Zuguang Gu
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/cola |
| Branch: master |
| Last Commit: 1f1010c |
| Last Changed Date: 2019-12-31 09:09:30 -0500 (Tue, 31 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:53:12 -0500 (Thu, 16 Jan 2020).
| Package 340/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cola 1.3.3 Zuguang Gu
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2020-01-16 03:07:56 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:11:35 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 219.7 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_1.3.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.3’
* 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 (user + system) or elapsed time > 5s
user system elapsed
consensus_partition 49.892 0.496 50.470
collect_plots-ConsensusPartitionList-method 20.815 0.917 21.603
collect_classes-ConsensusPartitionList-method 6.175 0.089 6.266
top_rows_heatmap-matrix-method 5.103 0.551 5.579
dimension_reduction-ConsensusPartition-method 3.110 2.171 5.606
* 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-3.11-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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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) (2019-12-14 r77572) -- "Unsuffered Consequences"
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: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
3.668 0.433 4.079
cola.Rcheck/cola-Ex.timings
| name | user | system | elapsed | |
| ATC | 0.225 | 0.044 | 0.268 | |
| ConsensusPartition-class | 0.001 | 0.000 | 0.000 | |
| ConsensusPartitionList-class | 0.001 | 0.000 | 0.001 | |
| Extract.ConsensusPartitionList | 0.690 | 0.067 | 0.757 | |
| ExtractExtract.ConsensusPartitionList | 0.141 | 0.033 | 0.175 | |
| FCC | 0.185 | 0.049 | 0.235 | |
| PAC | 0.171 | 0.034 | 0.206 | |
| aPAC | 0.159 | 0.031 | 0.191 | |
| adjust_matrix | 0.008 | 0.000 | 0.008 | |
| adjust_outlier | 0.001 | 0.000 | 0.002 | |
| all_partition_methods | 0.002 | 0.000 | 0.001 | |
| all_top_value_methods | 0.001 | 0.001 | 0.001 | |
| cola | 0.066 | 0.003 | 0.069 | |
| cola_opt | 0.078 | 0.004 | 0.081 | |
| cola_report-ConsensusPartition-method | 0.001 | 0.000 | 0.001 | |
| cola_report-ConsensusPartitionList-method | 0.000 | 0.001 | 0.001 | |
| cola_report-dispatch | 0.000 | 0.001 | 0.000 | |
| cola_rl | 0.198 | 0.038 | 0.236 | |
| collect_classes-ConsensusPartition-method | 3.200 | 0.106 | 3.308 | |
| collect_classes-ConsensusPartitionList-method | 6.175 | 0.089 | 6.266 | |
| collect_classes-dispatch | 0.000 | 0.001 | 0.001 | |
| collect_plots-ConsensusPartition-method | 0.001 | 0.001 | 0.000 | |
| collect_plots-ConsensusPartitionList-method | 20.815 | 0.917 | 21.603 | |
| collect_plots-dispatch | 0 | 0 | 0 | |
| collect_stats-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| collect_stats-ConsensusPartitionList-method | 1.166 | 0.072 | 1.238 | |
| collect_stats-dispatch | 0.000 | 0.000 | 0.001 | |
| colnames-ConsensusPartition-method | 0 | 0 | 0 | |
| colnames-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| colnames-dispatch | 0.001 | 0.001 | 0.001 | |
| compare_signatures-ConsensusPartition-method | 0 | 0 | 0 | |
| concordance | 0.162 | 0.040 | 0.203 | |
| consensus_heatmap-ConsensusPartition-method | 0.846 | 0.039 | 0.886 | |
| consensus_partition | 49.892 | 0.496 | 50.470 | |
| correspond_between_rankings | 0.117 | 0.002 | 0.120 | |
| correspond_between_two_rankings | 0.049 | 0.002 | 0.052 | |
| dim.ConsensusPartition | 0.000 | 0.001 | 0.000 | |
| dim.ConsensusPartitionList | 0 | 0 | 0 | |
| dimension_reduction-ConsensusPartition-method | 3.110 | 2.171 | 5.606 | |
| dimension_reduction-dispatch | 0.001 | 0.000 | 0.000 | |
| dimension_reduction-matrix-method | 0.000 | 0.001 | 0.000 | |
| find_best_km | 0.001 | 0.000 | 0.001 | |
| functional_enrichment-ANY-method | 0 | 0 | 0 | |
| functional_enrichment-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| functional_enrichment-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| functional_enrichment-dispatch | 0.000 | 0.001 | 0.000 | |
