Mike Jiang
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/CytoML |
| git_branch: devel |
| git_last_commit: b1c491e |
| git_last_commit_date: 2024-01-16 23:33:19 -0400 (Tue, 16 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:36 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 496/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoML 2.15.2 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the CytoML package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: CytoML |
| Version: 2.15.2 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings CytoML_2.15.2.tar.gz |
| StartedAt: 2024-03-28 04:24:55 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:28:00 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 185.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CytoML.Rcheck |
| Warnings: 5 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings CytoML_2.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoML.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘2.15.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CytoML’ can be installed ... WARNING
Found the following significant warnings:
../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoML.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 69.3Mb
sub-directories of 1Mb or more:
extdata 4.8Mb
libs 63.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
AGPL-3.0-only
Standardizable: FALSE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘jsonlite’ ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘openCyto’ ‘stats’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCustomInfo: no visible global function definition for
‘gh_get_transformations’
addGate: no visible binding for global variable ‘id’
addGate: no visible binding for global variable ‘gate_id’
addGate: no visible binding for global variable ‘fcs’
addGate: no visible binding for global variable ‘fcs_file_id’
addGate: no visible binding for global variable ‘gate_def’
addGate: no visible binding for global variable ‘name’
ce_get_panels: no visible binding for global variable ‘panel’
ce_get_panels: no visible binding for global variable ‘n’
constructTree: no visible binding for global variable ‘id’
constructTree: no visible binding for global variable ‘name’
createTransformIdentifier: no visible global function definition for
‘slotNames’
cytobank_to_gatingset.cytobank_experiment: no visible binding for
global variable ‘desc’
diva_to_gatingset: no visible binding for global variable ‘specimen’
diva_to_gatingset: no visible binding for global variable
‘sampleSelected’
diva_to_gatingset: no visible global function definition for
‘gh_apply_to_new_fcs’
export_comp_trans: no visible global function definition for
‘gh_get_compensations’
export_comp_trans: no visible global function definition for
‘gh_get_transformations’
export_gates_cytobank: no visible global function definition for
‘gs_get_pop_paths’
export_gates_cytobank: no visible global function definition for
‘gs_pop_get_gate’
extend.polygonGate: no visible binding for global variable ‘..dim’
extend.polygonGate : <anonymous>: no visible binding for global
variable ‘y’
extend.polygonGate : <anonymous>: no visible binding for global
variable ‘x’
extend.polygonGate: no visible binding for global variable ‘id’
extend.polygonGate: no visible binding for global variable ‘x’
extend.polygonGate: no visible binding for global variable ‘y’
extend.polygonGate: no visible binding for global variable ‘is.smaller’
flinTr: no visible global function definition for ‘lintGml2’
fratioTr: no visible global function definition for ‘ratiotGml2’
generate_trans: no visible global function definition for
‘flowjo_log_trans’
gs_compare_cytobank_counts: no visible binding for global variable
‘population’
gs_compare_cytobank_counts: no visible binding for global variable
‘parent’
gs_compare_cytobank_counts: no visible binding for global variable
‘parent_count’
gs_compare_cytobank_counts: no visible global function definition for
‘.’
gs_compare_cytobank_counts: no visible binding for global variable
‘fcs_filename’
hyperlogTr: no visible global function definition for ‘hyperlogtGml2’
open_cytobank_experiment: no visible global function definition for
‘unzip’
range.GatingHierarchy: no visible global function definition for
‘gh_get_transformations’
read.gatingML.cytobank: no visible binding for global variable ‘id’
read.gatingML.cytobank: no visible binding for global variable
‘comp_ref’
transDg1polynomial: no visible global function definition for
‘dg1polynomial’
transEH: no visible global function definition for ‘EHtrans’
transExponential: no visible global function definition for
‘exponential’
transHyperLog: no visible global function definition for ‘hyperlog’
transHyperbolicSin: no visible global function definition for ‘sinht’
transInvSplitScale: no visible global function definition for
‘invsplitscale’
transInverseHyperbolicSin: no visible global function definition for
‘asinht’
transLogarithm: no visible global function definition for ‘logarithm’
transQuadratic: no visible global function definition for ‘quadratic’
transRatio: no visible global function definition for ‘ratio’
transSplitScale: no visible global function definition for ‘splitscale’
transSquareroot: no visible global function definition for ‘squareroot’
write.gatingML: no visible global function definition for ‘sessionInfo’
xmlVertexNode : <anonymous>: no visible global function definition for
‘format_float’
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
no visible binding for global variable ‘expressionFilter’
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
no visible global function definition for ‘polytopeGate’
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
no visible global function definition for ‘pseudoinverse’
show,flowjo_workspace: no visible binding for global variable
‘groupName’
show,flowjo_workspace: no visible binding for global variable ‘groupID’
Undefined global functions or variables:
. ..dim EHtrans asinht comp_ref desc dg1polynomial exponential
expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans
format_float gate_def gate_id gh_apply_to_new_fcs
gh_get_compensations gh_get_transformations groupID groupName
gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id
invsplitscale is.smaller lintGml2 logarithm n name panel parent
parent_count polytopeGate population pseudoinverse quadratic ratio
ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen
splitscale squareroot unzip x y
Consider adding
importFrom("methods", "slotNames")
importFrom("utils", "sessionInfo", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) getNodes-graphGML-method.Rd:5: Lost braces; missing escapes or markup?
5 | \title{get nodes from {graphGML} object}
| ^
checkRd: (-1) getNodes-graphGML-method.Rd:22: Lost braces; missing escapes or markup?
