Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 403/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cola 2.13.0 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cola package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cola.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: cola |
Version: 2.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cola_2.13.0.tar.gz |
StartedAt: 2024-12-23 18:41:49 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:43:03 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 73.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cola.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cola_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cola.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cola/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cola’ version ‘2.13.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 27 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘cola’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... INFO installed size is 5.8Mb sub-directories of 1Mb or more: data 3.2Mb extdata 1.0Mb * 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 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 whether startup messages can be suppressed ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: predict_classes-ConsensusPartition-method.Rd: colorRamp2 predict_classes-matrix-method.Rd: colorRamp2 Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 consensus_partition 5.369 0.17 5.609 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/cola.Rcheck/00check.log’ for details.
cola.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cola ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘cola’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c atc.cpp -o atc.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cal_consensus_mat.cpp -o cal_consensus_mat.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pdist.cpp -o pdist.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-cola/00new/cola/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 (cola)
cola.Rcheck/tests/test-all.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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) > suppressWarnings(suppressPackageStartupMessages(library(cola))) > > test_check("cola") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ] > > > proc.time() user system elapsed 1.618 0.109 1.730
cola.Rcheck/cola-Ex.timings
name | user | system | elapsed | |
ATC | 0.011 | 0.002 | 0.013 | |
ATC_approx | 0 | 0 | 0 | |
ConsensusPartition-class | 0 | 0 | 0 | |
ConsensusPartitionList-class | 0 | 0 | 0 | |
DownSamplingConsensusPartition-class | 0 | 0 | 0 | |
Extract.ConsensusPartitionList | 0.162 | 0.010 | 0.175 | |
Extract.HierarchicalPartition | 0.069 | 0.002 | 0.073 | |
ExtractExtract.ConsensusPartitionList | 0.073 | 0.002 | 0.077 | |
ExtractExtract.HierarchicalPartition | 0 | 0 | 0 | |
FCC | 0.075 | 0.004 | 0.080 | |
HierarchicalPartition-class | 0 | 0 | 0 | |
PAC | 0.113 | 0.003 | 0.118 | |
aPAC | 0.066 | 0.002 | 0.069 | |
adjust_matrix | 0.002 | 0.000 | 0.004 | |
adjust_outlier | 0.000 | 0.001 | 0.000 | |
all_leaves-HierarchicalPartition-method | 0.061 | 0.001 | 0.061 | |
all_nodes-HierarchicalPartition-method | 0.062 | 0.001 | 0.064 | |
all_partition_methods | 0.001 | 0.001 | 0.001 | |
all_top_value_methods | 0 | 0 | 0 | |
cola | 0.016 | 0.000 | 0.016 | |
cola_opt | 0.010 | 0.001 | 0.011 | |
cola_report-ConsensusPartition-method | 0 | 0 | 0 | |
cola_report-ConsensusPartitionList-method | 0 | 0 | 0 | |
cola_report-HierarchicalPartition-method | 0 | 0 | 0 | |
cola_report-dispatch | 0 | 0 | 0 | |
cola_rl | 0.031 | 0.001 | 0.032 | |
collect_classes-ConsensusPartition-method | 0.548 | 0.013 | 0.571 | |
collect_classes-ConsensusPartitionList-method | 1.114 | 0.022 | 1.179 | |
collect_classes-HierarchicalPartition-method | 0.386 | 0.012 | 0.398 | |
collect_classes-dispatch | 0 | 0 | 0 | |
collect_plots-ConsensusPartition-method | 0 | 0 | 0 | |
