipped tests ===============================================================
* ###this will cause crashing error see #50 (2)
* file.exists(filename) is not TRUE (1)

[ FAIL 0 | WARN 42 | SKIP 3 | PASS 338 ]
There were 37 warnings (use warnings() to see them)
> #devtools::test("~/rglab/workspace/ncdfFlow")
> #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowSet_accessor.R")
> #test_file("~/rglab/workspace/ncdfFlow/inst/tests/test_ncdfFlowList.R")
> 
> 
> proc.time()
   user  system elapsed 
  11.64    0.75   12.42 

Example timings

ncdfFlow.Rcheck/examples_i386/ncdfFlow-Ex.timings

nameusersystemelapsed
Indices4.520.254.76
as.flowSet1.080.091.18
clone.ncdfFlowSet0.220.020.24
extractFlowFrame1.060.041.29
ncdfFlowList-class1.440.051.49
ncdfFlowSet-constructor1.050.021.06
ncfsApply-ncdfFlowSet-method1.080.041.13
rbind2-method1.070.051.12
read.ncdfFlowSet0.240.020.25
replacement-method-for-ncdfFlowSet1.060.041.11
save_ncfs000
subset-methods1.170.051.22
unlink-ncdfFlowSet-method0.810.060.87

ncdfFlow.Rcheck/examples_x64/ncdfFlow-Ex.timings

nameusersystemelapsed
Indices3.970.254.22
as.flowSet0.970.061.04
clone.ncdfFlowSet0.230.020.25
extractFlowFrame0.630.030.66
ncdfFlowList-class0.570.120.70
ncdfFlowSet-constructor0.880.050.92
ncfsApply-ncdfFlowSet-method0.560.050.61
rbind2-method0.810.070.99
read.ncdfFlowSet0.410.000.40
replacement-method-for-ncdfFlowSet0.730.000.74
save_ncfs000
subset-methods0.960.040.98
unlink-ncdfFlowSet-method0.580.040.63