Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 bigPint on tokay2


To the developers/maintainers of the bigPint package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bigPint.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 149/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigPint 1.10.0  (landing page)
Lindsay Rutter
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/bigPint
git_branch: RELEASE_3_14
git_last_commit: 8efcfe7
git_last_commit_date: 2021-10-26 12:49:05 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: bigPint
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigPint.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigPint_1.10.0.tar.gz
StartedAt: 2022-04-12 16:11:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:18:20 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 403.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: bigPint.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigPint.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigPint_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/bigPint.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bigPint/DESCRIPTION' ... OK
* this is package 'bigPint' 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 'bigPint' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.7Mb
  sub-directories of 1Mb or more:
    data              11.0Mb
    help               3.2Mb
    shiny-dashboards   5.0Mb
    shiny-examples     3.1Mb
* 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 ... WARNING
  LazyData DB of 11.0 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* 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
plotSM       44.33   0.24   44.58
plotClusters 14.46   1.06   15.51
plotLitre     4.36   1.38    5.79
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plotSM       48.09   0.50   48.94
plotClusters 13.81   0.63   14.47
plotLitre     4.25   0.98    5.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/bigPint.Rcheck/00check.log'
for details.



Installation output

bigPint.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/bigPint_1.10.0.tar.gz && rm -rf bigPint.buildbin-libdir && mkdir bigPint.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bigPint.buildbin-libdir bigPint_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bigPint_1.10.0.zip && rm bigPint_1.10.0.tar.gz bigPint_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
  0 56.8M    0 15985    0     0   135k      0  0:07:10 --:--:--  0:07:10  135k
  3 56.8M    3 2007k    0     0  1798k      0  0:00:32  0:00:01  0:00:31 1798k
  8 56.8M    8 4834k    0     0  2319k      0  0:00:25  0:00:02  0:00:23 2319k
 12 56.8M   12 7473k    0     0  2422k      0  0:00:24  0:00:03  0:00:21 2422k
 17 56.8M   17 10.1M    0     0  2530k      0  0:00:23  0:00:04  0:00:19 2530k
 23 56.8M   23 13.5M    0     0  2717k      0  0:00:21  0:00:05  0:00:16 2777k
 28 56.8M   28 16.0M    0     0  2694k      0  0:00:21  0:00:06  0:00:15 2895k
 34 56.8M   34 19.4M    0     0  2808k      0  0:00:20  0:00:07  0:00:13 3011k
 41 56.8M   41 23.8M    0     0  3010k      0  0:00:19  0:00:08  0:00:11 3372k
 46 56.8M   46 26.3M    0     0  2958k      0  0:00:19  0:00:09  0:00:10 3307k
 48 56.8M   48 27.5M    0     0  2785k      0  0:00:20  0:00:10  0:00:10 2854k
 52 56.8M   52 29.5M    0     0  2726k      0  0:00:21  0:00:11  0:00:10 2764k
 55 56.8M   55 31.4M    0     0  2661k      0  0:00:21  0:00:12  0:00:09 2452k
 59 56.8M   59 33.7M    0     0  2645k      0  0:00:22  0:00:13  0:00:09 2051k
 65 56.8M   65 37.0M    0     0  2692k      0  0:00:21  0:00:14  0:00:07 2207k
 72 56.8M   72 41.1M    0     0  2789k      0  0:00:20  0:00:15  0:00:05 2796k
 77 56.8M   77 43.8M    0     0  2789k      0  0:00:20  0:00:16  0:00:04 2929k
 80 56.8M   80 45.9M    0     0  2749k      0  0:00:21  0:00:17  0:00:04 2962k
 83 56.8M   83 47.7M    0     0  2703k      0  0:00:21  0:00:18  0:00:03 2857k
 87 56.8M   87 49.5M    0     0  2659k      0  0:00:21  0:00:19  0:00:02 2567k
 90 56.8M   90 51.5M    0     0  2630k      0  0:00:22  0:00:20  0:00:02 2149k
 95 56.8M   95 54.5M    0     0  2648k      0  0:00:21  0:00:21 --:--:-- 2195k
100 56.8M  100 56.8M    0     0  2682k      0  0:00:21  0:00:21 --:--:-- 2433k

install for i386

* installing *source* package 'bigPint' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bigPint'
    finding HTML links ... done
    bigPint                                 html  
    convertSEPair                           html  
    convertSESubsetGenes                    html  
    plotClusters                            html  
    plotLitre                               html  
    plotLitreApp                            html  
    plotPCP                                 html  
    plotPCPApp                              html  
    plotSM                                  html  
    plotSMApp                               html  
    plotVolcano                             html  
    plotVolcanoApp                          html  
    se_soybean_cn_sub                       html  
    se_soybean_ir_sub                       html  
    soybean_cn                              html  
    soybean_cn_metrics                      html  
    soybean_cn_sub                          html  
    soybean_cn_sub_metrics                  html  
    soybean_ir                              html  
    soybean_ir_metrics                      html  
    soybean_ir_sub                          html  
    soybean_ir_sub_metrics                  html  
*** copying figures
** 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 'bigPint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bigPint' as bigPint_1.10.0.zip
* DONE (bigPint)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'bigPint' successfully unpacked and MD5 sums checked

Tests output

bigPint.Rcheck/tests_i386/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> BiocGenerics:::testPackage("bigPint")


RUNIT TEST PROTOCOL -- Tue Apr 12 16:18:04 2022 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigPint RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In xtfrm.data.frame(x) : cannot xtfrm data frames
5: In xtfrm.data.frame(x) : cannot xtfrm data frames
6: In xtfrm.data.frame(x) : cannot xtfrm data frames
7: In xtfrm.data.frame(x) : cannot xtfrm data frames
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
> 
> proc.time()
   user  system elapsed 
   7.68    0.67    8.37 

bigPint.Rcheck/tests_x64/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.

> BiocGenerics:::testPackage("bigPint")


RUNIT TEST PROTOCOL -- Tue Apr 12 16:18:12 2022 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bigPint RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In xtfrm.data.frame(x) : cannot xtfrm data frames
5: In xtfrm.data.frame(x) : cannot xtfrm data frames
6: In xtfrm.data.frame(x) : cannot xtfrm data frames
7: In xtfrm.data.frame(x) : cannot xtfrm data frames
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
> 
> proc.time()
   user  system elapsed 
   7.18    0.37    7.54 

Example timings

bigPint.Rcheck/examples_i386/bigPint-Ex.timings

nameusersystemelapsed
convertSEPair0.190.000.18
convertSESubsetGenes0.260.080.35
plotClusters14.46 1.0615.51
plotLitre4.361.385.79
plotLitreApp0.040.000.04
plotPCP1.520.091.63
plotPCPApp0.90.00.9
plotSM44.33 0.2444.58
plotSMApp0.000.010.02
plotVolcano1.210.031.26
plotVolcanoApp0.090.000.10

bigPint.Rcheck/examples_x64/bigPint-Ex.timings

nameusersystemelapsed
convertSEPair0.180.000.18
convertSESubsetGenes0.180.040.23
plotClusters13.81 0.6314.47
plotLitre4.250.985.32
plotLitreApp0.030.000.03
plotPCP1.460.051.55
plotPCPApp1.340.021.36
plotSM48.09 0.5048.94
plotSMApp0.020.000.01
plotVolcano1.310.031.46
plotVolcanoApp0.160.010.17