collect_plots-ConsensusPartitionList-method | 0 | 0 | 0 | |
collect_plots-dispatch | 0 | 0 | 0 | |
collect_stats-ConsensusPartition-method | 0.001 | 0.000 | 0.000 | |
collect_stats-ConsensusPartitionList-method | 0.155 | 0.003 | 0.187 | |
collect_stats-dispatch | 0 | 0 | 0 | |
colnames-ConsensusPartition-method | 0 | 0 | 0 | |
colnames-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
colnames-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
colnames-HierarchicalPartition-method | 0.001 | 0.000 | 0.000 | |
colnames-dispatch | 0 | 0 | 0 | |
compare_partitions-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
compare_signatures-ConsensusPartition-method | 0 | 0 | 0 | |
compare_signatures-HierarchicalPartition-method | 1.823 | 0.073 | 1.953 | |
compare_signatures-dispatch | 0 | 0 | 0 | |
concordance | 0.067 | 0.003 | 0.070 | |
config_ATC | 0.001 | 0.000 | 0.001 | |
consensus_heatmap-ConsensusPartition-method | 0.179 | 0.005 | 0.193 | |
consensus_partition | 5.369 | 0.170 | 5.609 | |
consensus_partition_by_down_sampling | 0 | 0 | 0 | |
correspond_between_rankings | 0.022 | 0.001 | 0.023 | |
correspond_between_two_rankings | 0.011 | 0.001 | 0.011 | |
david_enrichment | 0 | 0 | 0 | |
dim.ConsensusPartition | 0 | 0 | 0 | |
dim.ConsensusPartitionList | 0 | 0 | 0 | |
dim.DownSamplingConsensusPartition | 0.000 | 0.001 | 0.000 | |
dim.HierarchicalPartition | 0 | 0 | 0 | |
dimension_reduction-ConsensusPartition-method | 0.262 | 0.019 | 0.284 | |
dimension_reduction-DownSamplingConsensusPartition-method | 0.442 | 0.034 | 0.493 | |
dimension_reduction-HierarchicalPartition-method | 0.230 | 0.012 | 0.244 | |
dimension_reduction-dispatch | 0 | 0 | 0 | |
dimension_reduction-matrix-method | 0 | 0 | 0 | |
find_best_km | 0 | 0 | 0 | |
functional_enrichment-ANY-method | 0 | 0 | 0 | |
functional_enrichment-ConsensusPartition-method | 0 | 0 | 0 | |
functional_enrichment-ConsensusPartitionList-method | 0 | 0 | 0 | |
functional_enrichment-HierarchicalPartition-method | 0 | 0 | 0 | |
functional_enrichment-dispatch | 0.000 | 0.001 | 0.000 | |
get_anno-ConsensusPartition-method | 0 | 0 | 0 | |
get_anno-ConsensusPartitionList-method | 0 | 0 | 0 | |
get_anno-DownSamplingConsensusPartition-method | 0.042 | 0.002 | 0.044 | |
get_anno-HierarchicalPartition-method | 0 | 0 | 0 | |
get_anno-dispatch | 0 | 0 | 0 | |
get_anno_col-ConsensusPartition-method | 0.000 | 0.001 | 0.000 | |
get_anno_col-ConsensusPartitionList-method | 0 | 0 | 0 | |
get_anno_col-HierarchicalPartition-method | 0 | 0 | 0 | |
get_anno_col-dispatch | 0 | 0 | 0 | |
get_children_nodes-HierarchicalPartition-method | 0 | 0 | 0 | |
get_classes-ConsensusPartition-method | 0.072 | 0.004 | 0.076 | |
get_classes-ConsensusPartitionList-method | 0.066 | 0.003 | 0.068 | |
get_classes-DownSamplingConsensusPartition-method | 0.041 | 0.002 | 0.043 | |
get_classes-HierarchicalPartition-method | 0.311 | 0.005 | 0.317 | |
get_classes-dispatch | 0 | 0 | 0 | |
get_consensus-ConsensusPartition-method | 0.068 | 0.009 | 0.078 | |
get_matrix-ConsensusPartition-method | 0.133 | 0.167 | 0.308 | |
get_matrix-ConsensusPartitionList-method | 0.134 | 0.162 | 0.299 | |
get_matrix-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
get_matrix-HierarchicalPartition-method | 0 | 0 | 0 | |
get_matrix-dispatch | 0 | 0 | 0 | |
get_membership-ConsensusPartition-method | 0.067 | 0.008 | 0.074 | |
get_membership-ConsensusPartitionList-method | 0.069 | 0.003 | 0.073 | |
get_membership-dispatch | 0.001 | 0.000 | 0.000 | |
get_param-ConsensusPartition-method | 0.068 | 0.004 | 0.072 | |
get_signatures-ConsensusPartition-method | 1.944 | 0.090 | 2.050 | |
get_signatures-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
get_signatures-HierarchicalPartition-method | 0 | 0 | 0 | |
get_signatures-dispatch | 0 | 0 | 0 | |
get_stats-ConsensusPartition-method | 0.066 | 0.003 | 0.069 | |
get_stats-ConsensusPartitionList-method | 0.067 | 0.002 | 0.069 | |
get_stats-dispatch | 0 | 0 | 0 | |
golub_cola | 0.074 | 0.003 | 0.077 | |
