Zuguang Gu
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/cola |
| git_branch: devel |
| git_last_commit: 1456cfb |
| git_last_commit_date: 2024-02-26 08:40:57 -0400 (Mon, 26 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:28 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 408/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cola 2.9.1 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: cola |
| Version: 2.9.1 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings cola_2.9.1.tar.gz |
| StartedAt: 2024-03-28 04:03:14 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:07:13 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 238.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cola.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings cola_2.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘2.9.1’
* 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 ‘cola’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 8.0Mb
sub-directories of 1Mb or more:
data 3.2Mb
extdata 1.0Mb
libs 2.3Mb
* 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 loading without being on the library search path ... 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 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 30.193 0.376 30.625
get_signatures-ConsensusPartition-method 6.877 0.056 6.944
compare_signatures-HierarchicalPartition-method 5.923 0.263 6.206
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck/00check.log’
for details.
cola.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL cola ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘cola’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atc.cpp -o atc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cal_consensus_mat.cpp -o cal_consensus_mat.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c pdist.cpp -o pdist.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-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) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
6.967 0.343 7.309
cola.Rcheck/cola-Ex.timings
| name | user | system | elapsed | |
| ATC | 0.166 | 0.004 | 0.170 | |
| ATC_approx | 0 | 0 | 0 | |
| ConsensusPartition-class | 0 | 0 | 0 | |
| ConsensusPartitionList-class | 0 | 0 | 0 | |
| DownSamplingConsensusPartition-class | 0 | 0 | 0 | |
| Extract.ConsensusPartitionList | 0.584 | 0.016 | 0.601 | |
| Extract.HierarchicalPartition | 0.289 | 0.008 | 0.297 | |
| ExtractExtract.ConsensusPartitionList | 0.167 | 0.016 | 0.183 | |
| ExtractExtract.HierarchicalPartition | 0 | 0 | 0 | |
| FCC | 0.183 | 0.008 | 0.192 | |
| HierarchicalPartition-class | 0.000 | 0.000 | 0.001 | |
| PAC | 0.539 | 0.366 | 0.908 | |
| aPAC | 0.138 | 0.022 | 0.160 | |
| adjust_matrix | 0.006 | 0.005 | 0.011 | |
| adjust_outlier | 0.001 | 0.000 | 0.001 | |
| all_leaves-HierarchicalPartition-method | 0.118 | 0.004 | 0.122 | |
| all_nodes-HierarchicalPartition-method | 0.125 | 0.008 | 0.134 | |
| all_partition_methods | 0.001 | 0.000 | 0.001 | |
| all_top_value_methods | 0 | 0 | 0 | |
| cola | 0.068 | 0.028 | 0.097 | |
| cola_opt | 0.030 | 0.004 | 0.034 | |
| cola_report-ConsensusPartition-method | 0 | 0 | 0 | |
| cola_report-ConsensusPartitionList-method | 0 | 0 | 0 | |
| cola_report-HierarchicalPartition-method | 0.001 | 0.000 | 0.000 | |
| cola_report-dispatch | 0.000 | 0.000 | 0.001 | |
