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BioC 3.6: CHECK report for CEMiTool on veracruz1

This page was generated on 2017-08-16 13:50:50 -0400 (Wed, 16 Aug 2017).

Package 191/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 0.99.8
Helder Nakaya
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CEMiTool
Last Changed Rev: 131779 / Revision: 131943
Last Changed Date: 2017-08-07 09:45:33 -0400 (Mon, 07 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CEMiTool
Version: 0.99.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CEMiTool_0.99.8.tar.gz
StartedAt: 2017-08-16 00:53:20 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:57:32 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 252.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CEMiTool_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CEMiTool/DESCRIPTION’ ... OK
* this is package ‘CEMiTool’ version ‘0.99.8’
* 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  9.0Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       2.7Mb
    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’
read_gmt: no visible binding for global variable ‘stack’
filter_expr,CEMiTool: no visible global function definition for ‘var’
find_modules,CEMiTool: no visible global function definition for ‘tail’
find_modules,CEMiTool: no visible global function definition for ‘head’
find_modules,CEMiTool: no visible global function definition for
  ‘hclust’
find_modules,CEMiTool: no visible global function definition for
  ‘as.dist’
get_hubs,CEMiTool : <anonymous>: 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_ora,CEMiTool : <anonymous>: no visible global function definition
  for ‘head’
Undefined global functions or variables:
  as.dist cem dist hclust head stack tail var
Consider adding
  importFrom("stats", "as.dist", "dist", "hclust", "var")
  importFrom("utils", "head", "stack", "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
generate_report   11.255  1.268  14.855
plot_interactions 10.726  0.155  11.277
* 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
  ‘/Users/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/CEMiTool-Ex.timings:

nameusersystemelapsed
CEMiTool-class0.0160.0040.021
cem0.0290.0030.037
cemitool0.0010.0000.001
cemoverlap0.0010.0000.000
expr0.0010.0010.002
expr_data0.0320.0020.041
filter_expr0.4240.0230.465
find_modules4.1230.0474.273
generate_report11.255 1.26814.855
get_hubs0.0150.0010.020
gsea_data3.7330.1423.611
interactions_data1.0710.0601.028
mod_colors0.0230.0010.025
mod_gsea3.4600.1283.327
mod_ora3.3880.1303.463
mod_summary0.0410.0070.033
module_genes0.0740.0220.033
module_names0.0770.0170.033
new_cem0.0410.0090.017
nmodules0.0450.0130.020
ora_data3.7830.1103.837
plot_beta_r20.8480.0040.870
plot_gsea4.0980.1753.807
plot_interactions10.726 0.15511.277
plot_mean_k0.3400.0040.350
plot_ora4.3880.1004.657
plot_profile2.2600.0202.369
read_gmt1.1020.0121.157
sample_annot0.0020.0010.004
sample_annotation0.0150.0010.016
show_plot0.2970.0030.310
write_files0.0200.0030.024