Zuguang Gu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/cola |
| Branch: RELEASE_3_9 |
| Last Commit: db87ed6 |
| Last Changed Date: 2019-09-16 15:12:51 -0400 (Mon, 16 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:04:08 -0400 (Wed, 16 Oct 2019).
| Package 324/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cola 1.0.1 Zuguang Gu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cola |
| Version: 1.0.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cola_1.0.1.tar.gz |
| StartedAt: 2019-10-16 01:40:39 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:44:18 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 219.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cola.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cola_1.0.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘1.0.1’
* 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
* 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 ... 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 or elapsed time > 5s
user system elapsed
consensus_partition 44.206 0.433 44.647
collect_plots-ConsensusPartitionList-method 20.648 0.872 21.371
top_rows_heatmap-matrix-method 5.769 0.447 6.148
collect_plots-HierarchicalPartition-method 5.454 0.417 5.826
dimension_reduction-ConsensusPartition-method 3.941 1.911 4.904
collect_classes-ConsensusPartitionList-method 5.112 0.099 5.212
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck/00check.log’
for details.
cola.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cola ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘cola’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c cal_consensus_mat.cpp -o cal_consensus_mat.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pdist.cpp -o pdist.o clang++ -std=gnu++11 -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 cola.so RcppExports.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/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> suppressWarnings(suppressPackageStartupMessages(library(cola)))
>
> test_check("cola")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
1.991 0.326 2.266
cola.Rcheck/cola-Ex.timings
| name | user | system | elapsed | |
| ATC | 0.219 | 0.051 | 0.269 | |
| ConsensusPartition-class | 0 | 0 | 0 | |
| ConsensusPartitionList-class | 0.001 | 0.000 | 0.000 | |
| Extract.ConsensusPartitionList | 0.734 | 0.107 | 0.841 | |
| Extract.HierarchicalPartition | 0.159 | 0.036 | 0.196 | |
| ExtractExtract.ConsensusPartitionList | 0.330 | 0.085 | 0.415 | |
| ExtractExtract.HierarchicalPartition | 0.161 | 0.037 | 0.200 | |
| FCC | 0.402 | 0.060 | 0.463 | |
| GO_enrichment-ANY-method | 0 | 0 | 0 | |
| GO_enrichment-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| GO_enrichment-ConsensusPartitionList-method | 0 | 0 | 0 | |
| GO_enrichment-HierarchicalPartition-method | 0 | 0 | 0 | |
| GO_enrichment-dispatch | 0.000 | 0.000 | 0.001 | |
| HierarchicalPartition-class | 0.001 | 0.001 | 0.000 | |
| PAC | 0.388 | 0.068 | 0.456 | |
| aPAC | 0.357 | 0.051 | 0.407 | |
| adjust_matrix | 0.007 | 0.001 | 0.008 | |
| adjust_outlier | 0.001 | 0.000 | 0.001 | |
| all_leaves-HierarchicalPartition-method | 0.079 | 0.031 | 0.110 | |
| all_nodes-HierarchicalPartition-method | 0.091 | 0.032 | 0.123 | |
| all_partition_methods | 0.002 | 0.001 | 0.002 | |
| all_top_value_methods | 0 | 0 | 0 | |
