Helder Nakaya
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CEMiTool |
| Branch: RELEASE_3_9 |
| Last Commit: 295c7f1 |
| Last Changed Date: 2019-07-10 21:52:25 -0400 (Wed, 10 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:39:03 -0400 (Wed, 16 Oct 2019).
| Package 237/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CEMiTool 1.8.3 Helder Nakaya
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CEMiTool |
| Version: 1.8.3 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CEMiTool_1.8.3.tar.gz |
| StartedAt: 2019-10-16 02:32:44 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:39:53 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 429.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CEMiTool.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CEMiTool_1.8.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CEMiTool.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.8.3'
* 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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespaces in Imports field not imported from:
'GeneOverlap' 'RColorBrewer' 'ff' 'ffbase' 'gRbase' 'limma' 'plyr'
'tidyr'
All declared Imports should be used.
* 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 : : 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 : : 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 : : 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_interactions 10.75 0.16 10.90
cemitool 8.97 0.15 9.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cemitool 10.48 0.16 10.67
plot_interactions 8.84 0.11 8.96
plot_ora 5.03 0.11 5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.
CEMiTool.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CEMiTool_1.8.3.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.8.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.8.3.zip && rm CEMiTool_1.8.3.tar.gz CEMiTool_1.8.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4048k 100 4048k 0 0 14.7M 0 --:--:-- --:--:-- --:--:-- 15.1M
install for i386
* 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
install for x64
* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.8.3.zip
* DONE (CEMiTool)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked
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CEMiTool.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
38.64 1.45 41.01
|
CEMiTool.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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')
== testthat results ===========================================================
[ OK: 105 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
>
> proc.time()
user system elapsed
31.67 0.81 32.50
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CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings
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CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings
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