Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-03-18 11:50:23 -0400 (Mon, 18 Mar 2019).
Package 1574/1676 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
TCseq 1.7.1 Mengjun Wu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] |
Package: TCseq |
Version: 1.7.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCseq_1.7.1.tar.gz |
StartedAt: 2019-03-18 05:28:21 -0400 (Mon, 18 Mar 2019) |
EndedAt: 2019-03-18 05:33:18 -0400 (Mon, 18 Mar 2019) |
EllapsedTime: 296.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: TCseq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCseq_1.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TCseq.Rcheck’ * using R Under development (unstable) (2019-01-22 r76000) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCseq’ version ‘1.7.1’ * 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 ‘TCseq’ can be installed ... WARNING Found the following significant warnings: The prototype for class “TCA” has undefined slot(s): '' See ‘/Users/biocbuild/bbs-3.9-bioc/meat/TCseq.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 ... OK * 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 ... NOTE DBresult: no visible global function definition for ‘as’ DBresult.cluster: no visible global function definition for ‘as’ TCA: no visible global function definition for ‘is’ TCA: no visible global function definition for ‘as’ TCAFromSummarizedExperiment: no visible global function definition for ‘is’ TCAFromSummarizedExperiment: no visible global function definition for ‘as’ countReads: no visible global function definition for ‘createAnnotationFile’ countReads: no visible global function definition for ‘featureCounts’ timeclustplot: no visible binding for global variable ‘group’ timecourseTable: no visible global function definition for ‘as’ Undefined global functions or variables: as createAnnotationFile featureCounts group is Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/TCseq.Rcheck/00check.log’ for details.
TCseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TCseq’ ... ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Warning in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : The prototype for class “TCA” has undefined slot(s): '' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (TCseq)
TCseq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-01-22 r76000) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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(TCseq) > > test_check("TCseq") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 8 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 12.982 1.134 14.081
TCseq.Rcheck/TCseq-Ex.timings
name | user | system | elapsed | |
DBanalysis | 1.325 | 0.077 | 1.401 | |
DBresult | 4.302 | 0.158 | 4.462 | |
TCA | 0.013 | 0.002 | 0.015 | |
TCA.accessors | 0.194 | 0.118 | 0.313 | |
counts | 0.067 | 0.011 | 0.079 | |
countsTable | 0.002 | 0.002 | 0.004 | |
experiment | 0.002 | 0.002 | 0.003 | |
experiment_BAMfile | 0.002 | 0.002 | 0.004 | |
genomicIntervals | 0.002 | 0.002 | 0.004 | |
peakreference | 0.017 | 0.001 | 0.018 | |
tca_ATAC | 0.001 | 0.001 | 0.002 | |
timeclust | 0.029 | 0.000 | 0.029 | |
timeclustplot | 2.927 | 0.045 | 2.975 | |
timecourseTable | 1.134 | 0.089 | 1.225 | |