| cola | 0.058 | 0.003 | 0.061 | |
| cola_opt | 0 | 0 | 0 | |
| cola_report-ConsensusPartition-method | 0 | 0 | 0 | |
| cola_report-ConsensusPartitionList-method | 0.001 | 0.001 | 0.000 | |
| cola_report-HierarchicalPartition-method | 0.000 | 0.000 | 0.001 | |
| cola_report-dispatch | 0.000 | 0.000 | 0.001 | |
| cola_rh | 0.132 | 0.032 | 0.164 | |
| cola_rl | 0.345 | 0.050 | 0.396 | |
| collect_classes-ConsensusPartition-method | 3.010 | 0.098 | 3.108 | |
| collect_classes-ConsensusPartitionList-method | 5.112 | 0.099 | 5.212 | |
| collect_classes-HierarchicalPartition-method | 2.418 | 0.145 | 2.565 | |
| collect_classes-dispatch | 0 | 0 | 0 | |
| collect_plots-ConsensusPartition-method | 0 | 0 | 0 | |
| collect_plots-ConsensusPartitionList-method | 20.648 | 0.872 | 21.371 | |
| collect_plots-HierarchicalPartition-method | 5.454 | 0.417 | 5.826 | |
| collect_plots-dispatch | 0 | 0 | 0 | |
| collect_stats-ConsensusPartition-method | 0.001 | 0.000 | 0.001 | |
| collect_stats-ConsensusPartitionList-method | 1.102 | 0.112 | 1.215 | |
| collect_stats-dispatch | 0.000 | 0.000 | 0.001 | |
| colnames-ConsensusPartition-method | 0 | 0 | 0 | |
| colnames-ConsensusPartitionList-method | 0.000 | 0.001 | 0.001 | |
| colnames-HierarchicalPartition-method | 0.001 | 0.001 | 0.001 | |
| colnames-dispatch | 0.000 | 0.000 | 0.001 | |
| compare_signatures-ConsensusPartition-method | 0.001 | 0.000 | 0.000 | |
| concordance | 0.285 | 0.084 | 0.370 | |
| consensus_heatmap-ConsensusPartition-method | 0.733 | 0.084 | 0.819 | |
| consensus_partition | 44.206 | 0.433 | 44.647 | |
| correspond_between_rankings | 0.127 | 0.003 | 0.130 | |
| correspond_between_two_rankings | 0.054 | 0.002 | 0.080 | |
| dim.ConsensusPartition | 0.000 | 0.000 | 0.001 | |
| dim.ConsensusPartitionList | 0.000 | 0.000 | 0.001 | |
| dim.HierarchicalPartition | 0.000 | 0.001 | 0.001 | |
| dimension_reduction-ConsensusPartition-method | 3.941 | 1.911 | 4.904 | |
| dimension_reduction-HierarchicalPartition-method | 0.336 | 0.013 | 0.350 | |
| dimension_reduction-dispatch | 0 | 0 | 0 | |
| dimension_reduction-matrix-method | 0 | 0 | 0 | |
| find_best_km | 0.001 | 0.000 | 0.001 | |
| get_anno-ConsensusPartition-method | 0 | 0 | 0 | |
| get_anno-ConsensusPartitionList-method | 0.000 | 0.001 | 0.001 | |
| get_anno-HierarchicalPartition-method | 0.001 | 0.000 | 0.001 | |
| get_anno-dispatch | 0 | 0 | 0 | |
| get_anno_col-ConsensusPartition-method | 0.001 | 0.000 | 0.001 | |
| get_anno_col-ConsensusPartitionList-method | 0.000 | 0.001 | 0.001 | |
| get_anno_col-HierarchicalPartition-method | 0 | 0 | 0 | |
| get_anno_col-dispatch | 0 | 0 | 0 | |
| get_classes-ConsensusPartition-method | 0.232 | 0.078 | 0.309 | |
| get_classes-ConsensusPartitionList-method | 0.289 | 0.075 | 0.363 | |
| get_classes-HierarchicalPartition-method | 0.077 | 0.034 | 0.110 | |
| get_classes-dispatch | 0 | 0 | 0 | |
| get_consensus-ConsensusPartition-method | 0.349 | 0.063 | 0.413 | |
| get_hierarchy | 0.000 | 0.000 | 0.001 | |
| get_matrix-ConsensusPartition-method | 0.271 | 0.081 | 0.352 | |
| get_matrix-ConsensusPartitionList-method | 0.316 | 0.089 | 0.406 | |
| get_matrix-HierarchicalPartition-method | 0 | 0 | 0 | |
| get_matrix-dispatch | 0.001 | 0.000 | 0.001 | |
| get_membership-ConsensusPartition-method | 0.698 | 0.178 | 0.877 | |
| get_membership-ConsensusPartitionList-method | 0.271 | 0.039 | 0.311 | |
