Package: cola

Version: 1.0.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cola_1.0.1.tar.gz

StartedAt: 2019-10-16 00:42:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:45:21 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 151.7 seconds

RetCode: 0

Status:  OK

CheckDir: cola.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cola_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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                           32.281  0.098  33.110
collect_plots-ConsensusPartitionList-method   11.703  0.188  11.892
dimension_reduction-ConsensusPartition-method  3.829  1.757   3.877
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/cola.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL cola
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cal_consensus_mat.cpp -o cal_consensus_mat.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pdist.cpp -o pdist.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o cola.so RcppExports.o cal_consensus_mat.o pdist.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.499   0.078   1.872 

name	user	system	elapsed
ATC	0.170	0.012	0.182
ConsensusPartition-class	0	0	0
ConsensusPartitionList-class	0	0	0
Extract.ConsensusPartitionList	0.601	0.032	0.633
Extract.HierarchicalPartition	0.141	0.004	0.145
ExtractExtract.ConsensusPartitionList	0.302	0.016	0.317
ExtractExtract.HierarchicalPartition	0.086	0.004	0.090
FCC	0.285	0.032	0.317
GO_enrichment-ANY-method	0	0	0
GO_enrichment-ConsensusPartition-method	0	0	0
GO_enrichment-ConsensusPartitionList-method	0	0	0
GO_enrichment-HierarchicalPartition-method	0	0	0
GO_enrichment-dispatch	0	0	0
HierarchicalPartition-class	0.001	0.000	0.000
PAC	0.358	0.016	0.373
aPAC	0.284	0.016	0.300
adjust_matrix	0.003	0.000	0.004
adjust_outlier	0.001	0.000	0.001
all_leaves-HierarchicalPartition-method	0.096	0.000	0.095
all_nodes-HierarchicalPartition-method	0.087	0.008	0.095
all_partition_methods	0.001	0.000	0.001
all_top_value_methods	0	0	0
cola	0.032	0.000	0.032
cola_opt	0	0	0
cola_report-ConsensusPartition-method	0	0	0
cola_report-ConsensusPartitionList-method	0	0	0
cola_report-HierarchicalPartition-method	0	0	0
cola_report-dispatch	0.001	0.000	0.000
cola_rh	0.121	0.004	0.124
cola_rl	0.387	0.024	0.411
collect_classes-ConsensusPartition-method	2.247	0.012	2.259
collect_classes-ConsensusPartitionList-method	4.067	0.028	4.095
collect_classes-HierarchicalPartition-method	1.435	0.016	1.450
collect_classes-dispatch	0	0	0
collect_plots-ConsensusPartition-method	0	0	0
collect_plots-ConsensusPartitionList-method	11.703	0.188	11.892
collect_plots-HierarchicalPartition-method	3.112	0.000	3.111
collect_plots-dispatch	0	0	0
collect_stats-ConsensusPartition-method	0.001	0.000	0.000
collect_stats-ConsensusPartitionList-method	0.884	0.008	0.891
collect_stats-dispatch	0	0	0
colnames-ConsensusPartition-method	0	0	0
colnames-ConsensusPartitionList-method	0	0	0
colnames-HierarchicalPartition-method	0	0	0
colnames-dispatch	0	0	0
compare_signatures-ConsensusPartition-method	0.001	0.000	0.000
concordance	0.276	0.004	0.279
consensus_heatmap-ConsensusPartition-method	0.821	0.016	0.836
consensus_partition	32.281	0.098	33.110
correspond_between_rankings	0.101	0.000	0.101
correspond_between_two_rankings	0.04	0.00	0.04
dim.ConsensusPartition	0	0	0
dim.ConsensusPartitionList	0.001	0.000	0.001
dim.HierarchicalPartition	0	0	0
dimension_reduction-ConsensusPartition-method	3.829	1.757	3.877
dimension_reduction-HierarchicalPartition-method	0.334	0.004	0.341
