Greg Finak
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/flowWorkspace |
| git_branch: master |
| git_last_commit: 9190b335 |
| git_last_commit_date: 2022-02-17 20:04:42 -0400 (Thu, 17 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:32 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the flowWorkspace package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowWorkspace.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. |
| Package 680/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowWorkspace 4.7.1 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: flowWorkspace |
| Version: 4.7.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowWorkspace.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowWorkspace_4.7.1.tar.gz |
| StartedAt: 2022-03-17 19:07:50 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:12:12 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 261.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowWorkspace.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowWorkspace.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings flowWorkspace_4.7.1.tar.gz
###
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##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.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 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '4.7.1'
* 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 'flowWorkspace' can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
lib 2.8Mb
libs 7.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Namespaces in Imports field not imported from:
'RBGL' 'RProtoBufLib' 'ggplot2' 'grDevices' 'graphics' 'utils'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'DelayedArray:::simplify_NULL_dimnames' 'flowCore:::.estimateLogicle'
'flowCore:::.spillover_pattern' 'flowCore:::checkClass'
'flowCore:::guid' 'flowCore:::logicle_transform'
'flowCore:::parse_pd_for_read_fs' 'flowCore:::txt2spillmatrix'
'flowCore:::updateTransformKeywords'
'flowCore:::validFilterResultList' 'graph:::.makeEdgeKeys'
'ncdfFlow:::.isValidSamples' 'stats:::.splinefun'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
print.cytoctx
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.computeCV : <anonymous>: no visible binding for global variable
'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
'median'
.graph_handler : asGraphNEL: no visible global function definition for
'new'
.graph_handler : asGraphNEL: no visible global function definition for
'validObject'
.load_legacy: no visible global function definition for 'is'
.load_legacy: no visible global function definition for 'new'
.load_legacy: no visible global function definition for '.hasSlot'
.load_legacy : <anonymous>: no visible global function definition for
'is'
.mergeGates : <anonymous>: no visible global function definition for
'extends'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
booleanFilter: no visible global function definition for 'is'
cf_append_cols: no visible global function definition for 'new'
cf_flush_meta: no visible global function definition for 'is'
cf_get_uri: no visible global function definition for 'is'
cf_keyword_delete: no visible global function definition for 'is'
cf_keyword_insert: no visible global function definition for 'is'
cf_keyword_rename: no visible global function definition for 'is'
cf_keyword_rename: no visible binding for global variable 'na_idx'
cf_keyword_set: no visible global function definition for 'is'
cf_load_meta: no visible global function definition for 'is'
cf_lock: no visible global function definition for 'is'
cf_rename_channel: no visible global function definition for 'is'
cf_rename_marker: no visible global function definition for 'is'
cf_rename_marker: no visible binding for global variable 'desc'
cf_scale_time_channel: no visible global function definition for 'is'
cf_unlock: no visible global function definition for 'is'
cf_write_disk: no visible global function definition for 'is'
char2booleanFilter: no visible global function definition for 'new'
check_comp: no visible global function definition for 'is'
convert_backend: no visible binding for global variable 'output'
copy_view.cytoframe: no visible global function definition for 'new'
copy_view.cytoset: no visible global function definition for 'new'
cs_add_cytoframe: no visible global function definition for 'is'
cs_get_cytoframe: no visible global function definition for 'is'
cs_get_cytoframe: no visible global function definition for 'new'
cs_get_uri: no visible global function definition for 'is'
cs_keyword_delete: no visible global function definition for 'is'
cs_keyword_insert: no visible global function definition for 'is'
cs_keyword_rename: no visible global function definition for 'is'
cs_keyword_rename : <anonymous>: no visible binding for global variable
'keys'
cs_keyword_set: no visible global function definition for 'is'
cs_set_cytoframe: no visible global function definition for 'is'
cytoframe_to_flowFrame: no visible global function definition for 'as'
cytoset: no visible global function definition for 'new'
cytoset_to_flowSet: no visible global function definition for 'as'
get_cytoframe_from_cs: no visible global function definition for 'is'
get_cytoframe_from_cs: no visible global function definition for 'new'
gh_apply_to_cs: no visible global function definition for 'new'
gh_pop_compare_stats: no visible binding for global variable 'node'
gh_pop_get_count: no visible binding for global variable 'count'
gh_pop_get_proportion: no visible binding for global variable 'percent'
