Helder Nakaya
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/CEMiTool |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8dd13b4 |
| git_last_commit_date: 2023-04-25 10:55:40 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:59 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 301/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CEMiTool 1.24.0 (landing page) Helder Nakaya
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the CEMiTool package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CEMiTool |
| Version: 1.24.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CEMiTool.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CEMiTool_1.24.0.tar.gz |
| StartedAt: 2023-10-16 00:26:54 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 00:31:15 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 261.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CEMiTool.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CEMiTool.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings CEMiTool_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/CEMiTool.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CEMiTool/DESCRIPTION' ... OK
* this is package 'CEMiTool' version '1.24.0'
* 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 ... OK
* checking for portable file names ... 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 10.25 0.20 10.52
plot_interactions 8.07 0.17 8.25
* 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
'F:/biocbuild/bbs-3.17-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.
CEMiTool.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL CEMiTool ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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)
CEMiTool.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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 13 | SKIP 0 | PASS 105 ]
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 105 ]
>
> proc.time()
user system elapsed
25.46 1.46 27.00
CEMiTool.Rcheck/CEMiTool-Ex.timings
| name | user | system | elapsed | |
| CEMiTool-class | 0.00 | 0.02 | 0.02 | |
| adj_data | 0.24 | 0.01 | 0.25 | |
| cem | 0.01 | 0.02 | 0.03 | |
| cemitool | 10.25 | 0.20 | 10.52 | |
| expr0 | 0 | 0 | 0 | |
| expr_data | 0.09 | 0.02 | 0.11 | |
| filter_expr | 0.15 | 0.01 | 0.16 | |
| find_modules | 1.60 | 0.05 | 1.65 | |
| fit_data | 1.60 | 0.01 | 1.61 | |
| generate_report | 0 | 0 | 0 | |
| get_adj | 0.09 | 0.02 | 0.11 | |
| get_beta_data | 0.69 | 0.00 | 0.68 | |
| get_cemitool_r2_beta | 1.55 | 0.01 | 1.57 | |
| get_connectivity | 1.61 | 0.00 | 1.61 | |
| get_hubs | 0.01 | 0.00 | 0.01 | |
| get_merged_mods | 0.81 | 0.05 | 0.86 | |
| get_mods | 0.74 | 0.01 | 0.75 | |
| get_phi | 1.67 | 0.00 | 1.67 | |
| gsea_data | 2.42 | 0.03 | 2.46 | |
| interactions_data | 0.25 | 0.02 | 3.70 | |
| mod_colors | 0.02 | 0.00 | 0.01 | |
| mod_gene_num | 0.06 | 0.00 | 0.07 | |
| mod_gsea | 1.31 | 0.00 | 1.31 | |
| mod_names | 0.05 | 0.00 | 0.05 | |
| mod_ora | 2.50 | 0.03 | 3.69 | |
| mod_summary | 0.14 | 0.00 | 0.14 | |
| module_genes | 0.01 | 0.00 | 0.02 | |
| new_cem | 0.02 | 0.02 | 0.03 | |
| nmodules | 0.03 | 0.00 | 0.03 | |
| ora_data | 1.83 | 0.08 | 1.90 | |
| plot_beta_r2 | 0.14 | 0.01 | 0.16 | |
| plot_gsea | 1.37 | 0.03 | 1.40 | |
| plot_hist | 0.31 | 0.00 | 0.31 | |
| plot_interactions | 8.07 | 0.17 | 8.25 | |
| plot_mean_k | 0.18 | 0.00 | 0.19 | |
| plot_mean_var | 0.33 | 0.02 | 0.39 | |
| plot_ora | 2.96 | 0.06 | 3.02 | |
| plot_profile | 1.76 | 0.06 | 2.09 | |
| plot_qq | 0.49 | 0.02 | 0.50 | |
| plot_sample_tree | 0.68 | 0.01 | 1.24 | |
| read_gmt | 0.49 | 0.02 | 0.50 | |
| sample_annot | 0.01 | 0.00 | 0.01 | |
| sample_annotation | 0.02 | 0.01 | 0.03 | |
| save_plots | 0.03 | 0.00 | 0.03 | |
| select_genes | 0.17 | 0.00 | 0.18 | |
| show_plot | 0.14 | 0.00 | 0.14 | |
| write_files | 0.47 | 0.03 | 0.50 | |