Tim Daniel Rose
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/mosbi |
| git_branch: RELEASE_3_15 |
| git_last_commit: 7649cab |
| git_last_commit_date: 2022-04-26 12:19:35 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:18 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 mosbi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mosbi.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 1229/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mosbi 1.2.0 (landing page) Tim Daniel Rose
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mosbi |
| Version: 1.2.0 |
| Command: _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosbi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosbi_1.2.0.tar.gz |
| StartedAt: 2022-10-19 05:00:39 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 05:01:33 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 54.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mosbi.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### _R_CHECK_FORCE_SUGGESTS_=0 /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mosbi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mosbi_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/mosbi.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mosbi/DESCRIPTION’ ... OK * this is package ‘mosbi’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘runibic’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mosbi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘get_communities’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/mosbi.Rcheck/00check.log’ for details.
mosbi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mosbi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘mosbi’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c attr_graph.cpp -o attr_graph.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c attributeConnector.cpp -o attributeConnector.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c attribute_overlap.cpp -o attribute_overlap.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bicluster_methods.cpp -o bicluster_methods.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_graph.cpp -o boost_graph.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_write.cpp -o boost_write.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c distance_matrix.cpp -o distance_matrix.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c extractBF.cpp -o extractBF.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c extractQUBIC2.cpp -o extractQUBIC2.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c full_graph.cpp -o full_graph.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c misc.cpp -o misc.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c network_edge_strength.cpp -o network_edge_strength.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sample_biclusters.cpp -o sample_biclusters.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c write_matrix.cpp -o write_matrix.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-mosbi/00new/mosbi/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 (mosbi)
mosbi.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(mosbi)
Attaching package: 'mosbi'
The following object is masked from 'package:testthat':
has_names
>
> test_check("mosbi")
6 6
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
1.771 0.166 1.913
mosbi.Rcheck/mosbi-Ex.timings
| name | user | system | elapsed | |
| NoBFBiclusters | 0.000 | 0.000 | 0.001 | |
| algohistogram | 0.002 | 0.000 | 0.001 | |
| apply_threshold-bicluster_net-method | 0 | 0 | 0 | |
| apply_threshold-cooccurrence_net-method | 0.000 | 0.000 | 0.001 | |
| apply_threshold | 0.000 | 0.001 | 0.000 | |
| attr_overlap | 0 | 0 | 0 | |
| attributeConnector | 0.001 | 0.000 | 0.001 | |
| attribute_graph | 0 | 0 | 0 | |
| bicluster-class | 0.004 | 0.000 | 0.005 | |
| bicluster_heatmap-bicluster-matrix-method | 0.058 | 0.002 | 0.059 | |
| bicluster_heatmap | 0.013 | 0.001 | 0.014 | |