gh_pop_get_stats_tfilter: no visible global function definition for
'is'
gh_pop_get_stats_tfilter : <anonymous>: no visible binding for global
variable 'Population'
gh_pop_set_gate: no visible global function definition for 'is'
gs_clone: no visible global function definition for 'new'
gs_copy_tree_only: no visible global function definition for 'new'
gs_get_singlecell_expression: no visible global function definition for
'is'
gs_get_singlecell_expression: no visible binding for global variable
'parallel'
gs_pop_add: no visible global function definition for 'is'
gs_pop_get_count_fast: no visible global function definition for 'is'
gs_pop_get_count_with_meta: no visible binding for global variable
'sampleName'
gs_pop_get_data: no visible global function definition for 'new'
gs_pop_set_gate: no visible global function definition for 'is'
gs_remove_redundant_nodes : <anonymous>: no visible global function
definition for 'is'
gslist_to_gs: no visible global function definition for 'new'
load_cytoframe: no visible global function definition for 'new'
load_cytoframe_from_fcs: no visible global function definition for
'new'
load_cytoset_from_fcs: no visible global function definition for 'new'
load_gs: no visible global function definition for 'new'
load_gslist : <anonymous>: no visible global function definition for
'is'
merge_list_to_gs: no visible global function definition for 'is'
merge_list_to_gs: no visible global function definition for 'new'
parse_transformer: no visible global function definition for 'is'
pop.MFI: no visible binding for global variable 'desc'
realize_view.cytoframe: no visible global function definition for 'new'
realize_view.cytoset: no visible global function definition for 'new'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
validitycheck: no visible global function definition for 'is'
GatingSet,cytoset-ANY: no visible global function definition for 'new'
Subset,cytoset-filterResultList : <anonymous>: no visible global
function definition for 'as'
Subset,cytoset-list: no visible global function definition for 'is'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSet-ANY: no visible global function definition for 'new'
[,GatingSetList-ANY: no visible global function definition for
'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'as'
compensate,GatingSet-ANY: no visible global function definition for
'selectMethod'
compensate,cytoset-ANY: no visible global function definition for
'selectMethod'
flowData,GatingSet: no visible binding for global variable 'obj'
fsApply,cytoset: no visible global function definition for
'callNextMethod'
gs_cyto_data,GatingSet: no visible global function definition for 'new'
keyword,GatingSetList-character: no visible global function definition
for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
for 'selectMethod'
keyword<-,cytoframe-list: no visible binding for global variable
'kwdError'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'as'
parameters,cytoframe: no visible global function definition for 'new'
phenoData,cytoset: no visible global function definition for 'new'
sampleNames<-,cytoset-ANY: no visible global function definition for
'selectMethod'
setNode,GatingSet-character-ANY: no visible global function definition
for 'is'
show,cytoframe: no visible global function definition for
'selectMethod'
transform,GatingSet: no visible global function definition for 'is'
transform,GatingSet : <anonymous>: no visible global function
definition for 'is'
transform,cytoframe: no visible global function definition for 'is'
transform,cytoset: no visible global function definition for 'is'
transform,cytoset : <anonymous>: no visible global function definition
for 'is'
Undefined global functions or variables:
. .hasSlot IQR Population as callNextMethod count desc extends is
keys kwdError median na_idx new node obj old openCyto.count output
parallel percent sampleName selectMethod validObject xml.count
Consider adding
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "validObject")
importFrom("stats", "IQR", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'gs_clone' 'gs_copy_tree_only'
Undocumented S4 methods:
generic 'dimnames' and siglist 'cytoframe'
generic 'rownames' and siglist 'cytoframe'
generic 'rownames<-' and siglist 'cytoframe'
generic 'show' and siglist 'cytoframe'
generic 'transform' and siglist 'cytoframe'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'GatingSet-methods':
'...'
Undocumented arguments in documentation object 'cf_append_cols'
'ctx'
Undocumented arguments in documentation object 'convert'
'backend'
Undocumented arguments in documentation object 'cs_get_uri'
'x'
Undocumented arguments in documentation object 'cytoctx'
'...'
Undocumented arguments in documentation object 'delete_gs'
'ctx'
Undocumented arguments in documentation object 'gh_apply_to_new_fcs'
'files'
Undocumented arguments in documentation object 'keyword-mutators'
'cs'
Undocumented arguments in documentation object 'load_cytoframe_from_fcs'
'backend' 'uri'
Undocumented arguments in documentation object 'load_cytoset_from_fcs'
'backend' 'backend_dir'
Undocumented arguments in documentation object 'save_gs'
'cdf' 'backend_readonly'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'cytoctx':
'print.cytoctx'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/flowWorkspace/libs/x64/flowWorkspace.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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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: 3 WARNINGs, 7 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.
