Helder Nakaya
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CEMiTool |
| Branch: RELEASE_3_8 |
| Last Commit: d4c4ae4 |
| Last Changed Date: 2019-03-15 14:27:37 -0400 (Fri, 15 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:28:07 -0400 (Sat, 13 Apr 2019).
| Package 224/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CEMiTool 1.6.11 Helder Nakaya
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CEMiTool |
| Version: 1.6.11 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CEMiTool_1.6.11.tar.gz |
| StartedAt: 2019-04-13 01:05:28 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:13:31 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 482.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CEMiTool.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CEMiTool_1.6.11.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CEMiTool.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.11'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cem_overlap : <anonymous>: no visible binding for global variable
'splitBy'
cem_overlap: no visible binding for global variable 'object'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable 'gene'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable 'P.Value'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'median'
enrich_mods : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'sd'
flip_vector: no visible global function definition for 'setNames'
makeContMatrix: no visible global function definition for
'model.matrix'
makeLimmaComp: no visible global function definition for 'setNames'
mod_activity : <anonymous>: no visible binding for global variable
'modules'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'gene'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'comparison'
mod_activity : <anonymous> : <anonymous>: no visible global function
definition for 'median'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'logFC'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'module'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'fc_median'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'parameter'
mod_activity : <anonymous> : <anonymous>: no visible binding for global
variable 'value'
mod_activity : <anonymous>: no visible binding for global variable
'new_col'
mod_activity : <anonymous>: no visible binding for global variable
'comparison'
mod_activity : <anonymous>: no visible binding for global variable
'parameter'
mod_activity : <anonymous>: no visible binding for global variable
'value'
mod_activity : <anonymous>: no visible binding for global variable
'module'
mod_compare : <anonymous>: no visible binding for global variable
'modules'
mod_compare: no visible binding for global variable 'first_mod'
mod_compare: no visible binding for global variable 'second_mod'
mod_compare: no visible global function definition for 'p.adjust'
mod_compare: no visible binding for global variable 'Jaccard'
mod_compare: no visible binding for global variable 'Fisherp'
mod_compare: no visible binding for global variable 'fdr'
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable 'value'
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable 'pathway'
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable 'module'
mod_info : <anonymous> : <anonymous>: no visible binding for global
variable 'metric'
mod_info : <anonymous>: no visible binding for global variable 'metric'
mod_info : <anonymous>: no visible binding for global variable
'modules'
mod_info : <anonymous>: no visible binding for global variable 'module'
mod_info: no visible binding for global variable 'value'
mod_info: no visible binding for global variable 'module'
plot_comembership: no visible binding for global variable 'Var1'
plot_comembership: no visible binding for global variable 'Freq'
plot_consensus: no visible global function definition for 'sd'
plot_consensus: no visible binding for global variable 'X1'
plot_consensus: no visible binding for global variable 'Y1'
plot_consensus: no visible binding for global variable 'X2'
plot_consensus: no visible binding for global variable 'Y2'
plot_consensus: no visible binding for global variable 'Communities'
plot_similarity: no visible binding for global variable 'X1'
plot_similarity: no visible binding for global variable 'Y1'
plot_similarity: no visible binding for global variable 'X2'
plot_similarity: no visible binding for global variable 'Y2'
plot_similarity: no visible binding for global variable 'Weight'
plot_similarity: no visible binding for global variable 'Names'
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
'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 : <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.. := Communities Fisherp Freq Jaccard Mean
Names P.Value Var1 Variance Weight X1 X2 Y1 Y2 as.dist comparison
data dev.off dist fc_median fdr first_mod gene hclust head logFC
median metric model.matrix module modules new_col num_genes object
p.adjust parameter pathway sd second_mod setNames splitBy tail value
var
Consider adding
importFrom("grDevices", "dev.off")
importFrom("stats", "as.dist", "dist", "hclust", "median",
"model.matrix", "p.adjust", "sd", "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
cemitool 10.82 0.19 11.05
plot_interactions 10.04 0.14 10.25
ora_data 9.63 0.14 9.77
plot_ora 8.56 0.01 8.57
mod_ora 8.00 0.11 8.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cemitool 9.15 0.25 9.40
plot_interactions 8.25 0.09 8.35
plot_ora 7.80 0.07 7.88
mod_ora 7.47 0.09 7.56
ora_data 6.97 0.00 6.97
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/CEMiTool_1.6.11.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.6.11.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.6.11.zip && rm CEMiTool_1.6.11.tar.gz CEMiTool_1.6.11.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 4060k 100 4060k 0 0 51.1M 0 --:--:-- --:--:-- --:--:-- 53.5M
install for i386
* installing *source* package 'CEMiTool' ...
** 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
cem_overlap html
cemitool html
diagnostic_report html
enrich_mods 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
makeContMatrix html
makeLimmaComp html
mod_activity html
mod_colors html
mod_compare html
mod_gene_num html
mod_gsea html
mod_info 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
outer_join_merge html
overlap_community html
plot_beta_r2 html
plot_comembership html
plot_consensus 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
plot_similarity html
read_gmt html
sample_annot html
sample_annotation html
save_plots html
select_genes html
show-CEMiTool-method html
show_plot html
stat_overlap_mods html
vst html
write_files html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.6.11.zip
* DONE (CEMiTool)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
CEMiTool.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 106 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
36.17 1.04 37.14
|
CEMiTool.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 106 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
34.73 0.82 35.45
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CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings
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CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings
|