Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 410/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cola 2.12.0 (landing page) Zuguang Gu
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 2.12.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cola.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cola_2.12.0.tar.gz |
StartedAt: 2024-12-20 00:15:36 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:20:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 301.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cola.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cola.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings cola_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'cola/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'cola' version '2.12.0' * 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 whether package 'cola' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... NOTE installed size is 6.6Mb 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 ... 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/cola/libs/x64/cola.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_signatures-ConsensusPartition-method 5.64 0.31 6.23 compare_signatures-HierarchicalPartition-method 5.19 0.28 5.67 consensus_partition 1.82 0.06 38.32 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck/00check.log' for details.
cola.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL cola ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'cola' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c atc.cpp -o atc.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cal_consensus_mat.cpp -o cal_consensus_mat.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pdist.cpp -o pdist.o g++ -std=gnu++17 -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o atc.o cal_consensus_mat.o pdist.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-cola/00new/cola/libs/x64 ** 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 ** 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 version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 5.23 0.45 28.31
cola.Rcheck/cola-Ex.timings
name | user | system | elapsed | |
ATC | 0.05 | 0.00 | 0.13 | |
ATC_approx | 0 | 0 | 0 | |
ConsensusPartition-class | 0 | 0 | 0 | |
ConsensusPartitionList-class | 0 | 0 | 0 | |
DownSamplingConsensusPartition-class | 0 | 0 | 0 | |
Extract.ConsensusPartitionList | 0.64 | 0.00 | 0.64 | |
Extract.HierarchicalPartition | 0.14 | 0.03 | 0.17 | |
ExtractExtract.ConsensusPartitionList | 0.24 | 0.03 | 0.27 | |
ExtractExtract.HierarchicalPartition | 0 | 0 | 0 | |
FCC | 0.12 | 0.02 | 0.14 | |
HierarchicalPartition-class | 0 | 0 | 0 | |
PAC | 0.50 | 0.01 | 0.52 | |
aPAC | 0.17 | 0.02 | 0.19 | |
adjust_matrix | 0 | 0 | 0 | |
adjust_outlier | 0.02 | 0.00 | 0.02 | |
all_leaves-HierarchicalPartition-method | 0.07 | 0.01 | 0.09 | |
all_nodes-HierarchicalPartition-method | 0.11 | 0.02 | 0.12 | |
all_partition_methods | 0 | 0 | 0 | |
all_top_value_methods | 0 | 0 | 0 | |
cola | 0.05 | 0.00 | 0.05 | |
cola_opt | 0.02 | 0.00 | 0.01 | |
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 | 0.04 | 0.03 | 0.08 | |
collect_classes-ConsensusPartition-method | 2.86 | 0.85 | 2.45 | |
collect_classes-ConsensusPartitionList-method | 4.08 | 0.07 | 4.16 | |
collect_classes-HierarchicalPartition-method | 1.61 | 0.07 | 1.80 | |
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 | 0 | 0 | |
collect_stats-ConsensusPartitionList-method | 0.57 | 0.00 | 0.58 | |
collect_stats-dispatch | 0 | 0 | 0 | |
colnames-ConsensusPartition-method | 0 | 0 | 0 | |
colnames-ConsensusPartitionList-method | 0 | 0 | 0 | |
colnames-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
colnames-HierarchicalPartition-method | 0 | 0 | 0 | |
colnames-dispatch | 0 | 0 | 0 | |
compare_partitions-ConsensusPartition-method | 0 | 0 | 0 | |
compare_signatures-ConsensusPartition-method | 0 | 0 | 0 | |
compare_signatures-HierarchicalPartition-method | 5.19 | 0.28 | 5.67 | |
compare_signatures-dispatch | 0 | 0 | 0 | |
concordance | 0.17 | 0.00 | 0.17 | |
config_ATC | 0 | 0 | 0 | |
consensus_heatmap-ConsensusPartition-method | 0.57 | 0.00 | 0.57 | |
consensus_partition | 1.82 | 0.06 | 38.32 | |
consensus_partition_by_down_sampling | 0 | 0 | 0 | |
correspond_between_rankings | 0.1 | 0.0 | 0.1 | |
correspond_between_two_rankings | 0.04 | 0.00 | 0.05 | |
david_enrichment | 0 | 0 | 0 | |
dim.ConsensusPartition | 0 | 0 | 0 | |
dim.ConsensusPartitionList | 0 | 0 | 0 | |
dim.DownSamplingConsensusPartition | 0 | 0 | 0 | |
dim.HierarchicalPartition | 0 | 0 | 0 | |
dimension_reduction-ConsensusPartition-method | 0.88 | 0.06 | 0.93 | |
dimension_reduction-DownSamplingConsensusPartition-method | 2.03 | 0.08 | 2.11 | |
