Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:06:50 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 rfaRm on palomino3


To the developers/maintainers of the rfaRm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rfaRm.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 1629/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfaRm 1.8.0  (landing page)
Lara Selles Vidal
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/rfaRm
git_branch: RELEASE_3_15
git_last_commit: 078e398
git_last_commit_date: 2022-04-26 12:04:36 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rfaRm
Version: 1.8.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rfaRm.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rfaRm_1.8.0.tar.gz
StartedAt: 2022-05-16 02:49:17 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 03:04:53 -0400 (Mon, 16 May 2022)
EllapsedTime: 935.8 seconds
RetCode: 0
Status:   OK  
CheckDir: rfaRm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rfaRm.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rfaRm_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/rfaRm.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rfaRm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rfaRm' version '1.8.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
rfamSequenceRegions 0.26      0    6.14
rfamSequenceSearch  0.05      0   10.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rfaRm
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rfaRm' ...
** using staged installation
** R
** 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
* DONE (rfaRm)

Tests output

rfaRm.Rcheck/tests/runTests.Rout


R version 4.2.0 (2022-04-22 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.

> BiocGenerics:::testPackage("rfaRm")
Linking to librsvg 2.48.8
No encoding supplied: defaulting to UTF-8.
# A tibble: 1 × 7
  format width height colorspace matte filesize density
  <chr>  <int>  <int> <chr>      <lgl>    <int> <chr>  
1 SVG      700    550 sRGB       TRUE     17458 96x96  
# A tibble: 1 × 7
  format width height colorspace matte filesize density
  <chr>  <int>  <int> <chr>      <lgl>    <int> <chr>  
1 GIF      600   2056 sRGB       FALSE    62234 72x72  
Running sequence search query. This might take a long time.
Sequence search is running, please wait.
Sequence search completed successfully.


RUNIT TEST PROTOCOL -- Mon May 16 03:04:43 2022 
*********************************************** 
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 
   6.81    0.70   83.59 

Example timings

rfaRm.Rcheck/rfaRm-Ex.timings

nameusersystemelapsed
rfamConsensusSecondaryStructure0.330.002.49
rfamCovarianceModel0.190.021.62
rfamFamilyAccessionToID0.010.000.18
rfamFamilyIDToAccession0.020.000.19
rfamFamilySummary0.040.011.25
rfamPDBMapping0.100.000.84
rfamSecondaryStructurePlot0.180.030.96
rfamSecondaryStructureXMLSVG0.110.020.86
rfamSeedAlignment0.680.002.67
rfamSeedTree0.090.020.91
rfamSeedTreeImage0.110.000.93
rfamSequenceRegions0.260.006.14
rfamSequenceSearch 0.05 0.0010.88
rfamTextSearchFamilyAccession0.200.010.64