| cola_rl | 0.081 | 0.004 | 0.085 | |
| collect_classes-ConsensusPartition-method | 2.654 | 0.264 | 2.923 | |
| collect_classes-ConsensusPartitionList-method | 4.318 | 0.128 | 4.453 | |
| collect_classes-HierarchicalPartition-method | 1.770 | 0.036 | 1.810 | |
| collect_classes-dispatch | 0.000 | 0.000 | 0.001 | |
| 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 | 0.532 | 0.040 | 0.574 | |
| collect_stats-dispatch | 0 | 0 | 0 | |
| colnames-ConsensusPartition-method | 0 | 0 | 0 | |
| colnames-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| colnames-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
| colnames-HierarchicalPartition-method | 0 | 0 | 0 | |
| colnames-dispatch | 0.000 | 0.000 | 0.001 | |
| compare_partitions-ConsensusPartition-method | 0 | 0 | 0 | |
| compare_signatures-ConsensusPartition-method | 0 | 0 | 0 | |
| compare_signatures-HierarchicalPartition-method | 5.923 | 0.263 | 6.206 | |
| compare_signatures-dispatch | 0 | 0 | 0 | |
| concordance | 0.146 | 0.000 | 0.147 | |
| config_ATC | 0.001 | 0.000 | 0.001 | |
| consensus_heatmap-ConsensusPartition-method | 0.717 | 0.000 | 0.718 | |
| consensus_partition | 30.193 | 0.376 | 30.625 | |
| consensus_partition_by_down_sampling | 0 | 0 | 0 | |
| correspond_between_rankings | 0.079 | 0.000 | 0.079 | |
| correspond_between_two_rankings | 0.038 | 0.000 | 0.038 | |
| 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 | 0.915 | 0.040 | 0.957 | |
| dimension_reduction-DownSamplingConsensusPartition-method | 2.263 | 0.024 | 2.291 | |
| dimension_reduction-HierarchicalPartition-method | 0.759 | 0.012 | 0.772 | |
| dimension_reduction-dispatch | 0 | 0 | 0 | |
| dimension_reduction-matrix-method | 0.000 | 0.000 | 0.001 | |
| find_best_km | 0 | 0 | 0 | |
| functional_enrichment-ANY-method | 0.000 | 0.001 | 0.000 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| get_anno-ConsensusPartitionList-method | 0 | 0 | 0 | |
| get_anno-DownSamplingConsensusPartition-method | 0.067 | 0.006 | 0.073 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| get_children_nodes-HierarchicalPartition-method | 0.001 | 0.000 | 0.000 | |
| get_classes-ConsensusPartition-method | 0.134 | 0.008 | 0.142 | |
| get_classes-ConsensusPartitionList-method | 0.136 | 0.004 | 0.139 | |
| get_classes-DownSamplingConsensusPartition-method | 0.070 | 0.004 | 0.074 | |
| get_classes-HierarchicalPartition-method | 0.128 | 0.004 | 0.132 | |
| get_classes-dispatch | 0 | 0 | 0 | |
| get_consensus-ConsensusPartition-method | 0.140 | 0.009 | 0.150 | |
| get_matrix-ConsensusPartition-method | 0.297 | 0.089 | 0.387 | |
| get_matrix-ConsensusPartitionList-method | 0.326 | 0.076 | 0.403 | |
| get_matrix-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
| get_matrix-HierarchicalPartition-method | 0 | 0 | 0 | |
| get_matrix-dispatch | 0.000 | 0.000 | 0.001 | |
| get_membership-ConsensusPartition-method | 0.139 | 0.004 | 0.144 | |
| get_membership-ConsensusPartitionList-method | 0.137 | 0.000 | 0.137 | |
| get_membership-dispatch | 0 | 0 | 0 | |
| get_param-ConsensusPartition-method | 0.146 | 0.000 | 0.147 | |
| get_signatures-ConsensusPartition-method | 6.877 | 0.056 | 6.944 | |
| get_signatures-DownSamplingConsensusPartition-method | 0 | 0 | 0 | |
| get_signatures-HierarchicalPartition-method | 0 | 0 | 0 | |
| get_signatures-dispatch | 0 | 0 | 0 | |
