Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:16:32 -0400 (Thu, 12 Apr 2018).
Package 199/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CEMiTool 1.0.3 Helder Nakaya
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: CEMiTool |
Version: 1.0.3 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_1.0.3.tar.gz |
StartedAt: 2018-04-11 22:05:28 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:09:37 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 249.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CEMiTool.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CEMiTool_1.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck’ * using R version 3.4.4 (2018-03-15) * 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 ‘1.0.3’ * 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 8.8Mb sub-directories of 1Mb or more: data 3.1Mb doc 2.4Mb 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 loading without being on the library search path ... 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 plot_interaction: no visible binding for global variable ‘cem’ filter_expr,CEMiTool: 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’ 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 cem data dev.off dist hclust head tail var Consider adding importFrom("grDevices", "dev.off") importFrom("stats", "as.dist", "dist", "hclust", "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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plot_interactions 8.648 0.048 8.701 generate_report 7.672 0.844 11.674 * 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-3.6-bioc/meat/CEMiTool.Rcheck/00check.log’ for details.
CEMiTool.Rcheck/00install.out
* installing *source* package ‘CEMiTool’ ... ** R ** data *** moving datasets to lazyload DB ** exec ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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: 86 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 29.356 0.696 30.122
CEMiTool.Rcheck/CEMiTool-Ex.timings
name | user | system | elapsed | |
CEMiTool-class | 0.028 | 0.004 | 0.032 | |
adj_data | 0.172 | 0.000 | 0.174 | |
cem | 0.028 | 0.000 | 0.027 | |
cem_overlap | 0.000 | 0.000 | 0.001 | |
cemitool | 0.000 | 0.000 | 0.001 | |
expr | 0.000 | 0.000 | 0.001 | |
expr_data | 0.284 | 0.004 | 0.289 | |
filter_expr | 0.596 | 0.000 | 0.596 | |
find_modules | 3.408 | 0.004 | 3.435 | |
fit_data | 3.696 | 0.012 | 3.708 | |
generate_report | 7.672 | 0.844 | 11.674 | |
geom_qq | 0.004 | 0.000 | 0.001 | |
get_adj | 0.208 | 0.016 | 0.226 | |
get_beta_data | 1.952 | 0.036 | 1.992 | |
get_cemitool_r2_beta | 2.984 | 0.004 | 2.987 | |
get_connectivity | 3.032 | 0.000 | 3.035 | |
get_hubs | 0.024 | 0.000 | 0.021 | |
get_merged_mods | 1.664 | 0.000 | 1.665 | |
get_mods | 0.460 | 0.004 | 0.464 | |
get_phi | 2.968 | 0.000 | 2.969 | |
gsea_data | 2.660 | 0.064 | 2.744 | |
interactions_data | 0.612 | 0.008 | 0.622 | |
mod_colors | 0.340 | 0.032 | 0.369 | |
mod_gsea | 2.672 | 0.004 | 2.677 | |
mod_names | 0.02 | 0.00 | 0.02 | |
mod_ora | 3.352 | 0.000 | 3.371 | |
mod_summary | 0.044 | 0.000 | 0.044 | |
module_genes | 0.024 | 0.000 | 0.025 | |
new_cem | 0.032 | 0.000 | 0.032 | |
nmodules | 0.02 | 0.00 | 0.02 | |
ora_data | 2.916 | 0.004 | 2.920 | |
plot_beta_r2 | 1.184 | 0.000 | 1.188 | |
plot_gsea | 3.364 | 0.000 | 3.368 | |
plot_hist | 0.836 | 0.008 | 0.845 | |
plot_interactions | 8.648 | 0.048 | 8.701 | |
plot_mean_k | 0.220 | 0.000 | 0.221 | |
plot_mean_var | 0.552 | 0.016 | 0.625 | |
plot_ora | 3.768 | 0.004 | 3.778 | |
plot_profile | 1.7 | 0.0 | 1.7 | |
plot_qq | 2.156 | 0.020 | 2.178 | |
plot_sample_tree | 0.532 | 0.008 | 0.540 | |
read_gmt | 0.528 | 0.000 | 0.526 | |
sample_annot | 0.000 | 0.000 | 0.002 | |
sample_annotation | 0.044 | 0.004 | 0.048 | |
save_plots | 0.056 | 0.000 | 0.056 | |
show_plot | 0.156 | 0.000 | 0.158 | |
write_files | 0.112 | 0.000 | 0.112 | |