Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-10-15 15:06:49 -0400 (Fri, 15 Oct 2021).

CHECK results for rfaRm on machv2

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? 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 1561/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfaRm 1.4.3  (landing page)
Lara Selles Vidal
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/rfaRm
git_branch: RELEASE_3_13
git_last_commit: f034172
git_last_commit_date: 2021-08-04 01:55:16 -0400 (Wed, 04 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: rfaRm
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rfaRm_1.4.3.tar.gz
StartedAt: 2021-10-14 23:06:54 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:29:08 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 1334.9 seconds
RetCode: 0
Status:   OK  
CheckDir: rfaRm.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rfaRm_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/rfaRm.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.4.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
rfamSequenceSearch 0.035  0.002  20.867
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/rfaRm.Rcheck/00check.log’
for details.



Installation output

rfaRm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rfaRm
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2.48.4
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 completed successfully.


RUNIT TEST PROTOCOL -- Thu Oct 14 23:29:01 2021 
*********************************************** 
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 
  7.600   0.614  81.207 

Example timings

rfaRm.Rcheck/rfaRm-Ex.timings

nameusersystemelapsed
rfamConsensusSecondaryStructure0.3860.0302.720
rfamCovarianceModel0.1300.0051.213
rfamFamilyAccessionToID0.0170.0000.233
rfamFamilyIDToAccession0.0110.0000.227
rfamFamilySummary0.1000.0041.468
rfamPDBMapping0.0760.0040.982
rfamSecondaryStructurePlot0.8870.0742.144
rfamSecondaryStructureXMLSVG0.0550.0021.127
rfamSeedAlignment0.5450.0233.836
rfamSeedTree0.0670.0031.035
rfamSeedTreeImage0.1480.0101.171
rfamSequenceRegions0.1360.0083.503
rfamSequenceSearch 0.035 0.00220.867
rfamTextSearchFamilyAccession0.1860.0090.667