golub_cola_ds | 0.049 | 0.003 | 0.051 | |
golub_cola_rh | 0.075 | 0.002 | 0.077 | |
hierarchical_partition | 0 | 0 | 0 | |
is_best_k-ConsensusPartition-method | 0.073 | 0.003 | 0.077 | |
is_best_k-ConsensusPartitionList-method | 0.068 | 0.001 | 0.075 | |
is_best_k-dispatch | 0 | 0 | 0 | |
is_leaf_node-HierarchicalPartition-method | 0.061 | 0.001 | 0.065 | |
is_stable_k-ConsensusPartition-method | 0.067 | 0.002 | 0.074 | |
is_stable_k-ConsensusPartitionList-method | 0.069 | 0.003 | 0.073 | |
is_stable_k-dispatch | 0 | 0 | 0 | |
knee_finder2 | 0.010 | 0.001 | 0.011 | |
knitr_add_tab_item | 0 | 0 | 0 | |
knitr_insert_tabs | 0.000 | 0.000 | 0.001 | |
map_to_entrez_id | 0 | 0 | 0 | |
max_depth-HierarchicalPartition-method | 0.060 | 0.001 | 0.063 | |
membership_heatmap-ConsensusPartition-method | 0.178 | 0.006 | 0.186 | |
merge_node-HierarchicalPartition-method | 0 | 0 | 0 | |
merge_node_param | 0 | 0 | 0 | |
ncol-ConsensusPartition-method | 0 | 0 | 0 | |
ncol-ConsensusPartitionList-method | 0 | 0 | 0 | |
ncol-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
ncol-HierarchicalPartition-method | 0.001 | 0.000 | 0.000 | |
ncol-dispatch | 0 | 0 | 0 | |
node_info-HierarchicalPartition-method | 0 | 0 | 0 | |
node_level-HierarchicalPartition-method | 0 | 0 | 0 | |
nrow-ConsensusPartition-method | 0 | 0 | 0 | |
nrow-ConsensusPartitionList-method | 0 | 0 | 0 | |
nrow-HierarchicalPartition-method | 0 | 0 | 0 | |
nrow-dispatch | 0 | 0 | 0 | |
plot_ecdf-ConsensusPartition-method | 0.070 | 0.003 | 0.073 | |
predict_classes-ConsensusPartition-method | 0 | 0 | 0 | |
predict_classes-dispatch | 0 | 0 | 0 | |
predict_classes-matrix-method | 0.000 | 0.000 | 0.001 | |
print.hc_table_suggest_best_k | 0 | 0 | 0 | |
recalc_stats | 0 | 0 | 0 | |
register_NMF | 0 | 0 | 0 | |
register_SOM | 0 | 0 | 0 | |
register_partition_methods | 0.307 | 0.006 | 0.316 | |
register_top_value_methods | 0.000 | 0.000 | 0.001 | |
relabel_class | 0.003 | 0.001 | 0.003 | |
remove_partition_methods | 0 | 0 | 0 | |
remove_top_value_methods | 0.000 | 0.000 | 0.001 | |
rownames-ConsensusPartition-method | 0 | 0 | 0 | |
rownames-ConsensusPartitionList-method | 0 | 0 | 0 | |
rownames-HierarchicalPartition-method | 0 | 0 | 0 | |
rownames-dispatch | 0.001 | 0.000 | 0.000 | |
run_all_consensus_partition_methods | 0.000 | 0.001 | 0.000 | |
select_partition_number-ConsensusPartition-method | 0.071 | 0.003 | 0.076 | |
show-ConsensusPartition-method | 0 | 0 | 0 | |
show-ConsensusPartitionList-method | 0 | 0 | 0 | |
show-DownSamplingConsensusPartition-method | 0.047 | 0.002 | 0.049 | |
show-HierarchicalPartition-method | 0.071 | 0.002 | 0.073 | |
show-dispatch | 0 | 0 | 0 | |
split_node-HierarchicalPartition-method | 0 | 0 | 0 | |
suggest_best_k-ConsensusPartition-method | 0.066 | 0.002 | 0.068 | |
suggest_best_k-ConsensusPartitionList-method | 0.068 | 0.002 | 0.070 | |
suggest_best_k-HierarchicalPartition-method | 0.061 | 0.002 | 0.063 | |
suggest_best_k-dispatch | 0 | 0 | 0 | |
test_between_factors | 0.003 | 0.000 | 0.003 | |
test_to_known_factors-ConsensusPartition-method | 0.073 | 0.003 | 0.076 | |
test_to_known_factors-ConsensusPartitionList-method | 0.098 | 0.003 | 0.102 | |
test_to_known_factors-DownSamplingConsensusPartition-method | 0.048 | 0.001 | 0.056 | |
test_to_known_factors-HierarchicalPartition-method | 0.064 | 0.002 | 0.065 | |
test_to_known_factors-dispatch | 0 | 0 | 0 | |
top_elements_overlap | 0.070 | 0.007 | 0.076 | |
top_rows_heatmap-ConsensusPartition-method | 0 | 0 | 0 | |
top_rows_heatmap-ConsensusPartitionList-method | 0 | 0 | 0 | |
top_rows_heatmap-HierarchicalPartition-method | 0 | 0 | 0 | |
top_rows_heatmap-dispatch | 0 | 0 | 0 | |
top_rows_heatmap-matrix-method | 1.562 | 0.100 | 1.681 | |
top_rows_overlap-ConsensusPartitionList-method | 0.293 | 0.018 | 0.318 | |
top_rows_overlap-HierarchicalPartition-method | 0.224 | 0.006 | 0.242 | |
top_rows_overlap-dispatch | 0 | 0 | 0 | |
top_rows_overlap-matrix-method | 0.045 | 0.003 | 0.048 | |