| get_anno-ConsensusPartition-method | 0 | 0 | 0 | |
| get_anno-ConsensusPartitionList-method | 0.001 | 0.000 | 0.000 | |
| 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-dispatch | 0.000 | 0.001 | 0.001 | |
| get_classes-ConsensusPartition-method | 0.152 | 0.023 | 0.175 | |
| get_classes-ConsensusPartitionList-method | 0.160 | 0.022 | 0.183 | |
| get_classes-dispatch | 0 | 0 | 0 | |
| get_consensus-ConsensusPartition-method | 0.133 | 0.045 | 0.180 | |
| get_matrix-ConsensusPartition-method | 0.173 | 0.058 | 0.231 | |
| get_matrix-ConsensusPartitionList-method | 0.187 | 0.057 | 0.247 | |
| get_matrix-dispatch | 0 | 0 | 0 | |
| get_membership-ConsensusPartition-method | 0.214 | 0.093 | 0.309 | |
| get_membership-ConsensusPartitionList-method | 0.159 | 0.031 | 0.190 | |
| get_membership-dispatch | 0.000 | 0.000 | 0.001 | |
| get_param-ConsensusPartition-method | 0.213 | 0.059 | 0.272 | |
| get_signatures-ConsensusPartition-method | 0.001 | 0.000 | 0.001 | |
| get_stats-ConsensusPartition-method | 0.142 | 0.022 | 0.163 | |
| get_stats-ConsensusPartitionList-method | 0.174 | 0.051 | 0.224 | |
| get_stats-dispatch | 0.000 | 0.001 | 0.000 | |
| is_best_k-ConsensusPartition-method | 0.001 | 0.000 | 0.000 | |
| is_best_k-ConsensusPartitionList-method | 0 | 0 | 0 | |
| is_best_k-dispatch | 0.000 | 0.001 | 0.000 | |
| is_stable_k-ConsensusPartition-method | 0.001 | 0.000 | 0.000 | |
| is_stable_k-ConsensusPartitionList-method | 0 | 0 | 0 | |
| is_stable_k-dispatch | 0 | 0 | 0 | |
| knitr_add_tab_item | 0.000 | 0.000 | 0.001 | |
| knitr_insert_tabs | 0.000 | 0.001 | 0.001 | |
| map_to_entrez_id | 0.000 | 0.000 | 0.001 | |
| membership_heatmap-ConsensusPartition-method | 0.856 | 0.029 | 0.886 | |
| ncol-ConsensusPartition-method | 0.000 | 0.000 | 0.001 | |
| ncol-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| ncol-dispatch | 0 | 0 | 0 | |
| nrow-ConsensusPartition-method | 0.001 | 0.001 | 0.000 | |
| nrow-ConsensusPartitionList-method | 0 | 0 | 0 | |
| nrow-dispatch | 0.001 | 0.000 | 0.001 | |
| plot_ecdf-ConsensusPartition-method | 0.170 | 0.024 | 0.200 | |
| recalc_stats | 0.000 | 0.000 | 0.001 | |
| register_NMF | 0.001 | 0.000 | 0.001 | |
| register_SOM | 0.000 | 0.001 | 0.000 | |
| register_partition_methods | 0.238 | 0.032 | 0.270 | |
| register_top_value_methods | 0.045 | 0.000 | 0.045 | |
| relabel_class | 0.019 | 0.003 | 0.023 | |
| remove_partition_methods | 0 | 0 | 0 | |
| remove_top_value_methods | 0.000 | 0.000 | 0.001 | |
| rownames-ConsensusPartition-method | 0.001 | 0.000 | 0.001 | |
| rownames-ConsensusPartitionList-method | 0.001 | 0.000 | 0.001 | |
| rownames-dispatch | 0.000 | 0.000 | 0.001 | |
| run_all_consensus_partition_methods | 0.187 | 0.023 | 0.210 | |
| select_partition_number-ConsensusPartition-method | 0.171 | 0.019 | 0.202 | |
| show-ConsensusPartition-method | 0.001 | 0.001 | 0.001 | |
| show-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| show-dispatch | 0.000 | 0.000 | 0.001 | |
| submit_to_david | 0.001 | 0.000 | 0.001 | |
| suggest_best_k-ConsensusPartition-method | 0.148 | 0.020 | 0.167 | |
| suggest_best_k-ConsensusPartitionList-method | 0.176 | 0.027 | 0.208 | |
| suggest_best_k-dispatch | 0.001 | 0.000 | 0.001 | |
| test_between_factors | 0.024 | 0.001 | 0.025 | |
| test_to_known_factors-ConsensusPartition-method | 0.210 | 0.019 | 0.228 | |
| test_to_known_factors-ConsensusPartitionList-method | 0.556 | 0.040 | 0.597 | |
| test_to_known_factors-dispatch | 0.001 | 0.000 | 0.001 | |
| top_elements_overlap | 0.117 | 0.009 | 0.138 | |
| top_rows_heatmap-ConsensusPartitionList-method | 0.000 | 0.000 | 0.001 | |
| top_rows_heatmap-dispatch | 0.001 | 0.000 | 0.001 | |
| top_rows_heatmap-matrix-method | 5.103 | 0.551 | 5.579 | |
| top_rows_overlap-ConsensusPartitionList-method | 0.436 | 0.041 | 0.476 | |
| top_rows_overlap-dispatch | 0.000 | 0.001 | 0.000 | |
| top_rows_overlap-matrix-method | 0.409 | 0.040 | 0.459 | |