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BioC 3.6: CHECK report for CEMiTool on tokay1

This page was generated on 2017-08-16 13:38:19 -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: rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_0.99.8.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_0.99.8.tar.gz
StartedAt: 2017-08-15 22:16:11 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:23:13 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 422.3 seconds
RetCode: 0
Status:  OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CEMiTool.buildbin-libdir CEMiTool.Rcheck && mkdir CEMiTool.buildbin-libdir CEMiTool.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CEMiTool.buildbin-libdir CEMiTool_0.99.8.tar.gz >CEMiTool.Rcheck\00install.out 2>&1 && cp CEMiTool.Rcheck\00install.out CEMiTool-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CEMiTool.buildbin-libdir --install="check:CEMiTool-install.out" --force-multiarch --no-vignettes --timings CEMiTool_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CEMiTool.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '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 whether package 'CEMiTool' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    doc       1.2Mb
    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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plot_interactions 11.32   0.13   11.44
generate_report    3.39   0.34   25.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plot_interactions 11.08   0.17   11.25
find_modules       6.10   0.02    6.12
generate_report    5.14   0.36   19.03
plot_ora           5.30   0.00    5.29
plot_gsea          5.15   0.00    5.16
* 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-3.6-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.


CEMiTool.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'CEMiTool' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_0.99.8.zip
* DONE (CEMiTool)

CEMiTool.Rcheck/examples_i386/CEMiTool-Ex.timings:

nameusersystemelapsed
CEMiTool-class0.020.000.02
cem0.030.000.04
cemitool000
cemoverlap000
expr0.000.010.01
expr_data0.030.000.03
filter_expr0.340.030.38
find_modules3.690.053.73
generate_report 3.39 0.3425.99
get_hubs0.030.000.03
gsea_data3.360.023.37
interactions_data0.670.050.74
mod_colors0.020.010.03
mod_gsea3.200.023.22
mod_ora3.340.063.41
mod_summary0.050.001.95
module_genes0.030.010.04
module_names0.360.000.36
new_cem0.020.020.03
nmodules0.010.000.02
ora_data3.300.043.34
plot_beta_r20.700.000.71
plot_gsea4.590.004.59
plot_interactions11.32 0.1311.44
plot_mean_k0.290.000.30
plot_ora4.350.094.68
plot_profile1.840.031.88
read_gmt0.860.000.86
sample_annot000
sample_annotation0.030.000.03
show_plot0.250.000.25
write_files0.030.000.06

CEMiTool.Rcheck/examples_x64/CEMiTool-Ex.timings:

nameusersystemelapsed
CEMiTool-class0.030.000.03
cem0.030.020.05
cemitool000
cemoverlap000
expr000
expr_data0.030.010.05
filter_expr0.440.060.50
find_modules6.100.026.12
generate_report 5.14 0.3619.03
get_hubs0.030.020.05
gsea_data3.730.003.73
interactions_data0.690.030.72
mod_colors0.050.000.05
mod_gsea2.480.002.48
mod_ora3.930.013.95
mod_summary0.050.000.05
module_genes0.030.000.03
module_names0.030.000.03
new_cem0.020.000.02
nmodules0.060.000.06
ora_data3.840.033.87
plot_beta_r20.930.020.94
plot_gsea5.150.005.16
plot_interactions11.08 0.1711.25
plot_mean_k0.340.000.35
plot_ora5.300.005.29
plot_profile3.200.003.21
read_gmt1.520.001.51
sample_annot000
sample_annotation0.010.020.03
show_plot0.270.000.27
write_files0.010.010.03