Package: cola

Version: 0.99.14

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_0.99.14.tar.gz

StartedAt: 2019-04-09 00:53:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:56:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 137.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cola.Rcheck

Warnings: 1

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### Running command:
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###   /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_0.99.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘0.99.14’
* 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 ... WARNING
Codoc mismatches from documentation object 'hierarchical_partition':
hierarchical_partition
  Code: function(data, top_value_method = "MAD", partition_method =
                 "kmeans", concordance_cutoff = 0.9, PAC_cutoff = 0.2,
                 silhouette_cutoff = 0.5, min_samples = 6,
                 min_signatures = 50, max_k = 4, verbose = TRUE,
                 mc.cores = 1, ...)
  Docs: function(data, top_value_method = "MAD", partition_method =
                 "kmeans", concordance_cutoff = 0.9, PAC_cutoff = 0.2,
                 silhouette_cutoff = 0.5, min_samples = 6, max_k = 4,
                 verbose = TRUE, mc.cores = 1, ...)
  Argument names in code not in docs:
    min_signatures
  Mismatches in argument names (first 3):
    Position: 8 Code: min_signatures Docs: max_k
    Position: 9 Code: max_k Docs: verbose
    Position: 10 Code: verbose Docs: mc.cores

* 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
top_rows_heatmap-matrix-method                5.186  0.656   5.719
collect_plots-ConsensusPartitionList-method   5.363  0.320   5.656
collect_classes-ConsensusPartitionList-method 5.631  0.033   5.665
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cola
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* 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" -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" -I/usr/local/include  -fPIC  -Wall -g -O2  -c cal_consensus_mat.cpp -o cal_consensus_mat.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 -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)

R Under development (unstable) (2019-03-18 r76245) -- "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: 1 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  1.704   0.318   1.970 

