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This page was generated on 2024-07-24 11:41 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1462/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
packFinder 1.17.0  (landing page)
Jack Gisby
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/packFinder
git_branch: devel
git_last_commit: 639edef
git_last_commit_date: 2024-04-30 11:20:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for packFinder on lconway

To the developers/maintainers of the packFinder package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/packFinder.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: packFinder
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:packFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings packFinder_1.17.0.tar.gz
StartedAt: 2024-07-23 23:07:44 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 23:09:05 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 81.0 seconds
RetCode: 0
Status:   OK  
CheckDir: packFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:packFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings packFinder_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/packFinder.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘packFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘packFinder’ version ‘1.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘packFinder’ 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 code 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 ... NOTE
checkRd: (-1) readBlast.Rd:100: Lost braces
   100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}},
       |     ^
checkRd: (-1) readBlast.Rd:100: Lost braces
   100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}},
       |                                 ^
checkRd: (-1) readBlast.Rd:101: Lost braces
   101 | code{\link{packAlign}}, 
       |     ^
checkRd: (-1) readBlast.Rd:102: Lost braces
   102 | code{\link{readUc}}, code{\link{packClust}}
       |     ^
checkRd: (-1) readBlast.Rd:102: Lost braces
   102 | code{\link{readUc}}, code{\link{packClust}}
       |                          ^
checkRd: (-1) readUc.Rd:98: Lost braces
    98 | code{\link{tirClust}}, code{\link{packAlign}}, 
       |     ^
checkRd: (-1) readUc.Rd:98: Lost braces
    98 | code{\link{tirClust}}, code{\link{packAlign}}, 
       |                            ^
checkRd: (-1) readUc.Rd:99: Lost braces
    99 | code{\link{readBlast}}, code{\link{packClust}}
       |     ^
checkRd: (-1) readUc.Rd:99: Lost braces
    99 | code{\link{readBlast}}, code{\link{packClust}}
       |                             ^
checkRd: (-1) tirClust.Rd:86: Lost braces
    86 | code{\link{packClust}}, code{\link{packAlign}},
       |     ^
checkRd: (-1) tirClust.Rd:86: Lost braces
    86 | code{\link{packClust}}, code{\link{packAlign}},
       |                             ^
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
arabidopsisThalianaRefseq 4.943  0.238    5.21
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/packFinder.Rcheck/00check.log’
for details.


Installation output

packFinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘packFinder’ ...
** using staged installation
** R
** data
** 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 (packFinder)

Tests output

packFinder.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(packFinder)
> 
> test_check("packFinder")
DNAStringSet object of length 1:
      width seq                                             names               
[1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3
[1] "File successfully written to tempTestOutput/packMatches.csv"
[1] "FASTA written to tempTestOutput/packMatches.fasta"
2024-07-23 23:08:34.384 R[11536:454307107] XType: com.apple.fonts is not accessible.
2024-07-23 23:08:34.385 R[11536:454307107] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
  7.122   0.437   7.589 

Example timings

packFinder.Rcheck/packFinder-Ex.timings

nameusersystemelapsed
arabidopsisThalianaRefseq4.9430.2385.210
blastAnalysis000
blastAnnotate0.0070.0020.009
collapseSeqs0.5730.0090.584
filterWildcards0.0970.0060.103
getPackSeqs1.1940.0131.226
getPacksFromCsv0.0030.0020.005
getPacksFromFasta0.0720.0070.083
getPacksFromGRanges0.1000.0030.104
getTsds0.0920.0060.098
identifyPotentialPackElements0.5470.0080.563
identifyTirMatches0.0870.0030.089
makeBlastDb000
packAlign0.0690.0040.073
packBlast0.0000.0010.000
packClust0.0730.0060.079
packMatches1.1250.0111.142
packSearch1.0920.0081.106
packsToCsv0.0030.0020.006
packsToFasta0.0950.0070.103
packsToGRanges0.0170.0020.018
readBlast0.0130.0020.015
readUc0.0030.0010.005
tirClust0.5080.0260.537