Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:58 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 TAPseq on nebbiolo1


To the developers/maintainers of the TAPseq package:
- Please 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 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 1979/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TAPseq 1.8.0  (landing page)
Andreas R. Gschwind
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TAPseq
git_branch: RELEASE_3_15
git_last_commit: a9faecb
git_last_commit_date: 2022-04-26 12:03:10 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TAPseq
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TAPseq_1.8.0.tar.gz
StartedAt: 2022-10-18 22:06:58 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:13:17 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 378.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TAPseq.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TAPseq_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TAPseq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TAPseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TAPseq’ version ‘1.8.0’
* 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 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 ‘/home/biocbuild/bbs-3.15-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 ... 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 ... 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 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 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 47.998  1.208  49.206
truncateTxsPolyA   6.825  0.124   6.949
TAPseqInput        5.661  0.264   5.925
pickPrimers        5.226  0.132   5.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TAPseq.Rcheck/00check.log’
for details.



Installation output

TAPseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TAPseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> 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 
 47.559   1.969  49.512 

Example timings

TAPseq.Rcheck/TAPseq-Ex.timings

nameusersystemelapsed
TAPseqInput5.6610.2645.925
TsIO-class0.0600.0040.064
TsIOList-class0.1640.0080.175
accessors0.3380.0120.350
checkPrimers2.3150.0322.347
createIORecord1.9410.0361.977
designPrimers0.0670.0000.067
estimateOffTargets000
exportPrimers3.9700.0724.042
getTxsSeq0.7980.0790.877
inferPolyASites3.7730.7733.265
parsePrimer3Output000
pickPrimers5.2260.1325.358
selectTargetGenes47.998 1.20849.206
truncateTxsPolyA6.8250.1246.949