Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:16 -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 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 1251/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mosbi 1.4.0 (landing page) Tim Daniel Rose
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: mosbi |
Version: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2023-04-10 21:20:37 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:21:15 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 37.6 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/mosbi.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘1.4.0’ * 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-3.16-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 bicluster_methods.cpp:130:18: warning: loop variable 'i' of type 'const int &' binds to a temporary constructed from type 'double &' [-Wrange-loop-construct] for(const int& i : row1){ ^ bicluster_methods.cpp:130:7: note: use non-reference type 'int' to make construction explicit or type 'const double &' to prevent copying for(const int& i : row1){ ^~~~~~~~~~~~~~ bicluster_methods.cpp:137:18: warning: loop variable 'j' of type 'const int &' binds to a temporary constructed from type 'double &' [-Wrange-loop-construct] for(const int& j : col1){ ^ bicluster_methods.cpp:137:7: note: use non-reference type 'int' to make construction explicit or type 'const double &' to prevent copying for(const int& j : col1){ ^~~~~~~~~~~~~~ 2 warnings generated. 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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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 0.995 0.134 1.124
mosbi.Rcheck/mosbi-Ex.timings
name | user | system | elapsed | |
NoBFBiclusters | 0.000 | 0.001 | 0.000 | |
algohistogram | 0.000 | 0.001 | 0.001 | |
apply_threshold-bicluster_net-method | 0.000 | 0.000 | 0.001 | |
apply_threshold-cooccurrence_net-method | 0 | 0 | 0 | |
apply_threshold | 0 | 0 | 0 | |
attr_overlap | 0 | 0 | 0 | |
attributeConnector | 0 | 0 | 0 | |
attribute_graph | 0.000 | 0.000 | 0.001 | |
bicluster-class | 0.002 | 0.001 | 0.004 | |
bicluster_heatmap-bicluster-matrix-method | 0.031 | 0.002 | 0.032 | |
bicluster_heatmap | 0.006 | 0.001 | 0.008 | |
bicluster_net-class | 0.001 | 0.001 | 0.002 | |
bicluster_net_to_igraph-bicluster_net-method | 0 | 0 | 0 | |
bicluster_net_to_igraph | 0.001 | 0.000 | 0.000 | |
bicluster_network | 0 | 0 | 0 | |
bicluster_to_matrix | 0.001 | 0.000 | 0.000 | |
check_names | 0 | 0 | 0 | |
clean_bicluster_list | 0.001 | 0.001 | 0.002 | |
colhistogram | 0.000 | 0.001 | 0.001 | |
cooccurrence_net-class | 0.001 | 0.000 | 0.002 | |
cooccurrence_net_to_igraph-cooccurrence_net-method | 0 | 0 | 0 | |
cooccurrence_net_to_igraph | 0 | 0 | 0 | |
cpp_matrix_subsetting | 0.000 | 0.001 | 0.001 | |
detect_elements | 0.000 | 0.000 | 0.001 | |
dim-bicluster-method | 0.000 | 0.000 | 0.001 | |
distance_matrix | 0.000 | 0.000 | 0.001 | |
ensemble_biclusters | 0.000 | 0.000 | 0.001 | |
feature_louvain_overlap | 0.000 | 0.001 | 0.000 | |
feature_network | 0 | 0 | 0 | |
filter_bicluster_size | 0.001 | 0.001 | 0.002 | |
filter_biclusters | 0.000 | 0.000 | 0.001 | |
filter_matrix | 0.000 | 0.000 | 0.001 | |
filter_subsets | 0.002 | 0.001 | 0.002 | |
full_graph | 0.001 | 0.000 | 0.001 | |
getAkmbiclustClusters | 0.000 | 0.001 | 0.000 | |
getBFCluster | 0 | 0 | 0 | |
getBicAREbiclusters | 0 | 0 | 0 | |
getBiclustClusters | 0 | 0 | 0 | |
getBiclustpyClusters | 0 | 0 | 0 | |
getFabiaClusters | 0.000 | 0.000 | 0.001 | |
getIsaClusters | 0.000 | 0.000 | 0.001 | |
getQUBIC2biclusters | 0.000 | 0.001 | 0.000 | |
get_adjacency-bicluster_net-method | 0 | 0 | 0 | |
get_adjacency | 0 | 0 | 0 | |
get_algorithms | 0.001 | 0.000 | 0.000 | |
get_bic_net_algorithms-bicluster_net-method | 0 | 0 | 0 | |
get_bic_net_algorithms | 0.001 | 0.000 | 0.000 | |
get_biclusters | 0 | 0 | 0 | |
get_louvain_communities-bicluster_net-method | 0.000 | 0.001 | 0.000 | |
get_louvain_communities-cooccurrence_net-method | 0 | 0 | 0 | |
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 | 0.000 | 0.000 | 0.001 | |
network_edge_strength | 0.000 | 0.000 | 0.001 | |
network_edge_strength_float | 0 | 0 | 0 | |
node_size | 0.000 | 0.001 | 0.000 | |
occurance_matrix | 0 | 0 | 0 | |
occurance_table | 0.000 | 0.001 | 0.000 | |
p_overlap | 0 | 0 | 0 | |
p_overlap_2d | 0.001 | 0.001 | 0.000 | |
p_overlap_2d_higher | 0 | 0 | 0 | |
p_overlap_higher | 0.000 | 0.000 | 0.001 | |
plot-bicluster_net-missing-method | 0.001 | 0.001 | 0.000 | |
plot-cooccurrence_net-missing-method | 0 | 0 | 0 | |
plot_algo_network | 0 | 0 | 0 | |
plot_piechart_bicluster_network | 0.000 | 0.000 | 0.001 | |
randomize_matrix | 0.001 | 0.000 | 0.001 | |
replace_threshold | 0.000 | 0.000 | 0.001 | |
replace_values | 0.000 | 0.000 | 0.001 | |
replace_values_float | 0.000 | 0.001 | 0.001 | |
rowhistogram | 0.000 | 0.001 | 0.000 | |
run_akmbiclust | 0 | 0 | 0 | |
run_bimax | 0.000 | 0.001 | 0.000 | |
run_cc | 0 | 0 | 0 | |
run_fabia | 0 | 0 | 0 | |
run_isa | 0 | 0 | 0 | |
run_plaid | 0 | 0 | 0 | |
run_qubic | 0.000 | 0.000 | 0.001 | |
run_quest | 0 | 0 | 0 | |
run_spectral | 0 | 0 | 0 | |
run_unibic | 0.000 | 0.000 | 0.001 | |
run_xmotifs | 0.000 | 0.000 | 0.001 | |
sample_biclusters | 0.000 | 0.000 | 0.001 | |
select_biclusters_from_bicluster_network-bicluster_net-list-method | 0 | 0 | 0 | |
select_biclusters_from_bicluster_network | 0.000 | 0.001 | 0.000 | |
set_bicluster_names | 0.001 | 0.000 | 0.002 | |
similarity_matrix | 0.001 | 0.000 | 0.001 | |
transpose_bicluster | 0.001 | 0.000 | 0.001 | |
validate_bicluster | 0.000 | 0.001 | 0.001 | |
write_graphml | 0 | 0 | 0 | |
write_matrix | 0.000 | 0.000 | 0.001 | |
zero_subsetting | 0 | 0 | 0 | |