Greg Finak
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/flowWorkspace |
| git_branch: RELEASE_3_14 |
| git_last_commit: 60bc06d |
| git_last_commit_date: 2021-10-26 11:59:12 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:22 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 [email protected]:packages/flowWorkspace.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 678/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowWorkspace 4.6.0 (landing page) Greg Finak
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: flowWorkspace |
| Version: 4.6.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowWorkspace_4.6.0.tar.gz |
| StartedAt: 2022-04-12 07:29:31 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:32:22 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 170.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowWorkspace.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flowWorkspace_4.6.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/flowWorkspace.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘4.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 94.7Mb
sub-directories of 1Mb or more:
libs 93.3Mb
* 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 is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/libs/flowWorkspace.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘srand’, possibly from ‘srand’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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
‘/home/biocbuild/bbs-3.14-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
flowWorkspace.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.14-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:
/home/biocbuild/bbs-3.14-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
/home/biocbuild/bbs-3.14-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]
31 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytoctxAPI.cpp -o cytoctxAPI.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.14-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
/home/biocbuild/bbs-3.14-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]
31 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.14-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
/home/biocbuild/bbs-3.14-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]
31 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/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]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so 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 /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/lib/libcytolib.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowWorkspace)
flowWorkspace.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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,
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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
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/home/biocbuild/bbs-3.14-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 3 | SKIP 21 | PASS 1668 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• 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 3 | SKIP 21 | PASS 1668 ]
>
> # 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
75.312 5.864 81.113
flowWorkspace.Rcheck/flowWorkspace-Ex.timings
| name | user | system | elapsed | |
| GatingHierarchy-class | 0.001 | 0.000 | 0.000 | |
| GatingSet-class | 0 | 0 | 0 | |
| GatingSet-methods | 0 | 0 | 0 | |
| GatingSetList-class | 0 | 0 | 0 | |
| asinh_Gml2 | 0.001 | 0.000 | 0.001 | |
| asinhtGml2_trans | 0.002 | 0.000 | 0.002 | |
| booleanFilter-class | 0.003 | 0.000 | 0.002 | |
| cf_append_cols | 0.973 | 0.124 | 1.097 | |
| compensate | 0 | 0 | 0 | |
| convert | 0.858 | 0.028 | 0.886 | |
| convert_legacy | 0 | 0 | 0 | |
| estimateLogicle | 0 | 0 | 0 | |
| extract_cluster_pop_name_from_node | 0 | 0 | 0 | |
| flow_breaks | 0.582 | 0.036 | 0.618 | |
| flowjo_biexp | 0.002 | 0.000 | 0.002 | |
| flowjo_biexp_trans | 0.600 | 0.031 | 0.631 | |
| flowjo_fasinh | 0.001 | 0.001 | 0.000 | |
| flowjo_fasinh_trans | 0.001 | 0.000 | 0.000 | |
| flowjo_log_trans | 0.001 | 0.000 | 0.000 | |
| gh_copy_gate | 0.086 | 0.016 | 0.102 | |
| gh_get_compensations | 0 | 0 | 0 | |
| gh_get_transformations | 0 | 0 | 0 | |
| gh_pop_get_data | 0 | 0 | 0 | |
| gh_pop_get_descendants | 0.014 | 0.000 | 0.014 | |
| gh_pop_get_indices | 0 | 0 | 0 | |
| gh_pop_move | 0.039 | 0.016 | 0.055 | |
| gh_pop_set_indices | 0.234 | 0.068 | 0.302 | |
| gh_pop_set_xml_count | 0 | 0 | 0 | |
| gs_check_redundant_nodes | 0 | 0 | 0 | |
| gs_get_pop_paths | 0.000 | 0.000 | 0.001 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| 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 | 0 | 0 | |
| 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 | 0.678 | 0.052 | 0.730 | |
| keyword | 0.000 | 0.000 | 0.001 | |
| logicleGml2_trans | 0.001 | 0.000 | 0.001 | |
| logicle_trans | 0.001 | 0.000 | 0.001 | |
| loglevel | 0 | 0 | 0 | |
| logtGml2_trans | 0.001 | 0.000 | 0.001 | |
| 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 | 0.799 | 0.060 | 0.859 | |
| transform | 0 | 0 | 0 | |
| transform_gate | 0 | 0 | 0 | |
| transformerList | 0.016 | 0.000 | 0.016 | |