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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1695/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rfaRm 1.12.1  (landing page)
Lara Selles Vidal
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/rfaRm
git_branch: RELEASE_3_17
git_last_commit: ee11154
git_last_commit_date: 2023-10-06 03:09:19 -0400 (Fri, 06 Oct 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for rfaRm on kjohnson2


To the developers/maintainers of the rfaRm package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rfaRm
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rfaRm_1.12.1.tar.gz
StartedAt: 2023-10-18 18:36:40 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 19:07:06 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 1826.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rfaRm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rfaRm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rfaRm_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/rfaRm.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rfaRm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rfaRm’ version ‘1.12.1’
* 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 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 startup messages can be suppressed ... 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 ... NOTE
rfamSeedAlignment: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 0.055   0.04  13.856
* 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-3.17-bioc-mac-arm64/meat/rfaRm.Rcheck/00check.log’
for details.



Installation output

rfaRm.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 2.50.3
No encoding supplied: defaulting to UTF-8.
2023-10-18 19:06:27.466 R[37338:44559054] XType: com.apple.fonts is not accessible.
2023-10-18 19:06:27.466 R[37338:44559054] XType: XTFontStaticRegistry is enabled.
# 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.


RUNIT TEST PROTOCOL -- Wed Oct 18 19:06:51 2023 
*********************************************** 
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 
 10.967   5.681 112.808 

Example timings

rfaRm.Rcheck/rfaRm-Ex.timings

nameusersystemelapsed
rfamConsensusSecondaryStructure0.2140.0471.847
rfamCovarianceModel0.1140.0060.784
rfamFamilyAccessionToID0.0110.0010.128
rfamFamilyIDToAccession0.0070.0010.119
rfamFamilySummary0.0580.0030.832
rfamPDBMapping0.0600.0030.833
rfamSecondaryStructurePlot0.3320.0591.433
rfamSecondaryStructureXMLSVG0.0410.0030.684
rfamSeedAlignment0.4480.0203.166
rfamSeedTree0.0600.0030.589
rfamSeedTreeImage0.1410.0070.755
rfamSequenceRegions0.1120.0073.149
rfamSequenceSearch 0.055 0.04013.856
rfamTextSearchFamilyAccession0.0400.0390.619