Mike Jiang
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/openCyto |
| git_branch: devel |
| git_last_commit: 3a74611 |
| git_last_commit_date: 2023-10-24 09:56:24 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:49 -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 1457/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| openCyto 2.15.0 (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 openCyto package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.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. |
| Package: openCyto |
| Version: 2.15.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:openCyto.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings openCyto_2.15.0.tar.gz |
| StartedAt: 2024-03-28 00:56:23 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 01:01:05 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 281.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: openCyto.Rcheck |
| Warnings: 4 |
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:openCyto.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings openCyto_2.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/openCyto.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘2.15.0’
* 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 ‘openCyto’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
AGPL-3.0-only
Standardizable: FALSE
* 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
Namespace in Imports field not imported from: ‘flowViz’
All declared Imports should be used.
Missing objects imported by ':::' calls:
‘ncdfFlow:::toBitVec’ ‘ncdfFlow:::toLogical’
Unexported objects imported by ':::' calls:
‘flowClust:::.ellipsePoints’ ‘flowWorkspace:::.addGate’
‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::cpp_addGate’
‘flowWorkspace:::cpp_boolGating’ ‘flowWorkspace:::cpp_setIndices’
‘flowWorkspace:::filter_to_list.booleanFilter’
‘flowWorkspace:::filter_to_list.rectangleGate’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’
* checking S3 generic/method consistency ... WARNING
as.data.table:
function(x, keep.rownames, ...)
as.data.table.gatingTemplate:
function(x, keep.rownames)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘openCyto/R/pluginFramework.R’:
unlockBinding(methodName, ENV)
unlockBinding(methodName, ENV)
.boundary: no visible global function definition for ‘rectangleGate’
.center_mode: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘density’
.find_peaks: no visible global function definition for ‘points’
.find_valleys: no visible global function definition for ‘density’
.gateToFilterResult: no visible global function definition for ‘exprs’
.gateToFilterResult: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘as’
.gatingTemplate: no visible global function definition for ‘new’
.gatingTemplate: no visible binding for global variable ‘pop’
.gatingTemplate: no visible binding for global variable ‘gating_method’
.gatingTemplate: no visible binding for global variable ‘gating_args’
.gatingTemplate: no visible binding for global variable
‘collapseDataForGating’
.gatingTemplate: no visible binding for global variable
‘preprocessing_method’
.gatingTemplate: no visible binding for global variable
‘preprocessing_args’
.gatingTemplate: no visible global function definition for ‘extends’
.gating_adaptor: no visible global function definition for ‘as’
.gating_adaptor: no visible global function definition for ‘na.omit’
.gating_adaptor: no visible global function definition for
‘rectangleGate’
.gating_adaptor: no visible global function definition for ‘filters’
.gating_adaptor: no visible global function definition for ‘extends’
.gating_gtMethod: no visible global function definition for ‘na.omit’
.gating_gtMethod : <anonymous>: no visible global function definition
for ‘extends’
.gating_gtMethod: no visible global function definition for ‘extends’
.gating_gtMethod: no visible global function definition for ‘is’
.gating_gtMethod : <anonymous>: no visible global function definition
for ‘filters’
.gating_polyFunctions: no visible global function definition for
‘permutations’
.gating_refGate : <anonymous>: no visible global function definition
for ‘rectangleGate’
.gating_refGate: no visible global function definition for ‘filterList’
.gating_refGate: no visible global function definition for ‘is’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘parent’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘gating_args’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘collapseDataForGating’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_method’
.gen_1dgate : <anonymous>: no visible binding for global variable
‘preprocessing_args’
.gen_dummy_ref_gate: no visible binding for global variable ‘parent’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘pop’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘gating_args’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘collapseDataForGating’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_method’
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
variable ‘preprocessing_args’
.gen_refGate: no visible binding for global variable ‘parent’
.gen_refGate: no visible binding for global variable ‘gating_args’
.getEllipse: no visible global function definition for ‘qf’
.getEllipse: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for ‘qf’
.getEllipseGate: no visible global function definition for ‘qchisq’
.getEllipseGate: no visible global function definition for
‘polygonGate’
.getEllipseGate: no visible global function definition for
‘ellipsoidGate’
.getFullPath: no visible binding for global variable ‘parent’
.improvedMindensity: no visible global function definition for
