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CHECK report for rfaRm on tokay2

This page was generated on 2020-10-17 11:57:36 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rfaRm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1470/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfaRm 1.0.0
Lara Selles Vidal
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rfaRm
Branch: RELEASE_3_11
Last Commit: 238d13d
Last Changed Date: 2020-04-27 15:35:59 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rfaRm
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rfaRm.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings rfaRm_1.0.0.tar.gz
StartedAt: 2020-10-17 07:27:12 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:31:16 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 243.3 seconds
RetCode: 0
Status:  OK  
CheckDir: rfaRm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rfaRm.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings rfaRm_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/rfaRm.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rfaRm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rfaRm' version '1.0.0'
* 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 'rfaRm' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
rfamSequenceSearch 0.01      0   10.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
rfamSecondaryStructurePlot 0.16   0.09   26.34
rfamSequenceSearch         0.05   0.00   10.89
* 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: OK


Installation output

rfaRm.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/rfaRm_1.0.0.tar.gz && rm -rf rfaRm.buildbin-libdir && mkdir rfaRm.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rfaRm.buildbin-libdir rfaRm_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL rfaRm_1.0.0.zip && rm rfaRm_1.0.0.tar.gz rfaRm_1.0.0.zip
###
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  % 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  124k  100  124k    0     0  2048k      0 --:--:-- --:--:-- --:--:-- 2309k

install for i386

* installing *source* package 'rfaRm' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rfaRm'
    finding HTML links ... done
    rfamConsensusSecondaryStructure         html  
    rfamCovarianceModel                     html  
    rfamFamilyAccessionToID                 html  
    rfamFamilyIDToAccession                 html  
    rfamFamilySummary                       html  
    rfamPDBMapping                          html  
    rfamSecondaryStructurePlot              html  
    rfamSecondaryStructureXMLSVG            html  
    rfamSeedAlignment                       html  
    rfamSeedTree                            html  
    rfamSeedTreeImage                       html  
    rfamSequenceRegions                     html  
    rfamSequenceSearch                      html  
    rfamTextSearchFamilyAccession           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 'rfaRm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rfaRm' as rfaRm_1.0.0.zip
* DONE (rfaRm)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'rfaRm' successfully unpacked and MD5 sums checked

Tests output

rfaRm.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("rfaRm")
No encoding supplied: defaulting to UTF-8.
  format width height colorspace matte filesize density
1    SVG   700    550       sRGB  TRUE    17458   96x96
  format width height colorspace matte filesize density
1    GIF   600   2056       sRGB FALSE    62234   72x72
Running sequence search query. This might take a long time.
Sequence search completed successfully.


RUNIT TEST PROTOCOL -- Sat Oct 17 07:30:39 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rfaRm RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.39    0.34   25.01 

rfaRm.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("rfaRm")
No encoding supplied: defaulting to UTF-8.
  format width height colorspace matte filesize density
1    SVG   700    550       sRGB  TRUE    17458   96x96
  format width height colorspace matte filesize density
1    GIF   600   2056       sRGB FALSE    62234   72x72
Running sequence search query. This might take a long time.
Sequence search completed successfully.


RUNIT TEST PROTOCOL -- Sat Oct 17 07:31:06 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rfaRm RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.59    0.29   26.71 

Example timings

rfaRm.Rcheck/examples_i386/rfaRm-Ex.timings

nameusersystemelapsed
rfamConsensusSecondaryStructure0.310.012.23
rfamCovarianceModel0.300.051.30
rfamFamilyAccessionToID0.000.020.19
rfamFamilyIDToAccession0.000.000.19
rfamFamilySummary0.100.031.22
rfamPDBMapping0.090.000.81
rfamSecondaryStructurePlot0.230.074.85
rfamSecondaryStructureXMLSVG0.040.010.94
rfamSeedAlignment0.890.032.70
rfamSeedTree0.090.000.80
rfamSeedTreeImage0.110.000.92
rfamSequenceRegions0.300.052.26
rfamSequenceSearch 0.01 0.0010.86
rfamTextSearchFamilyAccession0.080.020.50

rfaRm.Rcheck/examples_x64/rfaRm-Ex.timings

nameusersystemelapsed
rfamConsensusSecondaryStructure0.390.002.31
rfamCovarianceModel0.260.001.14
rfamFamilyAccessionToID0.030.000.20
rfamFamilyIDToAccession0.000.010.19
rfamFamilySummary0.090.021.16
rfamPDBMapping0.110.000.81
rfamSecondaryStructurePlot 0.16 0.0926.34
rfamSecondaryStructureXMLSVG0.060.000.92
rfamSeedAlignment0.860.022.82
rfamSeedTree0.110.000.79
rfamSeedTreeImage0.060.000.91
rfamSequenceRegions0.250.001.98
rfamSequenceSearch 0.05 0.0010.89
rfamTextSearchFamilyAccession0.030.000.40