Yuanhang Liu
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/XBSeq |
| Branch: RELEASE_3_9 |
| Last Commit: ccfb20d |
| Last Changed Date: 2019-05-02 11:53:55 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:55:55 -0400 (Wed, 16 Oct 2019).
| Package 1727/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| XBSeq 1.16.0 Yuanhang Liu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: XBSeq |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XBSeq_1.16.0.tar.gz |
| StartedAt: 2019-10-16 07:45:44 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 08:01:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 920.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: XBSeq.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:XBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings XBSeq_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/XBSeq.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘XBSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘XBSeq’ version ‘1.16.0’ * 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 ‘XBSeq’ can be installed ... OK * 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: no function found corresponding to methods exports from ‘XBSeq’ for: ‘conditions’, ‘conditions<-’, ‘dispTable’ 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 ... NOTE Loglikhood :: no visible global function definition for ‘ddelap’ Loglikhood : : no visible global function definition for ‘dpois’ Loglikhood_NB : : no visible global function definition for ‘dnbinom’ MAplot: no visible binding for global variable ‘baseMean’ MAplot: no visible global function definition for ‘quantile’ MAplot: no visible binding for global variable ‘log2FoldChange’ XBSeqDataSet: no visible global function definition for ‘DataFrame’ XBSeqDataSet: no visible global function definition for ‘SummarizedExperiment’ XBSeqDataSet: no visible global function definition for ‘formula’ XBSeqTest: no visible global function definition for ‘dispTable’ XBSeqTest: no visible global function definition for ‘conditions’ XBSeqTest: no visible global function definition for ‘p.adjust’ XBSeqTestForMatrices : : no visible global function definition for ‘dnbinom’ XBplot: no visible global function definition for ‘median’ XBplot: no visible binding for global variable ‘Sample’ XBplot: no visible binding for global variable ‘Group’ XBplot: no visible binding for global variable ‘..count..’ adjustScv: no visible global function definition for ‘data’ adjustScv: no visible binding for global variable ‘scvBiasCorrectionFits’ estimation_param_PoissonNB_MLE: no visible global function definition for ‘optim’ estimation_param_PoissonNB_MLE_NB: no visible global function definition for ‘optim’ exactTestBetaApprox: no visible global function definition for ‘qbeta’ exactTestBetaApprox: no visible global function definition for ‘pbeta’ getSignalVars: no visible global function definition for ‘cor’ parametricscvFit: no visible global function definition for ‘glm’ parametricscvFit: no visible global function definition for ‘Gamma’ parametricscvFit: no visible global function definition for ‘coefficients’ plotSCVEsts: no visible global function definition for ‘complete.cases’ predict_helper: no visible global function definition for ‘predict’ prepareScvBiasCorrectionFits : : : no visible global function definition for ‘rnbinom’ counts,XBSeqDataSet: no visible global function definition for ‘assays’ counts,XBSeqDataSet: no visible global function definition for ‘assay’ estimateRealCount,XBSeqDataSet: no visible global function definition for ‘assay’ estimateRealCount,XBSeqDataSet: no visible global function definition for ‘assay<-’ estimateSCV,XBSeqDataSet: no visible global function definition for ‘conditions’ estimateSCV,XBSeqDataSet: no visible global function definition for ‘dispTable<-’ Undefined global functions or variables: ..count.. DataFrame Gamma Group Sample SummarizedExperiment assay assay<- assays baseMean coefficients complete.cases conditions cor data ddelap dispTable dispTable<- dnbinom dpois formula glm log2FoldChange median optim p.adjust pbeta predict qbeta quantile rnbinom scvBiasCorrectionFits Consider adding importFrom("stats", "Gamma", "coefficients", "complete.cases", "cor", "dnbinom", "dpois", "formula", "glm", "median", "optim", "p.adjust", "pbeta", "predict", "qbeta", "quantile", "rnbinom") importFrom("utils", "data") to your NAMESPACE file. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed MAplot 86.634 33.433 120.070 XBSeq 75.575 30.512 106.085 XBSeqTest 72.415 29.992 102.404 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/XBSeq.Rcheck/00check.log’ for details.
XBSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL XBSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘XBSeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘XBSeq.Rmd’ using ‘UTF-8’ ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XBSeq)
XBSeq.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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> library(testthat)
> library(XBSeq)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Welcome to 'XBSeq'.
>
> test_check("XBSeq")
estimating parameters using MLE for group one
estimating parameters using MLE for group two
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 16 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
>
> proc.time()
user system elapsed
184.191 51.211 235.369
XBSeq.Rcheck/XBSeq-Ex.timings
| name | user | system | elapsed | |
| MAplot | 86.634 | 33.433 | 120.070 | |
| XBSeq | 75.575 | 30.512 | 106.085 | |
| XBSeqDataSet-class | 0.224 | 0.020 | 0.243 | |
| XBSeqTest | 72.415 | 29.992 | 102.404 | |
| XBplot | 1.158 | 0.055 | 1.213 | |
| conditions | 0.155 | 0.012 | 0.167 | |
| counts | 0.163 | 0.016 | 0.178 | |
| dispEst | 3.014 | 1.342 | 4.356 | |
| dispTable | 3.060 | 1.345 | 4.405 | |
| estimateRealCount | 0.183 | 0.016 | 0.199 | |
| estimateSCV | 3.011 | 1.284 | 4.296 | |
| fitInfo | 3.557 | 1.278 | 4.835 | |
| getSignalVars | 2.257 | 1.210 | 3.466 | |
| plotSCVEsts | 3.247 | 1.281 | 4.529 | |