‘density’
.improvedMindensity: no visible global function definition for
‘smooth.spline’
.improvedMindensity: no visible global function definition for
‘predict’
.improvedMindensity: no visible global function definition for ‘median’
.improvedMindensity : .plots: no visible global function definition for
‘abline’
.improvedMindensity: no visible global function definition for ‘par’
.improvedMindensity: no visible global function definition for ‘abline’
.plotTree: no visible global function definition for ‘as’
.plotTree: no visible global function definition for ‘par’
.plotTree: no visible global function definition for ‘legend’
.polyfunction_nodes: no visible global function definition for
‘permutations’
.preprocess_csv: no visible binding for global variable ‘pop’
.preprocess_csv: no visible binding for global variable ‘parent’
.preprocess_csv: no visible binding for global variable ‘gating_method’
.preprocess_csv: no visible binding for global variable ‘gating_args’
.preprocess_csv: no visible binding for global variable
‘collapseDataForGating’
.preprocess_csv: no visible binding for global variable
‘preprocessing_method’
.preprocess_csv: no visible binding for global variable
‘preprocessing_args’
.preprocess_row: no visible binding for global variable ‘pop’
.preprocess_row: no visible binding for global variable ‘gating_method’
.preprocess_row: no visible binding for global variable ‘parent’
.preprocess_row: no visible binding for global variable ‘gating_args’
.preprocess_row: no visible binding for global variable
‘preprocessing_method’
.preprocess_row: no visible binding for global variable
‘preprocessing_args’
.prior_flowClust1d: no visible global function definition for ‘fsApply’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘exprs’
.prior_flowClust1d: no visible global function definition for ‘hclust’
.prior_flowClust1d: no visible global function definition for ‘dist’
.prior_flowClust1d: no visible global function definition for ‘median’
.prior_flowClust1d: no visible global function definition for ‘cutree’
.prior_flowClust1d: no visible global function definition for ‘kmeans’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘sd’
.prior_flowClust1d: no visible binding for global variable ‘var’
.prior_flowClust1d : <anonymous>: no visible global function definition
for ‘embed’
.prior_flowClust1d : <anonymous>: no visible binding for global
variable ‘var’
.prior_kmeans : <anonymous>: no visible global function definition for
‘exprs’
.prior_kmeans : <anonymous>: no visible global function definition for
‘kmeans’
.prior_kmeans : <anonymous> : <anonymous>: no visible global function
definition for ‘cov’
.prior_kmeans : <anonymous>: no visible global function definition for
‘dist’
.prior_kmeans: no visible binding for global variable ‘cov.wt’
.quadGate2rectangleGates: no visible global function definition for
‘rectangleGate’
.quadGate2rectangleGates: no visible global function definition for
‘filters’
.quantile_flowClust : cdf_target : <anonymous>: no visible global
function definition for ‘pt’
.quantile_flowClust : cdf_target: no visible global function definition
for ‘weighted.mean’
.quantile_flowClust: no visible global function definition for
‘uniroot’
.read.FCS.csv: no visible global function definition for ‘new’
.read.flowSet.csv: no visible global function definition for ‘flowSet’
.scale_huber: no visible global function definition for ‘mad’
.standardize_flowFrame: no visible global function definition for
‘exprs’
.standardize_flowFrame: no visible global function definition for
‘exprs<-’
.standardize_flowset: no visible global function definition for
‘fsApply’
.standardize_flowset: no visible global function definition for
‘flowSet’
.standardize_flowset: no visible global function definition for ‘as’
.truncate_flowframe: no visible global function definition for
‘rectangleGate’
.truncate_flowframe: no visible global function definition for ‘Subset’
.truncate_flowset: no visible global function definition for
‘rectangleGate’
.truncate_flowset: no visible global function definition for ‘Subset’
.unique_check_alias: no visible binding for global variable ‘parent’
as.data.table.gatingTemplate : <anonymous>: no visible global function
definition for ‘extends’
fast_coerce: no visible global function definition for ‘fsApply’
fast_coerce : <anonymous>: no visible global function definition for
‘exprs’
fast_coerce: no visible global function definition for ‘new’
fcEllipsoidGate: no visible global function definition for ‘as’
fcFilterList : <anonymous>: no visible global function definition for
‘extends’
fcFilterList: no visible global function definition for ‘filterList’
fcFilterList: no visible global function definition for ‘as’
fcPolygonGate: no visible global function definition for ‘as’
fcRectangleGate: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘as’
fcTree: no visible global function definition for ‘new’
gate_flowclust_1d: no visible global function definition for ‘exprs’
gate_flowclust_1d: no visible global function definition for
‘rectangleGate’
gate_flowclust_1d: no visible global function definition for ‘abline’
gate_flowclust_1d: no visible global function definition for ‘rainbow’
gate_flowclust_1d: no visible global function definition for ‘lines’
gate_flowclust_2d: no visible global function definition for ‘new’
gate_flowclust_2d: no visible global function definition for ‘dist’
gate_flowclust_2d: no visible global function definition for ‘qchisq’
gate_flowclust_2d: no visible global function definition for ‘exprs’
gate_flowclust_2d: no visible global function definition for ‘sd’
gate_flowclust_2d: no visible global function definition for
