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This page was generated on 2024-03-04 11:40:03 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 2087/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TAPseq 1.15.2  (landing page)
Andreas R. Gschwind
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/TAPseq
git_branch: devel
git_last_commit: aff4998
git_last_commit_date: 2024-02-01 13:25:34 -0500 (Thu, 01 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for TAPseq on merida1


To the developers/maintainers of the TAPseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TAPseq.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: TAPseq
Version: 1.15.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TAPseq_1.15.2.tar.gz
StartedAt: 2024-03-02 11:36:39 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 11:57:12 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1232.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TAPseq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TAPseq_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TAPseq.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 ‘TAPseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TAPseq’ version ‘1.15.2’
* 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 ‘TAPseq’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Following software required by TAPseq is not installed or not in PATH:
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/TAPseq.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether 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 ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'get_gt_sequences.Rd':
  ‘compress’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
selectTargetGenes 310.307  5.523 364.322
truncateTxsPolyA   17.090  0.168  20.248
pickPrimers        14.444  0.568  17.346
TAPseqInput        11.092  0.277  11.866
inferPolyASites     8.534  2.071   8.308
exportPrimers      10.284  0.127  12.161
checkPrimers        5.621  0.118   6.767
createIORecord      5.194  0.058   6.084
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/TAPseq.Rcheck/00check.log’
for details.



Installation output

TAPseq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TAPseq’ ...
** 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
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!
** testing if installed package can be loaded from final location
Warning: Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package!
** testing if installed package keeps a record of temporary installation path
* DONE (TAPseq)

Tests output

TAPseq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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(TAPseq)

TAPseq is using the following tools:
primer3_core: NA
makeblastdb: NA
blastn: NA

Warning message:
Following software required by TAPseq is not installed or not in PATH:

	primer3_core
	makeblastdb
	blastn

Please install these tools before trying to use this package! 
> 
> test_check("TAPseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 209 ]
> 
> proc.time()
   user  system elapsed 
106.376   3.438 126.113 

Example timings

TAPseq.Rcheck/TAPseq-Ex.timings

nameusersystemelapsed
TAPseqInput11.092 0.27711.866
TsIO-class0.1160.0190.141
TsIOList-class0.3820.1423.926
accessors0.7680.0421.106
checkPrimers5.6210.1186.767
createIORecord5.1940.0586.084
designPrimers0.1450.0060.181
estimateOffTargets0.0010.0010.001
exportPrimers10.284 0.12712.161
getTxsSeq1.9190.1082.424
inferPolyASites8.5342.0718.308
parsePrimer3Output0.0000.0010.001
pickPrimers14.444 0.56817.346
selectTargetGenes310.307 5.523364.322
truncateTxsPolyA17.090 0.16820.248