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This page was generated on 2022-01-19 13:07:03 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 OmicsLonDA on tokay2


To the developers/maintainers of the OmicsLonDA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmicsLonDA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1326/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsLonDA 1.10.0  (landing page)
Ahmed A. Metwally
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/OmicsLonDA
git_branch: RELEASE_3_14
git_last_commit: a145163
git_last_commit_date: 2021-10-26 12:51:17 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OmicsLonDA
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicsLonDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OmicsLonDA_1.10.0.tar.gz
StartedAt: 2022-01-18 23:40:19 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 23:45:47 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 328.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OmicsLonDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicsLonDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OmicsLonDA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/OmicsLonDA.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicsLonDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmicsLonDA' version '1.10.0'
* 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 'OmicsLonDA' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
visualizeFeatureSpline 9.56   0.14    9.70
testStatPermutation    8.43   0.01    8.47
omicslonda             8.26   0.04    8.32
permutationMC          8.08   0.13    8.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
omicslonda             10.93   0.05   10.97
visualizeFeatureSpline 10.00   0.11   10.14
permutationMC           8.36   0.03    8.39
testStatPermutation     7.68   0.01    7.69
* 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: OK


Installation output

OmicsLonDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/OmicsLonDA_1.10.0.tar.gz && rm -rf OmicsLonDA.buildbin-libdir && mkdir OmicsLonDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmicsLonDA.buildbin-libdir OmicsLonDA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL OmicsLonDA_1.10.0.zip && rm OmicsLonDA_1.10.0.tar.gz OmicsLonDA_1.10.0.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
 78 4558k   78 3563k    0     0  4389k      0  0:00:01 --:--:--  0:00:01 4388k
100 4558k  100 4558k    0     0  4823k      0 --:--:-- --:--:-- --:--:-- 4824k

install for i386

* installing *source* package 'OmicsLonDA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OmicsLonDA'
    finding HTML links ... done
    adjustBaseline                          html  
    curveFitting                            html  
    findSigInterval                         html  
    omicslonda                              html  
    omicslonda_data_example                 html  
    permutationMC                           html  
    testStat                                html  
    testStatPermutation                     html  
    visualizeArea                           html  
    visualizeFeature                        html  
    visualizeFeatureSpline                  html  
    visualizeTestStatHistogram              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 'OmicsLonDA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsLonDA' as OmicsLonDA_1.10.0.zip
* DONE (OmicsLonDA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'OmicsLonDA' successfully unpacked and MD5 sums checked

Tests output

OmicsLonDA.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(OmicsLonDA)
> 
> test_check("OmicsLonDA")
[1] "Disease" "Healthy"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  15.21    0.98   16.18 

OmicsLonDA.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(OmicsLonDA)
> 
> test_check("OmicsLonDA")
[1] "Disease" "Healthy"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  15.31    0.48   15.78 

Example timings

OmicsLonDA.Rcheck/examples_i386/OmicsLonDA-Ex.timings

nameusersystemelapsed
adjustBaseline2.060.092.16
curveFitting3.390.183.56
findSigInterval0.110.000.11
omicslonda8.260.048.32
permutationMC8.080.138.20
testStat0.240.000.23
testStatPermutation8.430.018.47
visualizeArea1.070.211.27
visualizeFeature3.260.083.34
visualizeFeatureSpline9.560.149.70
visualizeTestStatHistogram0.330.200.54

OmicsLonDA.Rcheck/examples_x64/OmicsLonDA-Ex.timings

nameusersystemelapsed
adjustBaseline3.100.063.16
curveFitting3.150.023.17
findSigInterval0.120.010.14
omicslonda10.93 0.0510.97
permutationMC8.360.038.39
testStat0.210.020.23
testStatPermutation7.680.017.69
visualizeArea1.060.131.19
visualizeFeature3.580.063.74
visualizeFeatureSpline10.00 0.1110.14
visualizeTestStatHistogram0.500.310.82