‘polygonGate’
gate_flowclust_2d: no visible global function definition for ‘lines’
gate_flowclust_2d: no visible global function definition for ‘points’
gate_mindensity: no visible global function definition for ‘exprs’
gate_mindensity: no visible global function definition for
‘rectangleGate’
gate_mindensity2: no visible global function definition for ‘exprs’
gate_mindensity2: no visible global function definition for
‘rectangleGate’
gate_quad_sequential : <anonymous>: no visible global function
definition for ‘exprs’
gate_quad_sequential: no visible global function definition for
‘filter’
gate_quad_sequential: no visible global function definition for ‘as’
gate_quad_sequential : <anonymous>: no visible global function
definition for ‘rectangleGate’
gate_quad_sequential: no visible global function definition for
‘filters’
gate_quad_tmix: no visible global function definition for ‘filter’
gate_quad_tmix: no visible global function definition for ‘as’
gate_quad_tmix: no visible global function definition for ‘polygonGate’
gate_quad_tmix: no visible global function definition for ‘filters’
gate_quantile: no visible global function definition for ‘exprs’
gate_quantile: no visible global function definition for ‘quantile’
gate_quantile: no visible global function definition for ‘hist’
gate_quantile: no visible global function definition for ‘density’
gate_quantile: no visible global function definition for ‘abline’
gate_quantile: no visible global function definition for ‘text’
gate_quantile: no visible global function definition for
‘rectangleGate’
gate_singlet: no visible global function definition for ‘exprs’
gate_singlet: no visible global function definition for ‘as.formula’
gate_singlet: no visible global function definition for ‘predict’
gate_singlet: no visible global function definition for ‘polygonGate’
gs_add_gating_method: no visible global function definition for ‘is’
gs_add_gating_method_init: no visible global function definition for
‘is’
gs_remove_gating_method: no visible global function definition for ‘is’
mindensity: no visible global function definition for ‘exprs’
mindensity: no visible global function definition for ‘rectangleGate’
ocRectRefGate: no visible global function definition for ‘as’
prior_flowclust : <anonymous>: no visible global function definition
for ‘is’
quadGate.tmix: no visible global function definition for
‘quad_gate_tmix’
robust_m_estimator: no visible global function definition for ‘median’
singletGate: no visible global function definition for ‘exprs’
singletGate: no visible global function definition for ‘as.formula’
singletGate: no visible global function definition for ‘predict’
singletGate: no visible global function definition for ‘polygonGate’
coerce,ncdfFlowList-flowFrame: no visible global function definition
for ‘selectMethod’
gatingTemplate,character: no visible binding for global variable
‘isMultiPops’
gatingTemplate,character: no visible binding for global variable ‘pop’
gatingTemplate,character: no visible binding for global variable
‘gating_args’
gatingTemplate,data.table: no visible binding for global variable
‘isMultiPops’
gatingTemplate,data.table: no visible binding for global variable ‘pop’
gatingTemplate,data.table: no visible binding for global variable
‘gating_args’
plot,fcFilterList-ANY : <anonymous>: no visible global function
definition for ‘dnorm’
plot,fcFilterList-ANY: no visible global function definition for ‘hist’
plot,fcFilterList-ANY: no visible global function definition for
‘exprs’
plot,fcFilterList-ANY: no visible global function definition for
‘lines’
plot,fcFilterList-ANY: no visible global function definition for
‘rainbow’
plot,fcFilterList-ANY: no visible global function definition for
‘abline’
show,fcFilter: no visible global function definition for
‘callNextMethod’
Undefined global functions or variables:
Subset abline as as.formula callNextMethod collapseDataForGating cov
cov.wt cutree density dist dnorm ellipsoidGate embed exprs exprs<-
extends filter filterList filters flowSet fsApply gating_args
gating_method hclust hist is isMultiPops kmeans legend lines mad
median na.omit new par parent permutations points polygonGate pop
predict preprocessing_args preprocessing_method pt qchisq qf
quad_gate_tmix quantile rainbow rectangleGate sd selectMethod
smooth.spline text uniroot var weighted.mean
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "hist", "legend", "lines", "par",
"points", "text")
importFrom("methods", "as", "callNextMethod", "extends", "is", "new",
"selectMethod")
importFrom("stats", "as.formula", "cov", "cov.wt", "cutree", "density",
"dist", "dnorm", "embed", "filter", "hclust", "kmeans",
"mad", "median", "na.omit", "predict", "pt", "qchisq", "qf",
"quantile", "sd", "smooth.spline", "uniroot", "var",
"weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) gs_add_gating_method.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gs_add_gating_method.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gs_add_gating_method.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gt_gating.Rd:24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'gate_quad_sequential.Rd':
‘tailgate’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'robust_m_estimator.Rd'
‘x’ ‘sd’
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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/openCyto/libs/openCyto.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (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 ... NOTE
Package vignette with \VignetteEngine{} not specifying an engine package:
‘openCytoVignette.Rmd’
Engines should be specified as \VignetteEngine{PKG::ENG}.
