Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2116/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TAPseq 1.18.0 (landing page) Andreas R. Gschwind
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: TAPseq |
Version: 1.18.0 |
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_1.18.0.tar.gz |
StartedAt: 2024-12-20 10:37:07 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:54:57 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1069.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TAPseq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TAPseq.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TAPseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TAPseq’ version ‘1.18.0’ * 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 ‘/Users/biocbuild/bbs-3.20-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 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 ... 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 309.836 3.559 320.511 truncateTxsPolyA 17.725 0.089 18.663 pickPrimers 14.429 0.456 15.021 TAPseqInput 10.865 0.368 11.316 inferPolyASites 9.242 1.885 7.871 exportPrimers 10.163 0.040 10.228 checkPrimers 5.709 0.045 6.020 createIORecord 5.242 0.020 5.317 * 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-3.20-bioc/meat/TAPseq.Rcheck/00check.log’ for details.
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)
TAPseq.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 105.607 2.952 111.393
TAPseq.Rcheck/TAPseq-Ex.timings
name | user | system | elapsed | |
TAPseqInput | 10.865 | 0.368 | 11.316 | |
TsIO-class | 0.131 | 0.005 | 0.137 | |
TsIOList-class | 0.349 | 0.072 | 0.454 | |
accessors | 0.808 | 0.029 | 0.847 | |
checkPrimers | 5.709 | 0.045 | 6.020 | |
createIORecord | 5.242 | 0.020 | 5.317 | |
designPrimers | 0.146 | 0.004 | 0.151 | |
estimateOffTargets | 0.001 | 0.001 | 0.002 | |
exportPrimers | 10.163 | 0.040 | 10.228 | |
getTxsSeq | 1.795 | 0.123 | 2.004 | |
inferPolyASites | 9.242 | 1.885 | 7.871 | |
parsePrimer3Output | 0.001 | 0.001 | 0.001 | |
pickPrimers | 14.429 | 0.456 | 15.021 | |
selectTargetGenes | 309.836 | 3.559 | 320.511 | |
truncateTxsPolyA | 17.725 | 0.089 | 18.663 | |