Package: cola

Version: 1.2.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cola_1.2.1.tar.gz

StartedAt: 2020-04-15 06:15:39 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:17:56 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 136.6 seconds

RetCode: 0

Status:  OK

CheckDir: cola.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cola_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/cola.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.1’
* 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                         35.892  0.128  36.183
collect_plots-ConsensusPartitionList-method 11.676  0.140  11.858
* 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-3.10-bioc/meat/cola.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL cola
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o cola.so RcppExports.o cal_consensus_mat.o pdist.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  2.476   0.064   2.567 

name	user	system	elapsed
ATC	0.164	0.008	0.173
ConsensusPartition-class	0	0	0
ConsensusPartitionList-class	0.000	0.000	0.001
Extract.ConsensusPartitionList	0.568	0.004	0.580
ExtractExtract.ConsensusPartitionList	0.156	0.008	0.165
FCC	0.180	0.012	0.192
PAC	0.160	0.008	0.172
aPAC	0.160	0.016	0.176
adjust_matrix	0.008	0.000	0.007
adjust_outlier	0.000	0.000	0.001
all_partition_methods	0.000	0.004	0.002
all_top_value_methods	0	0	0
cola	0.040	0.000	0.052
cola_opt	0.028	0.012	0.043
cola_report-ConsensusPartition-method	0	0	0
cola_report-ConsensusPartitionList-method	0	0	0
cola_report-dispatch	0.000	0.000	0.001
cola_rl	0.184	0.008	0.194
collect_classes-ConsensusPartition-method	2.056	0.004	2.066
collect_classes-ConsensusPartitionList-method	4.452	0.016	4.500
collect_classes-dispatch	0	0	0
collect_plots-ConsensusPartition-method	0.004	0.000	0.000
collect_plots-ConsensusPartitionList-method	11.676	0.140	11.858
collect_plots-dispatch	0	0	0
collect_stats-ConsensusPartition-method	0	0	0
collect_stats-ConsensusPartitionList-method	1.112	0.004	1.118
collect_stats-dispatch	0	0	0
colnames-ConsensusPartition-method	0.004	0.000	0.000
colnames-ConsensusPartitionList-method	0	0	0
colnames-dispatch	0.000	0.000	0.001
compare_signatures-ConsensusPartition-method	0	0	0
concordance	0.156	0.008	0.162
consensus_heatmap-ConsensusPartition-method	0.680	0.016	0.699
consensus_partition	35.892	0.128	36.183
correspond_between_rankings	0.084	0.000	0.084
correspond_between_two_rankings	0.040	0.004	0.044
dim.ConsensusPartition	0.000	0.000	0.001
dim.ConsensusPartitionList	0.000	0.000	0.001
dimension_reduction-ConsensusPartition-method	2.040	0.016	2.059
dimension_reduction-dispatch	0	0	0
dimension_reduction-matrix-method	0	0	0
find_best_km	0	0	0
functional_enrichment-ANY-method	0.004	0.000	0.000
functional_enrichment-ConsensusPartition-method	0	0	0
functional_enrichment-ConsensusPartitionList-method	0	0	0
functional_enrichment-dispatch	0	0	0
get_anno-ConsensusPartition-method	0	0	0
get_anno-ConsensusPartitionList-method	0.000	0.000	0.001
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	0	0
get_classes-ConsensusPartition-method	0.160	0.012	0.170
get_classes-ConsensusPartitionList-method	0.164	0.008	0.173
get_classes-dispatch	0	0	0
get_consensus-ConsensusPartition-method	0.160	0.028	0.190
get_matrix-ConsensusPartition-method	0.168	0.020	0.188
get_matrix-ConsensusPartitionList-method	0.168	0.016	0.186
get_matrix-dispatch	0.000	0.000	0.001
get_membership-ConsensusPartition-method	0.192	0.028	0.217
get_membership-ConsensusPartitionList-method	0.144	0.020	0.163
get_membership-dispatch	0	0	0
get_param-ConsensusPartition-method	0.188	0.004	0.191
get_signatures-ConsensusPartition-method	0	0	0
get_stats-ConsensusPartition-method	0.160	0.004	0.164
get_stats-ConsensusPartitionList-method	0.168	0.004	0.170
get_stats-dispatch	0	0	0
is_best_k-ConsensusPartition-method	0	0	0
is_best_k-ConsensusPartitionList-method	0	0	0
is_best_k-dispatch	0.000	0.000	0.001
is_stable_k-ConsensusPartition-method	0	0	0
is_stable_k-ConsensusPartitionList-method	0	0	0
is_stable_k-dispatch	0	0	0
knitr_add_tab_item	0	0	0
knitr_insert_tabs	0	0	0
map_to_entrez_id	0	0	0
membership_heatmap-ConsensusPartition-method	0.824	0.004	0.832
ncol-ConsensusPartition-method	0	0	0
ncol-ConsensusPartitionList-method	0	0	0
ncol-dispatch	0	0	0
nrow-ConsensusPartition-method	0	0	0
nrow-ConsensusPartitionList-method	0	0	0
nrow-dispatch	0	0	0
plot_ecdf-ConsensusPartition-method	0.180	0.004	0.184
recalc_stats	0	0	0
register_NMF	0.000	0.000	0.001
register_SOM	0.000	0.004	0.000
register_partition_methods	0.344	0.144	0.510
register_top_value_methods	0.024	0.000	0.025
relabel_class	0.016	0.000	0.014
remove_partition_methods	0	0	0
remove_top_value_methods	0	0	0
rownames-ConsensusPartition-method	0	0	0
rownames-ConsensusPartitionList-method	0	0	0
rownames-dispatch	0	0	0
run_all_consensus_partition_methods	0.188	0.000	0.187
select_partition_number-ConsensusPartition-method	0.148	0.016	0.162
show-ConsensusPartition-method	0	0	0
show-ConsensusPartitionList-method	0	0	0
show-dispatch	0	0	0
submit_to_david	0	0	0
suggest_best_k-ConsensusPartition-method	0.144	0.004	0.152
suggest_best_k-ConsensusPartitionList-method	0.156	0.012	0.173
suggest_best_k-dispatch	0	0	0
test_between_factors	0.008	0.008	0.015
test_to_known_factors-ConsensusPartition-method	0.192	0.004	0.197
test_to_known_factors-ConsensusPartitionList-method	0.468	0.012	0.479
test_to_known_factors-dispatch	0	0	0
top_elements_overlap	0.096	0.004	0.103
top_rows_heatmap-ConsensusPartitionList-method	0	0	0
top_rows_heatmap-dispatch	0	0	0
top_rows_heatmap-matrix-method	2.984	0.072	3.068
top_rows_overlap-ConsensusPartitionList-method	0.368	0.008	0.376
top_rows_overlap-dispatch	0	0	0
top_rows_overlap-matrix-method	0.232	0.000	0.231