| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 388/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClustIRR 1.6.0 (landing page) Simo Kitanovski
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the ClustIRR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClustIRR.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: ClustIRR |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.6.0.tar.gz |
| StartedAt: 2025-10-14 01:39:24 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 01:58:26 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 1142.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClustIRR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClustIRR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 1.2Mb
libs 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘ggplot2’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_ag_summary: no visible binding for global variable ‘community’
get_beta_scatterplot : get_scatters: no visible binding for global
variable ‘mean_x’
get_beta_scatterplot : get_scatters: no visible binding for global
variable ‘mean_y’
get_beta_scatterplot : get_scatters: no visible binding for global
variable ‘specificity’
get_beta_scatterplot : get_scatters: no visible binding for global
variable ‘size_x’
get_beta_scatterplot : get_scatters: no visible binding for global
variable ‘size_y’
get_beta_scatterplot: no visible binding for global variable
‘community’
get_beta_violins : get_violins: no visible binding for global variable
‘specificity’
get_beta_violins : get_violins: no visible binding for global variable
‘size’
get_beta_violins: no visible binding for global variable ‘community’
get_honeycombs: no visible binding for global variable ‘x_adj’
get_honeycombs: no visible binding for global variable ‘y_adj’
get_honeycombs: no visible binding for global variable ‘..count..’
Undefined global functions or variables:
..count.. community mean_x mean_y size size_x size_y specificity
x_adj y_adj
* checking Rd files ... NOTE
prepare_Rd: decode_communities.Rd:21-23: Dropping empty section \details
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* 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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dco 180.069 4.913 230.746
get_beta_violins 178.430 5.620 214.982
get_beta_scatterplot 175.187 4.427 206.223
get_ag_summary 174.874 4.410 208.592
decode_communities 16.750 1.940 28.124
detect_communities 16.091 2.142 24.435
get_honeycombs 10.598 1.297 19.845
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck/00check.log’
for details.
ClustIRR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClustIRR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘ClustIRR’ ...
** this is package ‘ClustIRR’ version ‘1.6.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dm.cc -o stanExports_dm.o
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
virtual std::streamsize xsputn(const char_type* s, int n) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
virtual std::streamsize xsputn(const char_type* s, int n) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret = stan::services::error_codes::CONFIG;
^
In file included from stanExports_dm.cc:5:
./stanExports_dm.h:501:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_dmh.cc -o stanExports_dmh.o
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
virtual std::streamsize xsputn(const char_type* s, int n) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
virtual std::streamsize xsputn(const char_type* s, int n) {
^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int')
virtual streamsize xsputn(const char_type* __s, streamsize __n);
^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret = stan::services::error_codes::CONFIG;
^
In file included from stanExports_dmh.cc:5:
./stanExports_dmh.h:650:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
int pos__ = std::numeric_limits<int>::min();
^
5 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ClustIRR.so RcppExports.o stanExports_dm.o stanExports_dmh.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-ClustIRR/00new/ClustIRR/libs
** R
** data
** 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 (ClustIRR)
ClustIRR.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(ClustIRR)
> test_check("ClustIRR")
Analyze database: 100.0% (100.0)
Index database: 100.0% (100.0)
Read queries: 100.0% (1986.0 Bytes)
Read queries: 100.0% (1986.0 Bytes)
Search database: 100.0% (100.0)
Write hits: 100.0% (183.0)
Analyze database: 100.0% (100.0)
Index database: 100.0% (100.0)
Read queries: 100.0% (1946.0 Bytes)
Read queries: 100.0% (1946.0 Bytes)
Search database: 100.0% (100.0)
Write hits: 100.0% (159.0)
Analyze database: 100.0% (99.0)
Index database: 100.0% (99.0)
Read queries: 100.0% (1965.0 Bytes)
Read queries: 100.0% (1965.0 Bytes)
Search database: 100.0% (99.0)
Write hits: 100.0% (182.0)
Analyze database: 100.0% (100.0)
Index database: 100.0% (100.0)
Read queries: 100.0% (1946.0 Bytes)
Read queries: 100.0% (1946.0 Bytes)
Search database: 100.0% (100.0)
Write hits: 100.0% (159.0)
Analyze database: 100.0% (1.0)
Index database: 100.0% (1.0)
Read queries: 100.0% (19.0 Bytes)
Search database: 100.0% (1.0)
Write hits: 100.0% (1.0)
Analyze database: 100.0% (1.0)
Index database: 100.0% (1.0)
Read queries: 100.0% (18.0 Bytes)
Search database: 100.0% (1.0)
Write hits: 100.0% (1.0)
Analyze database: 100.0% (99.0)
Index database: 100.0% (99.0)
Read queries: 100.0% (1965.0 Bytes)
Read queries: 100.0% (1965.0 Bytes)
Search database: 100.0% (99.0)
Write hits: 100.0% (182.0)
Analyze database: 100.0% (99.0)
Index database: 100.0% (99.0)
Read queries: 100.0% (1926.0 Bytes)
Read queries: 100.0% (1926.0 Bytes)
Search database: 100.0% (99.0)
Write hits: 100.0% (150.0)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
14.202 1.367 23.717
ClustIRR.Rcheck/ClustIRR-Ex.timings
| name | user | system | elapsed | |
| BLOSUM62 | 0.004 | 0.009 | 0.017 | |
| CDR3ab | 0.060 | 0.006 | 0.071 | |
| clust_irr-class | 0.887 | 0.102 | 1.191 | |
| clustirr | 0.719 | 0.067 | 1.106 | |
| dco | 180.069 | 4.913 | 230.746 | |
| decode_communities | 16.750 | 1.940 | 28.124 | |
| detect_communities | 16.091 | 2.142 | 24.435 | |
| get_ag_summary | 174.874 | 4.410 | 208.592 | |
| get_beta_scatterplot | 175.187 | 4.427 | 206.223 | |
| get_beta_violins | 178.430 | 5.620 | 214.982 | |
| get_honeycombs | 10.598 | 1.297 | 19.845 | |
| mcpas | 0.074 | 0.002 | 0.085 | |
| plot_graph | 0.749 | 0.056 | 0.929 | |
| tcr3d | 0.001 | 0.001 | 0.003 | |
| vdjdb | 0.209 | 0.005 | 0.290 | |