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This page was generated on 2024-02-22 11:36:26 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 2105/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TAPseq 1.14.1  (landing page)
Andreas R. Gschwind
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/TAPseq
git_branch: RELEASE_3_18
git_last_commit: bc862df
git_last_commit_date: 2023-11-06 23:39:08 -0500 (Mon, 06 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for TAPseq on nebbiolo2


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: 1.14.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TAPseq_1.14.1.tar.gz
StartedAt: 2024-02-22 03:10:20 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 03:26:52 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 992.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TAPseq.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TAPseq_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TAPseq.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TAPseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TAPseq’ version ‘1.14.1’
* 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 ‘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-3.18-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 loading without being on the library search path ... 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 ... 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 272.109  3.180 275.290
truncateTxsPolyA    6.922  0.000   6.922
inferPolyASites     5.309  0.841   4.864
pickPrimers         5.374  0.072   5.446
* 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 ...
  ‘tapseq_primer_design.Rmd’ using ‘UTF-8’... OK
  ‘tapseq_target_genes.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/TAPseq.Rcheck/00check.log’
for details.



Installation output

TAPseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL TAPseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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 
 46.465   1.779  48.235 

Example timings

TAPseq.Rcheck/TAPseq-Ex.timings

nameusersystemelapsed
TAPseqInput4.220.124.34
TsIO-class0.0610.0000.062
TsIOList-class0.1720.0100.184
accessors0.3370.0040.341
checkPrimers2.2240.0082.232
createIORecord2.0020.0002.002
designPrimers0.0670.0000.066
estimateOffTargets0.0010.0000.000
exportPrimers4.0380.0204.059
getTxsSeq0.8100.0080.818
inferPolyASites5.3090.8414.864
parsePrimer3Output000
pickPrimers5.3740.0725.446
selectTargetGenes272.109 3.180275.290
truncateTxsPolyA6.9220.0006.922