Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:54 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE TAPseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1777/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TAPseq 1.0.0 Andreas Gschwind
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK |
Package: TAPseq |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TAPseq_1.0.0.tar.gz |
StartedAt: 2020-10-17 05:58:33 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 06:06:39 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 486.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TAPseq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TAPseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TAPseq_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TAPseq.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.0.0’ * 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-3.11-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 41.957 3.445 40.886 truncateTxsPolyA 8.567 0.080 8.645 inferPolyASites 5.568 1.181 5.479 TAPseqInput 6.400 0.108 6.508 pickPrimers 5.905 0.060 5.965 * 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-3.11-bioc/meat/TAPseq.Rcheck/00check.log’ for details.
TAPseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TAPseq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
TAPseq.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 209 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 52.777 1.703 57.706
TAPseq.Rcheck/TAPseq-Ex.timings
name | user | system | elapsed | |
TAPseqInput | 6.400 | 0.108 | 6.508 | |
TsIO-class | 0.074 | 0.008 | 0.082 | |
TsIOList-class | 0.223 | 0.076 | 0.810 | |
accessors | 0.681 | 0.064 | 0.744 | |
checkPrimers | 3.669 | 0.108 | 3.778 | |
createIORecord | 3.913 | 0.012 | 3.925 | |
designPrimers | 0.148 | 0.008 | 0.156 | |
estimateOffTargets | 0 | 0 | 0 | |
exportPrimers | 4.238 | 0.032 | 4.270 | |
getTxsSeq | 0.982 | 0.044 | 1.083 | |
inferPolyASites | 5.568 | 1.181 | 5.479 | |
parsePrimer3Output | 0.000 | 0.000 | 0.001 | |
pickPrimers | 5.905 | 0.060 | 5.965 | |
selectTargetGenes | 41.957 | 3.445 | 40.886 | |
truncateTxsPolyA | 8.567 | 0.080 | 8.645 | |