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This page was generated on 2021-06-18 14:06:38 -0400 (Fri, 18 Jun 2021).

CHECK results for CEMiTool on machv2

To the developers/maintainers of the CEMiTool package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CEMiTool.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 271/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.16.0  (landing page)
Helder Nakaya
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/CEMiTool
Branch: RELEASE_3_13
Last Commit: 6cf15bd
Last Changed Date: 2021-05-19 12:29:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CEMiTool
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.16.0.tar.gz
StartedAt: 2021-06-17 16:56:01 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 17:01:39 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 338.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CEMiTool.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CEMiTool_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CEMiTool.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
  ‘as.dist’
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 ‘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
  ‘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
  head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
cemitool          13.147  0.226  13.387
plot_interactions  8.948  0.171   9.125
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/CEMiTool.Rcheck/00check.log’
for details.



Installation output

CEMiTool.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CEMiTool
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> library(CEMiTool)

> test_check('CEMiTool')
[ FAIL 0 | WARN 17 | SKIP 0 | PASS 105 ]
> 
> proc.time()
   user  system elapsed 
 35.049   1.089  36.164 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.0400.0040.044
adj_data0.4110.0200.430
cem0.0460.0090.054
cemitool13.147 0.22613.387
expr00.0010.0010.003
expr_data0.1680.0120.181
filter_expr0.2700.0080.277
find_modules2.0380.0352.074
fit_data2.1470.0242.174
generate_report000
get_adj0.1590.0040.164
get_beta_data0.9230.0170.941
get_cemitool_r2_beta2.2010.0282.232
get_connectivity2.0900.0312.124
get_hubs0.0260.0040.029
get_merged_mods1.0850.0171.103
get_mods0.9090.0160.926
get_phi2.2170.0262.245
gsea_data3.5040.0393.552
interactions_data0.3180.0170.335
mod_colors0.0410.0150.055
mod_gene_num0.1300.0040.135
mod_gsea2.3460.0192.367
mod_names0.0210.0020.023
mod_ora3.4630.1423.607
mod_summary0.1770.0030.180
module_genes0.0430.0100.053
new_cem0.0210.0020.025
nmodules0.0210.0020.024
ora_data3.1500.0963.247
plot_beta_r20.1710.0030.174
plot_gsea2.6670.0152.684
plot_hist0.5090.0030.513
plot_interactions8.9480.1719.125
plot_mean_k0.2100.0030.214
plot_mean_var0.4240.0110.436
plot_ora4.2550.1044.363
plot_profile2.0780.0242.105
plot_qq0.4850.0190.504
plot_sample_tree0.9980.0131.013
read_gmt1.0510.0031.054
sample_annot0.0030.0030.006
sample_annotation0.0220.0030.025
save_plots0.0980.0100.107
select_genes0.2480.0050.254
show_plot0.2150.0050.221
write_files0.6290.0160.645