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/openCyto.Rcheck/00check.log’
for details.
openCyto.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL openCyto
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Hungarian.cpp -o Hungarian.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c rlm.cpp -o rlm.o
In file included from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/accumulators/statistics/median.hpp:11,
from rlm.cpp:8:
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.19-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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
rlm.cpp: In function ‘cpp11::list rlm_cpp(cpp11::doubles_matrix<>, cpp11::doubles, int)’:
rlm.cpp:55:10: warning: ‘scale’ may be used uninitialized in this function [-Wmaybe-uninitialized]
55 | double scale;
| ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c solve_LSAP.cpp -o solve_LSAP.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c unlockNamespace.cpp -o unlockNamespace.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o openCyto.so Hungarian.o cpp11.o misc.o rlm.o solve_LSAP.o unlockNamespace.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-openCyto/00new/openCyto/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 (openCyto)
openCyto.Rcheck/tests/testthat.Rout
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Platform: x86_64-pc-linux-gnu
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> library(testthat)
> library(openCyto)
>
> test_check("openCyto")
Loading required package: BH
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 145 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• dir.exists(file.path(localPath, "misc")) is not TRUE (1):
'test-gating-suite.R:8:1'
• no longer supported (1): 'test-polyfunction.R:4:3'
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 145 ]
>
>
> #taking quite some time , thus only for internal testing
> #test_file("~/rglab/workspace/openCyto/tests/testthat/gating-testSuite.R")
>
> proc.time()
user system elapsed
72.247 3.138 81.687
openCyto.Rcheck/openCyto-Ex.timings
| name | user | system | elapsed | |
| gate_flowclust_1d | 0 | 0 | 0 | |
| gate_flowclust_2d | 0 | 0 | 0 | |
| gate_mindensity | 0 | 0 | 0 | |
| gate_mindensity2 | 0 | 0 | 0 | |
| gate_quantile | 0.000 | 0.001 | 0.001 | |
| gatingTemplate-class | 0.000 | 0.001 | 0.001 | |
| gh_generate_template | 0.207 | 0.012 | 0.220 | |
| gs_add_gating_method | 0.001 | 0.000 | 0.001 | |
| gs_add_gating_method_init | 0 | 0 | 0 | |
| gs_remove_gating_method | 0.000 | 0.000 | 0.001 | |
| gtMethod-class | 0.000 | 0.000 | 0.001 | |
| gtPopulation-class | 0.000 | 0.000 | 0.001 | |
| gt_gating | 0.000 | 0.000 | 0.001 | |
| gt_get_children | 0 | 0 | 0 | |
| gt_get_gate | 0 | 0 | 0 | |
| gt_get_nodes | 0 | 0 | 0 | |
| gt_get_parent | 0 | 0 | 0 | |
| gt_toggle_helpergates | 0 | 0 | 0 | |
| names-gtMethod-method | 0 | 0 | 0 | |
| openCyto | 0 | 0 | 0 | |
| openCyto.options | 0.000 | 0.001 | 0.001 | |
| plot-fcFilterList-ANY-method | 0.000 | 0.000 | 0.001 | |
| plot-gatingTemplate-missing-method | 0.000 | 0.000 | 0.001 | |
| ppMethod-class | 0 | 0 | 0 | |
| ppMethod-gatingTemplate-character-method | 0 | 0 | 0 | |
| prior_flowclust | 0 | 0 | 0 | |