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 00:03:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:05:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 95.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cola.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### 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_0.99.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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
* 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.

##############################################################################
##############################################################################
###
### 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’ ...
** 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/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
* DONE (cola)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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 
  1.353   0.162   1.497 

name	user	system	elapsed
ATC	0.241	0.021	0.267
ConsensusPartition-class	0	0	0
ConsensusPartitionList-class	0	0	0
Extract.ConsensusPartitionList	0.420	0.020	0.446
Extract.HierarchicalPartition	0.079	0.011	0.091
ExtractExtract.ConsensusPartitionList	0.043	0.013	0.056
ExtractExtract.HierarchicalPartition	0.081	0.015	0.096
HierarchicalPartition-class	0.000	0.000	0.001
PAC	0.050	0.012	0.062
adjust_matrix	0.005	0.000	0.005
adjust_outlier	0.001	0.000	0.000
all_leaves-HierarchicalPartition-method	0.029	0.010	0.038
all_nodes-HierarchicalPartition-method	0.025	0.011	0.035
all_partition_methods	0.001	0.000	0.000
all_top_value_methods	0.001	0.000	0.001
cola	0.043	0.001	0.046
cola_report-ConsensusPartition-method	0	0	0
cola_report-ConsensusPartitionList-method	0	0	0
cola_report-HierarchicalPartition-method	0	0	0
cola_report-dispatch	0.000	0.000	0.001
cola_rh	0.055	0.013	0.068
cola_rl	0.079	0.013	0.095
collect_classes-ConsensusPartition-method	1.976	0.020	2.015
collect_classes-ConsensusPartitionList-method	3.842	0.017	3.884
collect_classes-HierarchicalPartition-method	2.873	0.142	3.053
collect_classes-dispatch	0	0	0
collect_plots-ConsensusPartition-method	0	0	0
collect_plots-ConsensusPartitionList-method	3.382	0.138	3.521
collect_plots-dispatch	0	0	0
concordance	0.046	0.006	0.053
consensus_heatmap-ConsensusPartition-method	0.812	0.036	0.866
consensus_partition	1.420	0.032	1.467
correspond_between_rankings	0.089	0.006	0.096
correspond_between_two_rankings	0.043	0.001	0.044
dimension_reduction-ConsensusPartition-method	0.085	0.009	0.096
dimension_reduction-HierarchicalPartition-method	0.162	0.009	0.175
dimension_reduction-dispatch	0	0	0
dimension_reduction-matrix-method	0	0	0
get_anno-ConsensusPartition-method	0	0	0
get_anno-ConsensusPartitionList-method	0	0	0
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	0.000	0.000	0.001
get_anno_col-dispatch	0	0	0
get_classes-ConsensusPartition-method	0.050	0.008	0.059
get_classes-ConsensusPartitionList-method	0.039	0.008	0.047
get_classes-HierarchicalPartition-method	0.031	0.007	0.038
get_classes-dispatch	0	0	0
get_consensus-ConsensusPartition-method	0.066	0.024	0.089
get_matrix-ConsensusPartition-method	0.060	0.024	0.085
get_matrix-ConsensusPartitionList-method	0.071	0.026	0.100
get_matrix-HierarchicalPartition-method	0.001	0.000	0.000
get_matrix-dispatch	0	0	0
get_membership-ConsensusPartition-method	0.084	0.035	0.121
get_membership-ConsensusPartitionList-method	0.056	0.009	0.064
get_membership-dispatch	0	0	0
get_param-ConsensusPartition-method	0.085	0.024	0.111
get_signatures-ConsensusPartition-method	0.000	0.000	0.001
get_signatures-HierarchicalPartition-method	0	0	0
get_signatures-dispatch	0.000	0.000	0.001
get_stats-ConsensusPartition-method	0.056	0.007	0.064
get_stats-ConsensusPartitionList-method	0.064	0.017	0.082
get_stats-dispatch	0	0	0
guess_best_k-ConsensusPartition-method	0.045	0.008	0.051
guess_best_k-ConsensusPartitionList-method	0.044	0.005	0.049
guess_best_k-HierarchicalPartition-method	0.035	0.007	0.042
guess_best_k-dispatch	0.000	0.000	0.001
hierarchical_partition	0.056	0.006	0.063
knitr_add_tab_item	0	0	0
knitr_insert_tabs	0.001	0.000	0.000
max_depth-HierarchicalPartition-method	0.024	0.008	0.031
membership_heatmap-ConsensusPartition-method	0.614	0.019	0.646
plot_ecdf-ConsensusPartition-method	0.054	0.010	0.065
register_NMF	0.001	0.000	0.000
register_SOM	0	0	0
register_partition_methods	0.244	0.006	0.254
register_top_value_methods	0.051	0.042	0.065
relabel_class	0.004	0.004	0.009
remove_partition_methods	0.001	0.000	0.000
remove_top_value_methods	0.001	0.000	0.001
run_all_consensus_partition_methods	0.096	0.021	0.118
select_partition_number-ConsensusPartition-method	0.085	0.018	0.104
show-ConsensusPartition-method	0.001	0.000	0.000
show-ConsensusPartitionList-method	0	0	0
show-HierarchicalPartition-method	0.061	0.012	0.073
show-dispatch	0	0	0
submit_to_david	0	0	0
test_between_factors	0.018	0.002	0.020
test_to_known_factors-ConsensusPartition-method	0.108	0.015	0.123
test_to_known_factors-ConsensusPartitionList-method	0.124	0.016	0.143
test_to_known_factors-HierarchicalPartition-method	0.033	0.009	0.043
test_to_known_factors-dispatch	0	0	0
top_elements_overlap	0.059	0.007	0.066
top_rows_heatmap-ConsensusPartitionList-method	0	0	0
top_rows_heatmap-dispatch	0.001	0.001	0.000
top_rows_heatmap-matrix-method	3.502	0.281	3.738
top_rows_overlap-ConsensusPartitionList-method	0.141	0.015	0.161
top_rows_overlap-dispatch	0.001	0.000	0.000
top_rows_overlap-matrix-method	2.191	0.219	2.092
venn_euler	0.749	0.021	0.748