Mike Jiang
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/CytoML |
| git_branch: RELEASE_3_16 |
| git_last_commit: a073fe2 |
| git_last_commit_date: 2022-11-01 11:14:00 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:02 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 CytoML package: - Please 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 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 469/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoML 2.10.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CytoML |
| Version: 2.10.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CytoML_2.10.0.tar.gz |
| StartedAt: 2023-04-10 20:06:50 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:09:40 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 170.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CytoML.Rcheck |
| Warnings: 4 |
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CytoML_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CytoML.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘CytoML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CytoML’ version ‘2.10.0’
* 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 ‘CytoML’ can be installed ... WARNING
Found the following significant warnings:
../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-3.16-bioc/meat/CytoML.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 80.6Mb
sub-directories of 1Mb or more:
extdata 4.8Mb
libs 74.8Mb
* 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 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 loading without being on the library search path ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'parseWorkspace'
‘backend_dir’ ‘backend’
Documented arguments not in \usage in documentation object 'parseWorkspace':
‘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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.16-bioc/R/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 ‘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 ...
‘HowToExportGatingSet.Rmd’ using ‘UTF-8’... OK
‘cytobank2GatingSet.Rmd’ using ‘UTF-8’... OK
‘flowjo_to_gatingset.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 7 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/CytoML.Rcheck/00check.log’
for details.
CytoML.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CytoML
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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
configure: CYTOLIBML_BIN=/usr/local/bin
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/cytolibml_bin_path.R
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace.h:6,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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.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/bbs-3.16-bioc/R/site-library/BH/include/boost/filesystem.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/global.hpp:21,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/GatingSet.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
577 | 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/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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.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/bbs-3.16-bioc/R/site-library/BH/include/boost/filesystem.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoVFS.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/global.hpp:21,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/CytoFrame.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/site-library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
577 | 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/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace.h:6,
from parseFlowJoWorkspace.cpp:11:
/home/biocbuild/bbs-3.16-bioc/R/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’:
/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/lib -L/usr/local/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/lib/libcytolib.a /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.16-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lxml2 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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(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 3 | SKIP 5 | PASS 66 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• (check_docker_status()[1] == "docker_ok" || check_binary_status() == (1)
• dir.exists("~/rglab/workspace/flowWorkspace/wsTestSuite") is not TRUE (1)
• dir.exists(path) is not TRUE (1)
• file.exists(acsfile) is not TRUE (2)
[ FAIL 0 | WARN 3 | 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
37.325 1.615 38.951
CytoML.Rcheck/CytoML-Ex.timings
| name | user | system | elapsed | |
| cytobank_to_gatingset | 0 | 0 | 0 | |
| extend | 0.093 | 0.000 | 0.093 | |
| fj_ws_get_keywords | 0.001 | 0.000 | 0.000 | |
| fj_ws_get_sample_groups | 0 | 0 | 0 | |
| fj_ws_get_samples | 0.001 | 0.000 | 0.000 | |
| flowjo_to_gatingset | 0 | 0 | 0 | |
| flowjo_workspace-class | 0.105 | 0.004 | 0.108 | |
| gatingset_to_cytobank | 1.250 | 0.036 | 1.287 | |
| gatingset_to_flowjo | 0 | 0 | 0 | |
| getChildren-graphGML-character-method | 0 | 0 | 0 | |
| getNodes-graphGML-method | 0 | 0 | 0 | |
| gs_compare_cytobank_counts | 1.978 | 0.128 | 2.109 | |
| open_diva_xml | 0 | 0 | 0 | |
| open_flowjo_xml | 0 | 0 | 0 | |
| plot-graphGML-missing-method | 0 | 0 | 0 | |
| range.GatingHierarchy | 0 | 0 | 0 | |
| read.gatingML.cytobank | 0 | 0 | 0 | |