flowWorkspace.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'flowWorkspace' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_API.cpp -o R_API.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_GatingHierarchy.cpp -o R_GatingHierarchy.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_GatingSet.cpp -o R_GatingSet.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:46,
from D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from ../inst/include/flowWorkspace.h:6,
from RcppExports.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
RcppExports.cpp:629:43: required from here
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete obj;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cytoctxAPI.cpp -o cytoctxAPI.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cytoframeAPI.cpp -o cytoframeAPI.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:46,
from D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytoframeAPI.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytoframeAPI.cpp:9:43: required from here
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete obj;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cytosetAPI.cpp -o cytosetAPI.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:46,
from D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytosetAPI.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytosetAPI.cpp:38:81: required from here
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:31:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete obj;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getDescendants.cpp -o getDescendants.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getPopStats.cpp -o getPopStats.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getSingleCellExpression.cpp -o getSingleCellExpression.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c h5_error_r_handler.cpp -o h5_error_r_handler.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c setCounts.cpp -o setCounts.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/range/iterator_range.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
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>::************
^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
mkdir -p "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
C:\rtools40\mingw64\bin\ar.exe: creating D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/x64/libflowWorkspace.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath D:/biocbuild/bbs-3.15-bioc/R/library/cytolib/lib/x64/libcytolib.a D:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LD:/biocbuild/bbs-3.15-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -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-flowWorkspace/00new/flowWorkspace/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowWorkspace'
finding HTML links ... done
GatingHierarchy-class html
GatingSet-class html
GatingSet-methods html
GatingSetList-class html
asinh_Gml2 html
asinhtGml2_trans html
booleanFilter-class html
finding level-2 HTML links ... done
brackets html
cf_append_cols html
cf_backend_type html
cf_get_uri html
cf_write_disk html
cf_write_h5 html
cf_write_tile html
cleanup html
cleanup_temp html
compensate html
convert html
convert_backend html
convert_legacy html
cs_add_cytoframe html
cs_get_uri html
cs_set_cytoframe html
cytoctx html
cytoframe-labels html
cytoframe html
cytoset html
default_backend html
delete_gs html
estimateLogicle html
extract_cluster_pop_name_from_node html
filter_to_list html
flowWorkspace-deprecated html
flowWorkspace-package html
flow_breaks html
flow_trans html
flowjo_biexp html
flowjo_biexp_trans html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_biexp_trans.html
flowjo_fasinh html
flowjo_fasinh_trans html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_fasinh_trans.html
flowjo_log_trans html
gh_apply_to_cs html
gh_apply_to_new_fcs html
gh_copy_gate html
gh_get_cluster_labels html
gh_get_compensations html
gh_get_transformations html
gh_pop_compare_stats html
gh_pop_get_cluster_name html
gh_pop_get_data html
gh_pop_get_descendants html
gh_pop_get_full_path html
gh_pop_get_indices html
gh_pop_get_indices_mat html
gh_pop_get_proportion html
gh_pop_move html
gh_pop_set_indices html
gh_pop_set_xml_count html
gs_check_redundant_nodes html
gs_cyto_data html
gs_get_compensation_internal html
gs_get_leaf_nodes html
gs_get_pop_paths html
gs_get_singlecell_expression html
gs_is_persistent html
gs_plot_diff_tree html
gs_plot_pop_count_cv html
gs_pop_add html
gs_pop_get_children html
gs_pop_get_count_fast html
gs_pop_get_gate html
gs_pop_get_gs html
gs_pop_get_stats html
gs_pop_get_stats_tfilter html
gs_pop_set_gate html
gs_pop_set_name html
gs_pop_set_visibility html
gs_remove_redundant_channels html
gs_remove_redundant_nodes html
gs_split_by_channels html
gs_split_by_tree html
gs_update_channels html
gslist_to_gs html
identifier-methods html
is_subsetted html
is_tiledb_support html
keyword-mutators html
keyword html
lapply-methods html
length html
load_cytoframe html
load_cytoframe_from_fcs html
load_cytoset_from_fcs html
load_meta html
lock html
logicleGml2_trans html
logicle_trans html
loglevel html
logtGml2_trans html
markernames html
merge_list_to_gs html
ncFlowSet-methods html
nodeflags html
openWorkspace html
pData-methods html
plot-methods html
plotGate-methods-defunct html
pop_add html
prettyAxis html
recompute html
rotate_gate html
sampleNames html
save_cytoset html
save_gs html
scale_gate html
shift_gate html
standardize-GatingSet html
stats.fun html
subset html
swap_data_cols html
transform html
transform_gate html
transformerList 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 (flowWorkspace)
Making 'packages.html' ... done
flowWorkspace.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
>
> test_check("flowWorkspace")
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object is masked from 'package:flowCore':
normalize
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
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, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
D:\biocbuild\bbs-3.15-bioc\R\library\flowWorkspaceData\extdata\legacy_gs\v2\gs_bcell_auto seems to be the legacy archive and it is recommended to convert to the new format by saving it to the new folder!
