Helder Nakaya
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CEMiTool |
| git_branch: master |
| git_last_commit: ca53a22 |
| git_last_commit_date: 2021-10-28 13:59:15 -0400 (Thu, 28 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:09 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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. |
| Package 275/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CEMiTool 1.19.1 (landing page) Helder Nakaya
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CEMiTool |
| Version: 1.19.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CEMiTool.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CEMiTool_1.19.1.tar.gz |
| StartedAt: 2022-03-17 18:41:22 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:45:03 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 221.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CEMiTool.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CEMiTool.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CEMiTool_1.19.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CEMiTool.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CEMiTool/DESCRIPTION' ... OK
* this is package 'CEMiTool' version '1.19.1'
* 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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
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 7.59 0.38 7.96
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.
CEMiTool.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CEMiTool
###
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##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'CEMiTool'
finding HTML links ... done
CEMiTool-class html
adj_data html
cem html
cemitool html
diagnostic_report html
expr0 html
expr_data html
expr_pct_filter html
filter_expr html
find_modules html
fit_data html
generate_report html
get_adj html
get_beta_data html
get_cemitool_r2_beta html
get_connectivity html
get_hubs html
get_merged_mods html
get_mods html
get_phi html
gsea_data html
interactions_data html
mod_colors html
mod_gene_num html
mod_gsea html
mod_names html
mod_ora html
mod_summary html
module_genes html
module_to_gmt html
new_cem html
nmodules html
ora_data html
plot_beta_r2 html
plot_gsea html
plot_hist html
plot_interactions html
plot_mean_k html
plot_mean_var html
plot_ora html
plot_ora_single html
plot_profile html
plot_qq html
plot_sample_tree html
read_gmt html
sample_annot html
sample_annotation html
save_plots html
select_genes html
show-CEMiTool-method html
show_plot html
vst html
write_files html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RcisTarget' is missing or broken
done
CEMiTool.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 18 | SKIP 0 | PASS 105 ]
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 105 ]
>
> proc.time()
user system elapsed
19.95 1.29 21.26
CEMiTool.Rcheck/CEMiTool-Ex.timings
| name | user | system | elapsed | |
| CEMiTool-class | 0.02 | 0.02 | 0.03 | |
| adj_data | 0.15 | 0.03 | 0.18 | |
| cem | 0.02 | 0.01 | 0.04 | |
| cemitool | 7.59 | 0.38 | 7.96 | |
| expr0 | 0 | 0 | 0 | |
| expr_data | 0.11 | 0.00 | 0.11 | |
| filter_expr | 0.13 | 0.02 | 0.14 | |
| find_modules | 1.39 | 0.01 | 1.41 | |
| fit_data | 1.32 | 0.03 | 1.36 | |
| generate_report | 0 | 0 | 0 | |
| get_adj | 0.08 | 0.03 | 0.11 | |
| get_beta_data | 0.56 | 0.00 | 0.56 | |
| get_cemitool_r2_beta | 1.60 | 0.07 | 1.66 | |
| get_connectivity | 1.55 | 0.03 | 1.58 | |
| get_hubs | 0.03 | 0.00 | 0.03 | |
| get_merged_mods | 0.81 | 0.04 | 0.86 | |
| get_mods | 0.83 | 0.02 | 0.84 | |
| get_phi | 1.68 | 0.01 | 1.70 | |
| gsea_data | 2.19 | 0.02 | 2.20 | |
| interactions_data | 0.22 | 0.11 | 0.33 | |
| mod_colors | 0.03 | 0.00 | 0.03 | |
| mod_gene_num | 0.08 | 0.01 | 0.10 | |
| mod_gsea | 1.27 | 0.02 | 1.28 | |
| mod_names | 0.03 | 0.01 | 0.04 | |
| mod_ora | 1.70 | 0.02 | 1.72 | |
| mod_summary | 0.13 | 0.01 | 0.14 | |
| module_genes | 0.01 | 0.02 | 0.03 | |
| new_cem | 0.02 | 0.00 | 0.02 | |
| nmodules | 0.03 | 0.02 | 0.05 | |
| ora_data | 2.48 | 0.06 | 2.54 | |
| plot_beta_r2 | 0.10 | 0.01 | 0.11 | |
| plot_gsea | 1.25 | 0.03 | 1.28 | |
| plot_hist | 0.23 | 0.00 | 0.24 | |
| plot_interactions | 3.95 | 0.35 | 4.34 | |
| plot_mean_k | 0.21 | 0.00 | 0.20 | |
| plot_mean_var | 0.32 | 0.03 | 0.38 | |
| plot_ora | 3.41 | 0.23 | 3.64 | |
| plot_profile | 1.11 | 0.00 | 1.11 | |
| plot_qq | 0.31 | 0.02 | 0.33 | |
| plot_sample_tree | 0.49 | 0.02 | 0.50 | |
| read_gmt | 0.33 | 0.01 | 0.34 | |
| sample_annot | 0 | 0 | 0 | |
| sample_annotation | 0.03 | 0.00 | 0.03 | |
| save_plots | 0.01 | 0.00 | 0.02 | |
| select_genes | 0.11 | 0.03 | 0.14 | |
| show_plot | 0.11 | 0.00 | 0.11 | |
| write_files | 0.31 | 0.03 | 0.34 | |