Helder Nakaya
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CEMiTool |
| Branch: RELEASE_3_8 |
| Last Commit: d4c4ae4 |
| Last Changed Date: 2019-03-15 14:27:37 -0400 (Fri, 15 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:56 -0400 (Tue, 16 Apr 2019).
| Package 224/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CEMiTool 1.6.11 Helder Nakaya
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CEMiTool |
| Version: 1.6.11 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CEMiTool_1.6.11.tar.gz |
| StartedAt: 2019-04-15 22:45:10 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:49:46 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 275.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CEMiTool.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CEMiTool_1.6.11.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CEMiTool.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.6.11’
* package encoding: UTF-8
* 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 ‘CEMiTool’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 3.1Mb
extdata 2.8Mb
* 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 ... NOTE
cem_overlap : <anonymous>: no visible binding for global variable
‘splitBy’
cem_overlap: no visible binding for global variable ‘object’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable ‘gene’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable ‘P.Value’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘median’
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘sd’
flip_vector: no visible global function definition for ‘setNames’
makeContMatrix: no visible global function definition for
‘model.matrix’
makeLimmaComp: no visible global function definition for ‘setNames’
mod_activity : <anonymous>: no visible binding for global variable
‘modules’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘gene’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘comparison’
mod_activity : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘logFC’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘module’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘fc_median’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘parameter’
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
mod_activity : <anonymous>: no visible binding for global variable
‘new_col’
mod_activity : <anonymous>: no visible binding for global variable
‘comparison’
mod_activity : <anonymous>: no visible binding for global variable
‘parameter’
mod_activity : <anonymous>: no visible binding for global variable
‘value’
mod_activity : <anonymous>: no visible binding for global variable
‘module’
mod_compare : <anonymous>: no visible binding for global variable
‘modules’
mod_compare: no visible binding for global variable ‘first_mod’
mod_compare: no visible binding for global variable ‘second_mod’
mod_compare: no visible global function definition for ‘p.adjust’
mod_compare: no visible binding for global variable ‘Jaccard’
mod_compare: no visible binding for global variable ‘Fisherp’
mod_compare: no visible binding for global variable ‘fdr’
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable ‘pathway’
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable ‘module’
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable ‘metric’
mod_info : <anonymous>: no visible binding for global variable
‘modules’
mod_info : <anonymous>: no visible binding for global variable ‘module’
mod_info: no visible binding for global variable ‘value’
mod_info: no visible binding for global variable ‘module’
plot_comembership: no visible binding for global variable ‘Var1’
plot_comembership: no visible binding for global variable ‘Freq’
plot_consensus: no visible global function definition for ‘sd’
plot_consensus: no visible binding for global variable ‘X1’
plot_consensus: no visible binding for global variable ‘Y1’
plot_consensus: no visible binding for global variable ‘X2’
plot_consensus: no visible binding for global variable ‘Y2’
plot_consensus: no visible binding for global variable ‘Communities’
plot_similarity: no visible binding for global variable ‘X1’
plot_similarity: no visible binding for global variable ‘Y1’
plot_similarity: no visible binding for global variable ‘X2’
plot_similarity: no visible binding for global variable ‘Y2’
plot_similarity: no visible binding for global variable ‘Weight’
plot_similarity: no visible binding for global variable ‘Names’
select_genes: no visible global function definition for ‘var’
get_hubs,CEMiTool : <anonymous>: no visible global function definition
for ‘head’
get_merged_mods,CEMiTool: no visible global function definition for
‘hclust’
get_merged_mods,CEMiTool: no visible global function definition for
‘as.dist’
get_mods,CEMiTool: no visible global function definition for ‘hclust’
get_mods,CEMiTool: no visible global function definition for ‘as.dist’
get_phi,CEMiTool: no visible global function definition for ‘tail’
get_phi,CEMiTool: no visible global function definition for ‘head’
mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’
mod_gene_num,CEMiTool: no visible binding for global variable
‘num_genes’
mod_summary,CEMiTool: no visible global function definition for ‘:=’
plot_gsea,CEMiTool: no visible global function definition for ‘hclust’
plot_gsea,CEMiTool: no visible global function definition for ‘dist’
plot_mean_var,CEMiTool: no visible binding for global variable ‘var’
plot_mean_var,CEMiTool: no visible binding for global variable ‘Mean’
plot_mean_var,CEMiTool: no visible binding for global variable
‘Variance’
plot_mean_var,CEMiTool: no visible binding for global variable
‘..eq.label..’
plot_mean_var,CEMiTool: no visible binding for global variable
‘..rr.label..’