| get_stats-ConsensusPartition-method | 0.133 | 0.004 | 0.137 | |
| get_stats-ConsensusPartitionList-method | 0.132 | 0.004 | 0.137 | |
| get_stats-dispatch | 0 | 0 | 0 | |
| golub_cola | 0.172 | 0.000 | 0.172 | |
| golub_cola_ds | 0.109 | 0.000 | 0.108 | |
| golub_cola_rh | 0.169 | 0.004 | 0.174 | |
| hierarchical_partition | 0 | 0 | 0 | |
| is_best_k-ConsensusPartition-method | 0.137 | 0.000 | 0.137 | |
| is_best_k-ConsensusPartitionList-method | 0.162 | 0.000 | 0.163 | |
| is_best_k-dispatch | 0 | 0 | 0 | |
| is_leaf_node-HierarchicalPartition-method | 0.117 | 0.000 | 0.117 | |
| is_stable_k-ConsensusPartition-method | 0.14 | 0.00 | 0.14 | |
| is_stable_k-ConsensusPartitionList-method | 0.146 | 0.000 | 0.146 | |
| is_stable_k-dispatch | 0 | 0 | 0 | |
| knee_finder2 | 0.031 | 0.000 | 0.031 | |
| knitr_add_tab_item | 0 | 0 | 0 | |
| knitr_insert_tabs | 0 | 0 | 0 | |
| map_to_entrez_id | 0.001 | 0.000 | 0.000 | |
| max_depth-HierarchicalPartition-method | 0.117 | 0.000 | 0.117 | |
| membership_heatmap-ConsensusPartition-method | 0.572 | 0.000 | 0.573 | |
| merge_node-HierarchicalPartition-method | 0 | 0 | 0 | |
| merge_node_param | 0 | 0 | 0 | |
| ncol-ConsensusPartition-method | 0 | 0 | 0 | |
| ncol-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| 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 | 0.163 | 0.004 | 0.166 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| register_SOM | 0 | 0 | 0 | |
| register_partition_methods | 0.682 | 0.052 | 0.735 | |
| register_top_value_methods | 0.001 | 0.000 | 0.002 | |
| relabel_class | 0.01 | 0.00 | 0.01 | |
| remove_partition_methods | 0.001 | 0.000 | 0.000 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| run_all_consensus_partition_methods | 0 | 0 | 0 | |
| select_partition_number-ConsensusPartition-method | 0.155 | 0.000 | 0.155 | |
| show-ConsensusPartition-method | 0 | 0 | 0 | |
| show-ConsensusPartitionList-method | 0 | 0 | 0 | |
| show-DownSamplingConsensusPartition-method | 0.107 | 0.000 | 0.108 | |
| show-HierarchicalPartition-method | 0.167 | 0.004 | 0.171 | |
| show-dispatch | 0 | 0 | 0 | |
| split_node-HierarchicalPartition-method | 0 | 0 | 0 | |
| suggest_best_k-ConsensusPartition-method | 0.133 | 0.008 | 0.141 | |
| suggest_best_k-ConsensusPartitionList-method | 0.137 | 0.012 | 0.150 | |
| suggest_best_k-HierarchicalPartition-method | 0.125 | 0.000 | 0.126 | |
| suggest_best_k-dispatch | 0 | 0 | 0 | |
| test_between_factors | 0.011 | 0.000 | 0.011 | |
| test_to_known_factors-ConsensusPartition-method | 0.163 | 0.000 | 0.163 | |
| test_to_known_factors-ConsensusPartitionList-method | 0.317 | 0.004 | 0.322 | |
| test_to_known_factors-DownSamplingConsensusPartition-method | 0.104 | 0.000 | 0.104 | |
| test_to_known_factors-HierarchicalPartition-method | 0.137 | 0.000 | 0.137 | |
| test_to_known_factors-dispatch | 0 | 0 | 0 | |
| top_elements_overlap | 0.291 | 0.004 | 0.295 | |
| top_rows_heatmap-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| 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 | 4.342 | 0.092 | 4.430 | |
| top_rows_overlap-ConsensusPartitionList-method | 1.592 | 0.008 | 1.602 | |
| top_rows_overlap-HierarchicalPartition-method | 0.558 | 0.004 | 0.563 | |
| top_rows_overlap-dispatch | 0.001 | 0.000 | 0.000 | |
| top_rows_overlap-matrix-method | 0.183 | 0.000 | 0.183 | |