Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:12 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CEMiTool on palomino4


To the developers/maintainers of the CEMiTool package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CEMiTool.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 282/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CEMiTool 1.21.0  (landing page)
Helder Nakaya
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CEMiTool
git_branch: master
git_last_commit: c3c8961
git_last_commit_date: 2022-04-26 11:42:23 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CEMiTool
Version: 1.21.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CEMiTool_1.21.0.tar.gz
StartedAt: 2022-06-24 00:03:21 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:07:57 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 275.2 seconds
RetCode: 0
Status:   OK  
CheckDir: CEMiTool.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CEMiTool.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CEMiTool_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CEMiTool.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CEMiTool/DESCRIPTION' ... OK
* this is package 'CEMiTool' version '1.21.0'
* 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  6.5Mb
  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
* 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
flip_vector: no visible global function definition for 'setNames'
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
  'as.dist'
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 '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
  '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 data dev.off dist
  head modules num_genes setNames tail var
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "as.dist", "dist", "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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
cemitool          9.82   0.32   10.16
plot_interactions 8.14   0.10    8.24
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/CEMiTool.Rcheck/00check.log'
for details.



Installation output

CEMiTool.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/CEMiTool_1.21.0.tar.gz && rm -rf CEMiTool.buildbin-libdir && mkdir CEMiTool.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CEMiTool.buildbin-libdir CEMiTool_1.21.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CEMiTool_1.21.0.zip && rm CEMiTool_1.21.0.tar.gz CEMiTool_1.21.0.zip
###
##############################################################################
##############################################################################


  % 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  13.3M      0 --:--:-- --:--:-- --:--:-- 13.4M
only one architecture so ignoring '--merge-multiarch'
* 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
** 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
* MD5 sums
packaged installation of 'CEMiTool' as CEMiTool_1.21.0.zip
* DONE (CEMiTool)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'CEMiTool' successfully unpacked and MD5 sums checked

Tests output

CEMiTool.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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')
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 105 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 105 ]
> 
> proc.time()
   user  system elapsed 
  25.35    1.20   26.48 

Example timings

CEMiTool.Rcheck/CEMiTool-Ex.timings

nameusersystemelapsed
CEMiTool-class0.020.000.02
adj_data0.830.010.84
cem0.020.000.01
cemitool 9.82 0.3210.16
expr0000
expr_data0.150.010.15
filter_expr0.140.020.16
find_modules1.890.011.91
fit_data1.860.041.89
generate_report000
get_adj0.110.000.11
get_beta_data0.840.030.87
get_cemitool_r2_beta1.840.031.88
get_connectivity1.920.031.95
get_hubs0.020.000.02
get_merged_mods101
get_mods0.940.000.93
get_phi1.970.032.00
gsea_data2.070.012.09
interactions_data0.320.000.32
mod_colors0.010.020.03
mod_gene_num0.100.010.11
mod_gsea1.430.001.43
mod_names0.020.000.02
mod_ora2.260.082.36
mod_summary0.140.000.14
module_genes0.020.020.04
new_cem0.010.000.01
nmodules0.020.000.02
ora_data2.190.042.24
plot_beta_r20.140.000.14
plot_gsea2.270.022.28
plot_hist0.360.010.37
plot_interactions8.140.108.24
plot_mean_k0.170.000.17
plot_mean_var0.280.000.34
plot_ora3.610.193.80
plot_profile1.360.031.39
plot_qq0.390.000.39
plot_sample_tree0.750.000.75
read_gmt0.370.040.42
sample_annot0.000.000.02
sample_annotation0.020.000.01
save_plots0.010.020.03
select_genes0.160.000.16
show_plot0.140.000.14
write_files0.410.000.41