dimension_reduction-dispatch	0.000	0.000	0.001
dimension_reduction-matrix-method	0	0	0
find_best_km	0	0	0
get_anno-ConsensusPartition-method	0.001	0.000	0.000
get_anno-ConsensusPartitionList-method	0.001	0.000	0.000
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	0.001	0.000
get_anno_col-dispatch	0.000	0.000	0.001
get_classes-ConsensusPartition-method	0.265	0.021	0.287
get_classes-ConsensusPartitionList-method	0.253	0.032	0.290
get_classes-HierarchicalPartition-method	0.095	0.000	0.096
get_classes-dispatch	0.000	0.000	0.001
get_consensus-ConsensusPartition-method	0.265	0.028	0.293
get_hierarchy	0	0	0
get_matrix-ConsensusPartition-method	0.267	0.020	0.319
get_matrix-ConsensusPartitionList-method	0.288	0.024	0.352
get_matrix-HierarchicalPartition-method	0	0	0
get_matrix-dispatch	0	0	0
get_membership-ConsensusPartition-method	0.324	0.052	0.385
get_membership-ConsensusPartitionList-method	0.245	0.027	0.485
get_membership-dispatch	0.001	0.000	0.000
get_param-ConsensusPartition-method	0.282	0.032	0.361
get_signatures-ConsensusPartition-method	0	0	0
get_signatures-HierarchicalPartition-method	0	0	0
get_signatures-dispatch	0.001	0.000	0.000
get_stats-ConsensusPartition-method	0.281	0.020	0.304
get_stats-ConsensusPartitionList-method	0.555	0.036	0.607
get_stats-dispatch	0	0	0
hierarchical_partition	0.115	0.000	0.116
knitr_add_tab_item	0	0	0
knitr_insert_tabs	0	0	0
map_to_entrez_id	0.000	0.000	0.001
max_depth-HierarchicalPartition-method	0.083	0.004	0.088
membership_heatmap-ConsensusPartition-method	0.796	0.019	0.840
ncol-ConsensusPartition-method	0	0	0
ncol-ConsensusPartitionList-method	0.000	0.000	0.001
ncol-HierarchicalPartition-method	0.001	0.000	0.000
ncol-dispatch	0	0	0
nrow-ConsensusPartition-method	0	0	0
nrow-ConsensusPartitionList-method	0.000	0.000	0.001
nrow-HierarchicalPartition-method	0.001	0.000	0.000
nrow-dispatch	0	0	0
plot_ecdf-ConsensusPartition-method	0.251	0.032	0.282
recalc_stats	0	0	0
register_NMF	0	0	0
register_SOM	0	0	0
register_partition_methods	0.475	0.143	0.793
register_top_value_methods	0.022	0.000	0.022
relabel_class	0.004	0.000	0.003
remove_partition_methods	0	0	0
remove_top_value_methods	0.001	0.000	0.000
rownames-ConsensusPartition-method	0	0	0
rownames-ConsensusPartitionList-method	0	0	0
rownames-HierarchicalPartition-method	0.000	0.000	0.001
rownames-dispatch	0	0	0
run_all_consensus_partition_methods	0.283	0.012	0.298
select_partition_number-ConsensusPartition-method	0.262	0.023	0.327
show-ConsensusPartition-method	0	0	0
show-ConsensusPartitionList-method	0.001	0.000	0.001
show-HierarchicalPartition-method	0.119	0.000	0.137
show-dispatch	0	0	0
submit_to_david	0	0	0
suggest_best_k-ConsensusPartition-method	0.252	0.028	0.295
suggest_best_k-ConsensusPartitionList-method	0.282	0.008	0.295
suggest_best_k-HierarchicalPartition-method	0.086	0.008	0.094
suggest_best_k-dispatch	0.001	0.000	0.000
test_between_factors	0.015	0.000	0.014
test_to_known_factors-ConsensusPartition-method	0.271	0.027	0.335
test_to_known_factors-ConsensusPartitionList-method	0.481	0.016	0.622
test_to_known_factors-HierarchicalPartition-method	0.094	0.004	0.099
test_to_known_factors-dispatch	0	0	0
top_elements_overlap	0.105	0.004	0.137
top_rows_heatmap-ConsensusPartitionList-method	0	0	0
top_rows_heatmap-dispatch	0	0	0
top_rows_heatmap-matrix-method	2.507	0.091	2.676
top_rows_overlap-ConsensusPartitionList-method	0.454	0.024	0.504
top_rows_overlap-dispatch	0	0	0
top_rows_overlap-matrix-method	0.312	0.000	0.369