plot_ora,CEMiTool : <anonymous>: no visible global function definition
for ‘head’
plot_qq,CEMiTool: no visible binding for global variable ‘data’
plot_sample_tree,CEMiTool: no visible global function definition for
‘hclust’
plot_sample_tree,CEMiTool: no visible global function definition for
‘dist’
plot_sample_tree,CEMiTool: no visible global function definition for
‘dev.off’
save_plots,CEMiTool : <anonymous>: no visible global function
definition for ‘dev.off’
save_plots,CEMiTool: no visible global function definition for
‘dev.off’
Undefined global functions or variables:
..eq.label.. ..rr.label.. := Communities Fisherp Freq Jaccard Mean
Names P.Value Var1 Variance Weight X1 X2 Y1 Y2 as.dist comparison
data dev.off dist fc_median fdr first_mod gene hclust head logFC
median metric model.matrix module modules new_col num_genes object
p.adjust parameter pathway sd second_mod setNames splitBy tail value
var
Consider adding
importFrom("grDevices", "dev.off")
importFrom("stats", "as.dist", "dist", "hclust", "median",
"model.matrix", "p.adjust", "sd", "setNames", "var")
importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cemitool 10.648 0.052 10.713
plot_ora 9.492 0.004 9.525
plot_interactions 8.300 0.048 8.352
ora_data 8.008 0.036 8.055
mod_ora 7.140 0.052 7.227
plot_gsea 5.140 0.016 4.217
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘CEMiTool’ ... ** R ** data *** moving datasets to lazyload DB ** exec ** 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 (CEMiTool)
CEMiTool.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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)
> library(CEMiTool)
> test_check('CEMiTool')
══ testthat results ═══════════════════════════════════════════════════════════
OK: 106 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
46.756 0.636 41.035
CEMiTool.Rcheck/CEMiTool-Ex.timings
| name | user | system | elapsed | |
| CEMiTool-class | 0.056 | 0.004 | 0.062 | |
| adj_data | 0.476 | 0.000 | 0.476 | |
| cem | 0.572 | 0.000 | 0.572 | |
| cem_overlap | 0 | 0 | 0 | |
| cemitool | 10.648 | 0.052 | 10.713 | |
| enrich_mods | 0 | 0 | 0 | |
| expr0 | 0.000 | 0.000 | 0.001 | |
| expr_data | 0.116 | 0.000 | 0.116 | |
| filter_expr | 0.152 | 0.004 | 0.156 | |
| find_modules | 1.472 | 0.004 | 1.476 | |
| fit_data | 1.720 | 0.000 | 1.719 | |
| generate_report | 0 | 0 | 0 | |
| get_adj | 0.128 | 0.000 | 0.129 | |
| get_beta_data | 0.604 | 0.004 | 0.605 | |
| get_cemitool_r2_beta | 1.500 | 0.004 | 1.507 | |
| get_connectivity | 2.016 | 0.000 | 2.018 | |
| get_hubs | 0.028 | 0.000 | 0.027 | |
| get_merged_mods | 1.16 | 0.00 | 1.16 | |
| get_mods | 0.700 | 0.000 | 0.701 | |
| get_phi | 1.476 | 0.000 | 1.477 | |
| gsea_data | 4.316 | 0.088 | 3.506 | |
| interactions_data | 0.432 | 0.020 | 0.451 | |
| makeContMatrix | 0 | 0 | 0 | |
| makeLimmaComp | 0 | 0 | 0 | |
| mod_colors | 0.020 | 0.000 | 0.021 | |
| mod_gene_num | 0.124 | 0.008 | 0.132 | |
| mod_gsea | 4.288 | 0.008 | 3.481 | |
| mod_names | 0.02 | 0.00 | 0.02 | |
| mod_ora | 7.140 | 0.052 | 7.227 | |
| mod_summary | 2.040 | 0.008 | 0.614 | |
| module_genes | 0.032 | 0.000 | 0.028 | |
| new_cem | 0.020 | 0.000 | 0.019 | |
| nmodules | 0.04 | 0.00 | 0.04 | |
| ora_data | 8.008 | 0.036 | 8.055 | |
| overlap_community | 0.000 | 0.000 | 0.001 | |
| plot_beta_r2 | 0.348 | 0.000 | 0.350 | |
| plot_comembership | 0.004 | 0.000 | 0.000 | |
| plot_consensus | 0.000 | 0.000 | 0.001 | |
| plot_gsea | 5.140 | 0.016 | 4.217 | |
| plot_hist | 0.616 | 0.004 | 0.621 | |
| plot_interactions | 8.300 | 0.048 | 8.352 | |
| plot_mean_k | 0.180 | 0.004 | 0.184 | |
| plot_mean_var | 0.332 | 0.008 | 0.340 | |
| plot_ora | 9.492 | 0.004 | 9.525 | |
| plot_profile | 1.824 | 0.000 | 1.825 | |
| plot_qq | 0.332 | 0.000 | 0.332 | |
| plot_sample_tree | 0.480 | 0.004 | 0.483 | |
| plot_similarity | 0 | 0 | 0 | |
| read_gmt | 0.628 | 0.000 | 0.632 | |
| sample_annot | 0.000 | 0.000 | 0.002 | |
| sample_annotation | 0.020 | 0.000 | 0.019 | |
| save_plots | 0.036 | 0.000 | 0.035 | |
| select_genes | 0.184 | 0.000 | 0.186 | |
| show_plot | 0.164 | 0.000 | 0.161 | |
| stat_overlap_mods | 0 | 0 | 0 | |
| write_files | 4.500 | 0.024 | 1.613 | |