dimension_reduction-HierarchicalPartition-method | 0.67 | 0.02 | 0.69 | |
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 | 0 | 0 | |
get_anno-ConsensusPartition-method | 0 | 0 | 0 | |
get_anno-ConsensusPartitionList-method | 0 | 0 | 0 | |
get_anno-DownSamplingConsensusPartition-method | 0.05 | 0.03 | 0.07 | |
get_anno-HierarchicalPartition-method | 0 | 0 | 0 | |
get_anno-dispatch | 0 | 0 | 0 | |
get_anno_col-ConsensusPartition-method | 0 | 0 | 0 | |
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 | 0.17 | 0.02 | 0.19 | |
get_classes-ConsensusPartitionList-method | 0.16 | 0.00 | 0.16 | |
get_classes-DownSamplingConsensusPartition-method | 0.08 | 0.00 | 0.08 | |
get_classes-HierarchicalPartition-method | 0.09 | 0.07 | 0.16 | |
get_classes-dispatch | 0 | 0 | 0 | |
get_consensus-ConsensusPartition-method | 0.12 | 0.03 | 0.15 | |
get_matrix-ConsensusPartition-method | 0.75 | 0.28 | 1.03 | |
get_matrix-ConsensusPartitionList-method | 0.66 | 0.41 | 1.06 | |
get_matrix-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
get_matrix-HierarchicalPartition-method | 0 | 0 | 0 | |
get_matrix-dispatch | 0 | 0 | 0 | |
get_membership-ConsensusPartition-method | 0.16 | 0.05 | 0.21 | |
get_membership-ConsensusPartitionList-method | 0.15 | 0.03 | 0.18 | |
get_membership-dispatch | 0 | 0 | 0 | |
get_param-ConsensusPartition-method | 0.16 | 0.05 | 0.21 | |
get_signatures-ConsensusPartition-method | 5.64 | 0.31 | 6.23 | |
get_signatures-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
get_signatures-HierarchicalPartition-method | 0 | 0 | 0 | |
get_signatures-dispatch | 0 | 0 | 0 | |
get_stats-ConsensusPartition-method | 0.2 | 0.0 | 0.2 | |
get_stats-ConsensusPartitionList-method | 0.19 | 0.00 | 0.19 | |
get_stats-dispatch | 0 | 0 | 0 | |
golub_cola | 0.12 | 0.03 | 0.15 | |
golub_cola_ds | 0.11 | 0.00 | 0.11 | |
golub_cola_rh | 0.14 | 0.03 | 0.17 | |
hierarchical_partition | 0 | 0 | 0 | |
is_best_k-ConsensusPartition-method | 0.15 | 0.02 | 0.17 | |
is_best_k-ConsensusPartitionList-method | 0.14 | 0.01 | 0.16 | |
is_best_k-dispatch | 0 | 0 | 0 | |
is_leaf_node-HierarchicalPartition-method | 0.10 | 0.03 | 0.12 | |
is_stable_k-ConsensusPartition-method | 0.14 | 0.02 | 0.16 | |
is_stable_k-ConsensusPartitionList-method | 0.17 | 0.01 | 0.19 | |
is_stable_k-dispatch | 0 | 0 | 0 | |
knee_finder2 | 0.03 | 0.00 | 0.03 | |
knitr_add_tab_item | 0 | 0 | 0 | |
knitr_insert_tabs | 0 | 0 | 0 | |
map_to_entrez_id | 0 | 0 | 0 | |
max_depth-HierarchicalPartition-method | 0.11 | 0.04 | 0.14 | |
membership_heatmap-ConsensusPartition-method | 0.45 | 0.00 | 0.45 | |
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 | 0 | 0 | |
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 | 0.09 | 0.01 | 0.11 | |
predict_classes-ConsensusPartition-method | 0 | 0 | 0 | |
predict_classes-dispatch | 0 | 0 | 0 | |
predict_classes-matrix-method | 0 | 0 | 0 | |
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 | 0.58 | 0.00 | 0.58 | |
register_top_value_methods | 0 | 0 | 0 | |
relabel_class | 0.00 | 0.01 | 0.02 | |
remove_partition_methods | 0 | 0 | 0 | |
remove_top_value_methods | 0 | 0 | 0 | |
rownames-ConsensusPartition-method | 0 | 0 | 0 | |
rownames-ConsensusPartitionList-method | 0 | 0 | 0 | |
rownames-HierarchicalPartition-method | 0 | 0 | 0 | |
rownames-dispatch | 0 | 0 | 0 | |
run_all_consensus_partition_methods | 0 | 0 | 0 | |
select_partition_number-ConsensusPartition-method | 0.09 | 0.01 | 0.11 | |
show-ConsensusPartition-method | 0 | 0 | 0 | |
show-ConsensusPartitionList-method | 0 | 0 | 0 | |
show-DownSamplingConsensusPartition-method | 0.10 | 0.00 | 0.09 | |
show-HierarchicalPartition-method | 0.17 | 0.00 | 0.17 | |
show-dispatch | 0 | 0 | 0 | |
split_node-HierarchicalPartition-method | 0 | 0 | 0 | |
suggest_best_k-ConsensusPartition-method | 0.14 | 0.03 | 0.17 | |
suggest_best_k-ConsensusPartitionList-method | 0.14 | 0.02 | 0.16 | |
suggest_best_k-HierarchicalPartition-method | 0.14 | 0.00 | 0.14 | |
suggest_best_k-dispatch | 0 | 0 | 0 | |
test_between_factors | 0.02 | 0.00 | 0.02 | |
test_to_known_factors-ConsensusPartition-method | 0.12 | 0.03 | 0.15 | |
test_to_known_factors-ConsensusPartitionList-method | 0.24 | 0.01 | 0.25 | |
test_to_known_factors-DownSamplingConsensusPartition-method | 0.09 | 0.00 | 0.10 | |
test_to_known_factors-HierarchicalPartition-method | 0.16 | 0.00 | 0.15 | |
test_to_known_factors-dispatch | 0 | 0 | 0 | |
top_elements_overlap | 0.33 | 0.03 | 0.36 | |
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 | 3.96 | 0.22 | 4.32 | |
top_rows_overlap-ConsensusPartitionList-method | 0.97 | 0.07 | 1.03 | |
top_rows_overlap-HierarchicalPartition-method | 0.49 | 0.01 | 0.50 | |
top_rows_overlap-dispatch | 0 | 0 | 0 | |
top_rows_overlap-matrix-method | 0.18 | 0.00 | 0.18 | |