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CHECK report for CEMiTool on malbec1

This page was generated on 2020-04-15 12:13:01 -0400 (Wed, 15 Apr 2020).

Package 251/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.10.2
Helder Nakaya
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_10
Last Commit: b2830d1
Last Changed Date: 2020-03-27 11:45:16 -0400 (Fri, 27 Mar 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CEMiTool
Version: 1.10.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CEMiTool_1.10.2.tar.gz
StartedAt: 2020-04-15 05:00:36 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:05:33 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 296.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CEMiTool_1.10.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CEMiTool.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 ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.10.2’
* 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  6.5Mb
  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
flip_vector: no visible global function definition for ‘setNames’
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.. := Mean Variance as.dist data dev.off dist
  hclust head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "hclust", "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          13.844  0.092  14.007
plot_interactions 10.220  0.088  10.403
gsea_data          7.720  0.276   5.388
plot_gsea          7.808  0.016   5.378
mod_gsea           6.408  0.016   4.047
write_files        5.156  0.012   2.369
plot_ora           4.968  0.008   5.018
* 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-3.10-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.



Installation output

CEMiTool.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CEMiTool
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘CEMiTool’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CEMiTool)

Tests output

CEMiTool.Rcheck/tests/testthat.Rout


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)
> library(CEMiTool)

> test_check('CEMiTool')
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 105 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 56.248   0.716  44.412 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0120.0080.021
adj_data0.3080.0000.309
cem0.0240.0000.023
cemitool13.844 0.09214.007
expr00.0000.0000.001
expr_data0.2400.0000.238
filter_expr0.2960.0000.297
find_modules2.1520.0042.160
fit_data1.8680.0001.872
generate_report0.0000.0000.001
get_adj0.1640.0000.164
get_beta_data0.8400.0000.858
get_cemitool_r2_beta2.1120.0042.120
get_connectivity1.6960.0001.697
get_hubs0.020.000.02
get_merged_mods1.1800.0041.199
get_mods0.9040.0040.909
get_phi1.8080.0001.807
gsea_data7.7200.2765.388
interactions_data0.4440.0160.474
mod_colors0.0280.0000.028
mod_gene_num0.0840.0040.090
mod_gsea6.4080.0164.047
mod_names0.0480.0000.050
mod_ora3.5120.0083.527
mod_summary2.2440.0080.780
module_genes0.0320.0040.034
new_cem0.0200.0000.023
nmodules0.0200.0040.027
ora_data3.5040.0003.523
plot_beta_r20.1920.0000.189
plot_gsea7.8080.0165.378
plot_hist0.5800.0040.584
plot_interactions10.220 0.08810.403
plot_mean_k0.2800.0000.364
plot_mean_var0.5640.0280.594
plot_ora4.9680.0085.018
plot_profile2.9400.0042.958
plot_qq0.6320.0040.655
plot_sample_tree0.8280.0080.851
read_gmt0.9880.0000.995
sample_annot0.0040.0000.003
sample_annotation0.0200.0040.023
save_plots0.0560.0000.056
select_genes0.3080.0040.317
show_plot0.2400.0040.249
write_files5.1560.0122.369