| get_membership-dispatch | 0 | 0 | 0 | |
| get_param-ConsensusPartition-method | 0.307 | 0.077 | 0.384 | |
| get_signatures-ConsensusPartition-method | 0.000 | 0.001 | 0.000 | |
| get_signatures-HierarchicalPartition-method | 0.000 | 0.000 | 0.001 | |
| get_signatures-dispatch | 0.000 | 0.000 | 0.001 | |
| get_stats-ConsensusPartition-method | 0.273 | 0.075 | 0.348 | |
| get_stats-ConsensusPartitionList-method | 0.261 | 0.042 | 0.302 | |
| get_stats-dispatch | 0.000 | 0.001 | 0.001 | |
| hierarchical_partition | 0.140 | 0.040 | 0.179 | |
| knitr_add_tab_item | 0 | 0 | 0 | |
| knitr_insert_tabs | 0 | 0 | 0 | |
| map_to_entrez_id | 0.001 | 0.000 | 0.001 | |
| max_depth-HierarchicalPartition-method | 0.073 | 0.029 | 0.102 | |
| membership_heatmap-ConsensusPartition-method | 1.067 | 0.064 | 1.131 | |
| ncol-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| ncol-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| ncol-HierarchicalPartition-method | 0 | 0 | 0 | |
| ncol-dispatch | 0.000 | 0.001 | 0.001 | |
| nrow-ConsensusPartition-method | 0 | 0 | 0 | |
| nrow-ConsensusPartitionList-method | 0 | 0 | 0 | |
| nrow-HierarchicalPartition-method | 0 | 0 | 0 | |
| nrow-dispatch | 0.001 | 0.000 | 0.001 | |
| plot_ecdf-ConsensusPartition-method | 0.296 | 0.036 | 0.333 | |
| recalc_stats | 0 | 0 | 0 | |
| register_NMF | 0.001 | 0.000 | 0.000 | |
| register_SOM | 0.000 | 0.001 | 0.000 | |
| register_partition_methods | 0.397 | 0.036 | 0.433 | |
| register_top_value_methods | 0.034 | 0.000 | 0.034 | |
| relabel_class | 0.006 | 0.001 | 0.007 | |
| remove_partition_methods | 0.000 | 0.001 | 0.001 | |
| remove_top_value_methods | 0 | 0 | 0 | |
| rownames-ConsensusPartition-method | 0 | 0 | 0 | |
| rownames-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| rownames-HierarchicalPartition-method | 0 | 0 | 0 | |
| rownames-dispatch | 0 | 0 | 0 | |
| run_all_consensus_partition_methods | 0.313 | 0.042 | 0.355 | |
| select_partition_number-ConsensusPartition-method | 0.273 | 0.041 | 0.313 | |
| show-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| show-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| show-HierarchicalPartition-method | 0.116 | 0.028 | 0.144 | |
| show-dispatch | 0.000 | 0.000 | 0.001 | |
| submit_to_david | 0 | 0 | 0 | |
| suggest_best_k-ConsensusPartition-method | 0.274 | 0.078 | 0.354 | |
| suggest_best_k-ConsensusPartitionList-method | 0.280 | 0.043 | 0.323 | |
| suggest_best_k-HierarchicalPartition-method | 0.096 | 0.030 | 0.127 | |
| suggest_best_k-dispatch | 0.000 | 0.000 | 0.001 | |
| test_between_factors | 0.017 | 0.000 | 0.017 | |
| test_to_known_factors-ConsensusPartition-method | 0.348 | 0.052 | 0.399 | |
| test_to_known_factors-ConsensusPartitionList-method | 0.564 | 0.058 | 0.622 | |
| test_to_known_factors-HierarchicalPartition-method | 0.085 | 0.031 | 0.115 | |
| test_to_known_factors-dispatch | 0.000 | 0.000 | 0.001 | |
| top_elements_overlap | 0.127 | 0.010 | 0.140 | |
| top_rows_heatmap-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| top_rows_heatmap-dispatch | 0.000 | 0.000 | 0.001 | |
| top_rows_heatmap-matrix-method | 5.769 | 0.447 | 6.148 | |
| top_rows_overlap-ConsensusPartitionList-method | 0.518 | 0.082 | 0.602 | |
| top_rows_overlap-dispatch | 0 | 0 | 0 | |
| top_rows_overlap-matrix-method | 0.406 | 0.050 | 0.462 | |