22 | get nodes from {graphGML} object
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'flowjo_to_gatingset.Rd'
‘backend_dir’ ‘backend’
Documented arguments not in \usage in Rd file 'flowjo_to_gatingset.Rd':
‘h5_dir’
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.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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’
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars.in’
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/CytoML/libs/CytoML.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 ‘sprintf’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 8 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/CytoML.Rcheck/00check.log’
for details.
CytoML.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL CytoML
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘CytoML’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: setting cytolib-ml commandline tool path...
configure: Using the following compilation and linking flags
configure: PKG_CPPFLAGS=-I/usr/include/libxml2
configure: PKG_LIBS=-lxml2 -lz -llzma -lm
configure: CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cpp11.cpp -o cpp11.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
|
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace.h:6,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
33 | for (auto j = 0; j < m; j++) {
| ~~^~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
34 | for (auto i = 0; i < n; i++) {
| ~~^~~
In file included from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/wsNode.hpp: In member function ‘virtual std::streamsize CytoML::Cytostreambuf::xsputn(const char*, std::streamsize)’:
../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
27 | Rprintf("%.*s", n, s);
| ~~^~ ~
| | |
| int std::streamsize {aka long int}
In file included from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)’:
../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
| ^
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/filesystem.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/global.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/filesystem/directory.hpp:923:5: note: declared here
923 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::unique_ptr<cytolib::GatingSet> CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CytoML::SampleInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
201 | for (int i = 0; i < sample_infos.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
585 | for(int j = 0; j < sample_ids.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include' -I/usr/local/include -fPIC -g -O2 -Wall -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
|
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-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/R/R-4.4-devel-2024.03.20/site-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 ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/wsNode.hpp: In member function ‘virtual std::streamsize CytoML::Cytostreambuf::xsputn(const char*, std::streamsize)’:
../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
27 | Rprintf("%.*s", n, s);
| ~~^~ ~
| | |
| int std::streamsize {aka long int}
In file included from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)’:
../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
| ^
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/filesystem.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/global.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/compensation.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/filesystem/directory.hpp:923:5: note: declared here
923 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::unique_ptr<cytolib::GatingSet> CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<CytoML::SampleInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
201 | for (int i = 0; i < sample_infos.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
585 | for(int j = 0; j < sample_ids.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace.h:6,
from parseFlowJoWorkspace.cpp:11:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
33 | for (auto j = 0; j < m; j++) {
| ~~^~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
34 | for (auto i = 0; i < n; i++) {
| ~~^~~
parseFlowJoWorkspace.cpp: In function ‘cpp11::external_pointer<cytolib::GatingSet> parse_workspace(cpp11::external_pointer<CytoML::flowJoWorkspace>, int, cpp11::list, bool, std::string, cpp11::external_pointer<cytolib::GatingSet>, std::string, std::string, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, bool, float, float, bool, bool, bool, bool, cpp11::list, bool, std::string, bool, SEXP, int)’:
parseFlowJoWorkspace.cpp:103:21: 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]
103 | for(int i = 0; i < filter_names.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/cytolib/lib/libcytolib.a /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lopenblas -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-CytoML/00new/CytoML/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 (CytoML)
CytoML.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
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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(CytoML)
>
> win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
> if(!win32_flag)
+ test_check("CytoML")
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")
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: BH
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.
[ FAIL 0 | WARN 2 | SKIP 5 | PASS 66 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• (check_docker_status()[1] == "docker_ok" || check_binary_status() == (1):
'test-GatingSet2flowJo.R:2:1'
• dir.exists("~/rglab/workspace/flowWorkspace/wsTestSuite") is not TRUE (1):
'test-internal-suite.R:2:1'
• dir.exists(path) is not TRUE (1): 'test-cytobank.R:50:3'
• file.exists(acsfile) is not TRUE (2): 'test-cytobank.R:6:3',
'test-cytobank.R:28:3'
[ FAIL 0 | WARN 2 | SKIP 5 | PASS 66 ]
>
> #devtools::test()
>
> # test_file("~/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
>
> proc.time()
user system elapsed
56.201 1.814 58.192
CytoML.Rcheck/CytoML-Ex.timings
| name | user | system | elapsed | |
| cytobank_to_gatingset | 0 | 0 | 0 | |
| extend | 0.122 | 0.004 | 0.126 | |
| fj_ws_get_keywords | 0 | 0 | 0 | |
| fj_ws_get_sample_groups | 0 | 0 | 0 | |
| fj_ws_get_samples | 0 | 0 | 0 | |
| flowjo_to_gatingset | 0.000 | 0.000 | 0.001 | |
| flowjo_workspace-class | 0.092 | 0.000 | 0.101 | |
| gatingset_to_cytobank | 2.005 | 0.092 | 2.103 | |
| gatingset_to_flowjo | 0 | 0 | 0 | |
| getChildren-graphGML-character-method | 0 | 0 | 0 | |
| getNodes-graphGML-method | 0.001 | 0.000 | 0.000 | |
| gs_compare_cytobank_counts | 2.852 | 0.108 | 2.976 | |
| open_diva_xml | 0 | 0 | 0 | |
| open_flowjo_xml | 0.000 | 0.000 | 0.001 | |
| plot-graphGML-missing-method | 0 | 0 | 0 | |
| range.GatingHierarchy | 0 | 0 | 0 | |
| read.gatingML.cytobank | 0 | 0 | 0 | |