| bicluster_net-class | 0.003 | 0.001 | 0.003 | |
| bicluster_net_to_igraph-bicluster_net-method | 0.000 | 0.000 | 0.001 | |
| bicluster_net_to_igraph | 0 | 0 | 0 | |
| bicluster_network | 0.000 | 0.000 | 0.001 | |
| bicluster_to_matrix | 0.001 | 0.000 | 0.001 | |
| check_names | 0.001 | 0.000 | 0.001 | |
| clean_bicluster_list | 0.003 | 0.001 | 0.004 | |
| colhistogram | 0.000 | 0.000 | 0.001 | |
| cooccurrence_net-class | 0.002 | 0.000 | 0.002 | |
| cooccurrence_net_to_igraph-cooccurrence_net-method | 0 | 0 | 0 | |
| cooccurrence_net_to_igraph | 0.000 | 0.000 | 0.001 | |
| cpp_matrix_subsetting | 0.001 | 0.000 | 0.001 | |
| detect_elements | 0.002 | 0.000 | 0.001 | |
| dim-bicluster-method | 0.001 | 0.000 | 0.001 | |
| distance_matrix | 0.001 | 0.000 | 0.002 | |
| ensemble_biclusters | 0.001 | 0.000 | 0.002 | |
| feature_louvain_overlap | 0 | 0 | 0 | |
| feature_network | 0.000 | 0.000 | 0.001 | |
| filter_bicluster_size | 0.003 | 0.001 | 0.003 | |
| filter_biclusters | 0.002 | 0.000 | 0.002 | |
| filter_matrix | 0.000 | 0.001 | 0.000 | |
| filter_subsets | 0.002 | 0.000 | 0.003 | |
| full_graph | 0.001 | 0.000 | 0.001 | |
| getAkmbiclustClusters | 0 | 0 | 0 | |
| getBFCluster | 0.000 | 0.000 | 0.001 | |
| getBicAREbiclusters | 0.001 | 0.000 | 0.001 | |
| getBiclustClusters | 0.001 | 0.000 | 0.000 | |
| getBiclustpyClusters | 0.000 | 0.001 | 0.000 | |
| getFabiaClusters | 0 | 0 | 0 | |
| getIsaClusters | 0 | 0 | 0 | |
| getQUBIC2biclusters | 0.000 | 0.000 | 0.001 | |
| get_adjacency-bicluster_net-method | 0 | 0 | 0 | |
| get_adjacency | 0.000 | 0.001 | 0.000 | |
| get_algorithms | 0.001 | 0.000 | 0.002 | |
| get_bic_net_algorithms-bicluster_net-method | 0.001 | 0.000 | 0.000 | |
| get_bic_net_algorithms | 0.001 | 0.000 | 0.001 | |
| get_biclusters | 0.001 | 0.000 | 0.000 | |
| get_louvain_communities-bicluster_net-method | 0.001 | 0.000 | 0.001 | |
| get_louvain_communities-cooccurrence_net-method | 0.001 | 0.000 | 0.000 | |
| get_louvain_communities | 0 | 0 | 0 | |
| getallBFClusters | 0 | 0 | 0 | |
| has_names | 0.001 | 0.000 | 0.000 | |
| is_subset_or_identical | 0.001 | 0.000 | 0.001 | |
| mouse_data | 0 | 0 | 0 | |
| network_edge_strength | 0.001 | 0.000 | 0.000 | |
| network_edge_strength_float | 0.001 | 0.001 | 0.001 | |
| node_size | 0.000 | 0.000 | 0.001 | |
| occurance_matrix | 0 | 0 | 0 | |
| occurance_table | 0 | 0 | 0 | |
| p_overlap | 0.000 | 0.000 | 0.001 | |
| p_overlap_2d | 0.000 | 0.001 | 0.000 | |
| p_overlap_2d_higher | 0.000 | 0.000 | 0.001 | |
| p_overlap_higher | 0 | 0 | 0 | |
| plot-bicluster_net-missing-method | 0 | 0 | 0 | |
| plot-cooccurrence_net-missing-method | 0.000 | 0.000 | 0.001 | |
| plot_algo_network | 0.000 | 0.001 | 0.000 | |
| plot_piechart_bicluster_network | 0 | 0 | 0 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| replace_threshold | 0.000 | 0.000 | 0.001 | |
| replace_values | 0.001 | 0.000 | 0.000 | |
| replace_values_float | 0.001 | 0.000 | 0.001 | |
| rowhistogram | 0 | 0 | 0 | |
| run_akmbiclust | 0 | 0 | 0 | |
| run_bimax | 0.000 | 0.001 | 0.000 | |
| run_cc | 0 | 0 | 0 | |
| run_fabia | 0.001 | 0.001 | 0.001 | |
| run_isa | 0.001 | 0.000 | 0.000 | |
| run_plaid | 0.001 | 0.000 | 0.000 | |
| run_qubic | 0.000 | 0.000 | 0.001 | |
| run_quest | 0 | 0 | 0 | |
| run_spectral | 0.000 | 0.000 | 0.001 | |
| run_unibic | 0.000 | 0.000 | 0.001 | |
| run_xmotifs | 0.000 | 0.000 | 0.001 | |
| sample_biclusters | 0 | 0 | 0 | |
| select_biclusters_from_bicluster_network-bicluster_net-list-method | 0.000 | 0.000 | 0.001 | |
| select_biclusters_from_bicluster_network | 0.000 | 0.000 | 0.001 | |
| set_bicluster_names | 0.001 | 0.000 | 0.002 | |
| similarity_matrix | 0.002 | 0.000 | 0.002 | |
| transpose_bicluster | 0.002 | 0.000 | 0.002 | |
| validate_bicluster | 0.000 | 0.001 | 0.000 | |
| write_graphml | 0 | 0 | 0 | |
| write_matrix | 0.000 | 0.001 | 0.001 | |
| zero_subsetting | 0.001 | 0.000 | 0.001 | |