name	user	system	elapsed
ATC	0.216	0.053	0.269
ConsensusPartition-class	0	0	0
ConsensusPartitionList-class	0.000	0.001	0.001
Extract.ConsensusPartitionList	0.489	0.028	0.517
Extract.HierarchicalPartition	0.101	0.020	0.121
ExtractExtract.ConsensusPartitionList	0.062	0.023	0.085
ExtractExtract.HierarchicalPartition	0.113	0.018	0.131
HierarchicalPartition-class	0.000	0.000	0.001
PAC	0.074	0.021	0.095
adjust_matrix	0.009	0.001	0.009
adjust_outlier	0.001	0.001	0.001
all_leaves-HierarchicalPartition-method	0.032	0.017	0.050
all_nodes-HierarchicalPartition-method	0.030	0.017	0.047
all_partition_methods	0.001	0.000	0.001
all_top_value_methods	0.000	0.000	0.001
cola	0.040	0.002	0.042
cola_report-ConsensusPartition-method	0	0	0
cola_report-ConsensusPartitionList-method	0	0	0
cola_report-HierarchicalPartition-method	0.001	0.000	0.001
cola_report-dispatch	0.000	0.000	0.001
cola_rh	0.061	0.014	0.075
cola_rl	0.097	0.020	0.117
collect_classes-ConsensusPartition-method	2.903	0.042	2.946
collect_classes-ConsensusPartitionList-method	5.631	0.033	5.665
collect_classes-HierarchicalPartition-method	3.933	0.327	4.261
collect_classes-dispatch	0.000	0.001	0.001
collect_plots-ConsensusPartition-method	0.001	0.001	0.001
collect_plots-ConsensusPartitionList-method	5.363	0.320	5.656
collect_plots-dispatch	0.000	0.000	0.001
concordance	0.052	0.010	0.062
consensus_heatmap-ConsensusPartition-method	1.134	0.065	1.201
consensus_partition	1.852	0.079	1.932
correspond_between_rankings	0.124	0.010	0.135
correspond_between_two_rankings	0.065	0.003	0.069
dimension_reduction-ConsensusPartition-method	0.099	0.019	0.119
dimension_reduction-HierarchicalPartition-method	0.212	0.024	0.236
dimension_reduction-dispatch	0.001	0.001	0.001
dimension_reduction-matrix-method	0.000	0.000	0.001
get_anno-ConsensusPartition-method	0.000	0.000	0.001
get_anno-ConsensusPartitionList-method	0.000	0.001	0.000
get_anno-HierarchicalPartition-method	0	0	0
get_anno-dispatch	0.000	0.000	0.001
get_anno_col-ConsensusPartition-method	0.000	0.001	0.001
get_anno_col-ConsensusPartitionList-method	0.000	0.000	0.001
get_anno_col-HierarchicalPartition-method	0.000	0.000	0.001
get_anno_col-dispatch	0.001	0.001	0.001
get_classes-ConsensusPartition-method	0.057	0.018	0.076
get_classes-ConsensusPartitionList-method	0.051	0.016	0.068
get_classes-HierarchicalPartition-method	0.033	0.012	0.046
get_classes-dispatch	0.001	0.000	0.001
get_consensus-ConsensusPartition-method	0.078	0.046	0.125
get_matrix-ConsensusPartition-method	0.083	0.044	0.128
get_matrix-ConsensusPartitionList-method	0.091	0.056	0.148
get_matrix-HierarchicalPartition-method	0.001	0.000	0.001
get_matrix-dispatch	0.000	0.000	0.001
get_membership-ConsensusPartition-method	0.111	0.087	0.198
get_membership-ConsensusPartitionList-method	0.059	0.019	0.078
get_membership-dispatch	0	0	0
get_param-ConsensusPartition-method	0.100	0.045	0.146
get_signatures-ConsensusPartition-method	0.001	0.000	0.000
get_signatures-HierarchicalPartition-method	0.000	0.000	0.001
get_signatures-dispatch	0	0	0
get_stats-ConsensusPartition-method	0.055	0.017	0.072
get_stats-ConsensusPartitionList-method	0.085	0.044	0.127
get_stats-dispatch	0.000	0.001	0.001
guess_best_k-ConsensusPartition-method	0.056	0.014	0.070
guess_best_k-ConsensusPartitionList-method	0.063	0.014	0.077
guess_best_k-HierarchicalPartition-method	0.034	0.012	0.046
guess_best_k-dispatch	0.001	0.001	0.000
hierarchical_partition	0.069	0.013	0.082
knitr_add_tab_item	0.000	0.000	0.001
knitr_insert_tabs	0.001	0.000	0.001
max_depth-HierarchicalPartition-method	0.030	0.012	0.042
membership_heatmap-ConsensusPartition-method	0.831	0.041	0.867
plot_ecdf-ConsensusPartition-method	0.079	0.022	0.102
register_NMF	0	0	0
register_SOM	0.000	0.000	0.001
register_partition_methods	0.278	0.010	0.287
register_top_value_methods	0.074	0.063	0.100
relabel_class	0.008	0.005	0.012
remove_partition_methods	0.001	0.000	0.000
remove_top_value_methods	0.001	0.000	0.001
run_all_consensus_partition_methods	0.134	0.044	0.178
select_partition_number-ConsensusPartition-method	0.111	0.028	0.140
show-ConsensusPartition-method	0.001	0.000	0.000
show-ConsensusPartitionList-method	0.001	0.000	0.000
show-HierarchicalPartition-method	0.054	0.016	0.069
show-dispatch	0.000	0.000	0.001
submit_to_david	0	0	0
test_between_factors	0.019	0.004	0.024
test_to_known_factors-ConsensusPartition-method	0.135	0.038	0.174
test_to_known_factors-ConsensusPartitionList-method	0.167	0.042	0.210
test_to_known_factors-HierarchicalPartition-method	0.043	0.020	0.062
test_to_known_factors-dispatch	0.001	0.001	0.000
top_elements_overlap	0.098	0.018	0.116
top_rows_heatmap-ConsensusPartitionList-method	0.000	0.001	0.000
top_rows_heatmap-dispatch	0.000	0.000	0.001
top_rows_heatmap-matrix-method	5.186	0.656	5.719
top_rows_overlap-ConsensusPartitionList-method	0.153	0.029	0.182
top_rows_overlap-dispatch	0.000	0.001	0.000
top_rows_overlap-matrix-method	2.083	0.415	2.133
venn_euler	0.690	0.053	0.713