Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-21 12:04:38 -0400 (Thu, 21 Oct 2021).

CHECK results for bigPint on riesling1

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? 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 149/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bigPint 1.9.0  (landing page)
Lindsay Rutter
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/bigPint
git_branch: master
git_last_commit: cc84061
git_last_commit_date: 2021-05-19 12:40:30 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: bigPint
Version: 1.9.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigPint.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigPint_1.9.0.tar.gz
StartedAt: 2021-10-21 00:33:45 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 00:39:42 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 356.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: bigPint.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:bigPint.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings bigPint_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/bigPint.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.9.0'
* 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 22.6Mb
  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       33.33   0.28   33.78
plotClusters 10.27   0.20   10.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plotSM       31.01   0.29   31.67
plotClusters 10.11   0.42   11.59
* 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
  'D:/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_1.9.0.tar.gz && rm -rf bigPint.buildbin-libdir && mkdir bigPint.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bigPint.buildbin-libdir bigPint_1.9.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL bigPint_1.9.0.zip && rm bigPint_1.9.0.tar.gz bigPint_1.9.0.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
  1 56.8M    1  945k    0     0  2305k      0  0:00:25 --:--:--  0:00:25 2305k
 11 56.8M   11 6532k    0     0  4645k      0  0:00:12  0:00:01  0:00:11 4642k
 22 56.8M   22 12.7M    0     0  5428k      0  0:00:10  0:00:02  0:00:08 5426k
 30 56.8M   30 17.1M    0     0  4940k      0  0:00:11  0:00:03  0:00:08 4938k
 41 56.8M   41 23.5M    0     0  5465k      0  0:00:10  0:00:04  0:00:06 5464k
 55 56.8M   55 31.3M    0     0  5935k      0  0:00:09  0:00:05  0:00:04 6232k
 71 56.8M   71 40.7M    0     0  6509k      0  0:00:08  0:00:06  0:00:02 7034k
 84 56.8M   84 47.8M    0     0  6598k      0  0:00:08  0:00:07  0:00:01 7160k
 92 56.8M   92 52.4M    0     0  6398k      0  0:00:09  0:00:08  0:00:01 7469k
100 56.8M  100 56.8M    0     0  6563k      0  0:00:08  0:00:08 --:--:-- 7649k

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_1.9.0.zip
* DONE (bigPint)
* installing to library 'D:/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 4.1.1 (2021-08-10) -- "Kick Things"
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.

> BiocGenerics:::testPackage("bigPint")


RUNIT TEST PROTOCOL -- Thu Oct 21 00:37:55 2021 
*********************************************** 
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 
   4.85    0.32    5.17 

bigPint.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> BiocGenerics:::testPackage("bigPint")


RUNIT TEST PROTOCOL -- Thu Oct 21 00:38:01 2021 
*********************************************** 
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 
   4.45    0.59    5.04 

Example timings

bigPint.Rcheck/examples_i386/bigPint-Ex.timings

nameusersystemelapsed
convertSEPair0.180.000.17
convertSESubsetGenes0.170.040.20
plotClusters10.27 0.2010.47
plotLitre2.531.203.76
plotLitreApp0.030.000.03
plotPCP1.110.031.14
plotPCPApp0.530.000.53
plotSM33.33 0.2833.78
plotSMApp000
plotVolcano0.870.050.92
plotVolcanoApp0.080.000.08

bigPint.Rcheck/examples_x64/bigPint-Ex.timings

nameusersystemelapsed
convertSEPair0.120.010.20
convertSESubsetGenes0.200.000.22
plotClusters10.11 0.4211.59
plotLitre2.561.073.77
plotLitreApp0.030.010.04
plotPCP1.050.021.19
plotPCPApp0.530.000.53
plotSM31.01 0.2931.67
plotSMApp0.020.000.02
plotVolcano0.860.020.87
plotVolcanoApp0.060.000.06