[ FAIL 0 | WARN 240 | SKIP 23 | PASS 1659 ]
== Skipped tests ===============================================================
* On Windows (2)
* dir.exists(legacy) is not TRUE (2)
* empty test (2)
* get_default_backend() != "h5" is TRUE (1)
* get_default_backend() != "mem" is TRUE (1)
* get_default_backend() == "mem" is TRUE (13)
* get_default_backend() == "tile" is not TRUE (2)
[ FAIL 0 | WARN 240 | SKIP 23 | PASS 1659 ]
There were 36 warnings (use warnings() to see them)
>
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-main.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
>
>
>
> proc.time()
user system elapsed
76.06 26.65 128.14
flowWorkspace.Rcheck/flowWorkspace-Ex.timings
| name | user | system | elapsed | |
| GatingHierarchy-class | 0 | 0 | 0 | |
| GatingSet-class | 0 | 0 | 0 | |
| GatingSet-methods | 0 | 0 | 0 | |
| GatingSetList-class | 0 | 0 | 0 | |
| asinh_Gml2 | 0 | 0 | 0 | |
| asinhtGml2_trans | 0.02 | 0.00 | 0.02 | |
| booleanFilter-class | 0 | 0 | 0 | |
| cf_append_cols | 0.67 | 0.00 | 0.73 | |
| compensate | 0 | 0 | 0 | |
| convert | 0.61 | 0.06 | 0.69 | |
| convert_legacy | 0 | 0 | 0 | |
| estimateLogicle | 0 | 0 | 0 | |
| extract_cluster_pop_name_from_node | 0 | 0 | 0 | |
| flow_breaks | 0.40 | 0.04 | 0.42 | |
| flowjo_biexp | 0.01 | 0.00 | 0.01 | |
| flowjo_biexp_trans | 0.33 | 0.14 | 0.47 | |
| flowjo_fasinh | 0 | 0 | 0 | |
| flowjo_fasinh_trans | 0 | 0 | 0 | |
| flowjo_log_trans | 0 | 0 | 0 | |
| gh_copy_gate | 0.09 | 0.02 | 0.11 | |
| gh_get_compensations | 0 | 0 | 0 | |
| gh_get_transformations | 0 | 0 | 0 | |
| gh_pop_get_data | 0 | 0 | 0 | |
| gh_pop_get_descendants | 0.00 | 0.01 | 0.01 | |
| gh_pop_get_indices | 0 | 0 | 0 | |
| gh_pop_move | 0.07 | 0.02 | 0.08 | |
| gh_pop_set_indices | 0.35 | 0.28 | 0.64 | |
| gh_pop_set_xml_count | 0 | 0 | 0 | |
| gs_check_redundant_nodes | 0 | 0 | 0 | |
| gs_get_pop_paths | 0 | 0 | 0 | |
| gs_get_singlecell_expression | 0 | 0 | 0 | |
| gs_plot_diff_tree | 0 | 0 | 0 | |
| gs_plot_pop_count_cv | 0 | 0 | 0 | |
| gs_pop_add | 0 | 0 | 0 | |
| gs_pop_get_children | 0 | 0 | 0 | |
| gs_pop_get_count_fast | 0 | 0 | 0 | |
| gs_pop_get_gate | 0 | 0 | 0 | |
| gs_pop_get_stats | 0.02 | 0.00 | 0.02 | |
| gs_pop_set_gate | 0 | 0 | 0 | |
| gs_pop_set_name | 0 | 0 | 0 | |
| gs_pop_set_visibility | 0 | 0 | 0 | |
| gs_remove_redundant_channels | 0 | 0 | 0 | |
| gs_remove_redundant_nodes | 0 | 0 | 0 | |
| gs_split_by_channels | 0 | 0 | 0 | |
| gs_split_by_tree | 0 | 0 | 0 | |
| gs_update_channels | 0 | 0 | 0 | |
| keyword-mutators | 0.63 | 0.19 | 0.94 | |
| keyword | 0 | 0 | 0 | |
| logicleGml2_trans | 0 | 0 | 0 | |
| logicle_trans | 0 | 0 | 0 | |
| loglevel | 0 | 0 | 0 | |
| logtGml2_trans | 0 | 0 | 0 | |
| markernames | 0 | 0 | 0 | |
| plot-methods | 0 | 0 | 0 | |
| plotGate-methods-defunct | 0 | 0 | 0 | |
| prettyAxis | 0 | 0 | 0 | |
| rotate_gate | 0 | 0 | 0 | |
| sampleNames | 0 | 0 | 0 | |
| save_cytoset | 0 | 0 | 0 | |
| save_gs | 0 | 0 | 0 | |
| scale_gate | 0 | 0 | 0 | |
| shift_gate | 0 | 0 | 0 | |
| swap_data_cols | 0.44 | 0.03 | 0.47 | |
| transform | 0 | 0 | 0 | |
| transform_gate | 0 | 0 | 0 | |
| transformerList | 0.03 | 0.00 | 0.03 | |