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This page was generated on 2017-10-18 14:16:57 -0400 (Wed, 18 Oct 2017).
| Package 1371/1381 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| XBSeq 1.6.0 Yuanhang Liu
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: XBSeq |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings XBSeq_1.6.0.tar.gz |
| StartedAt: 2017-10-18 03:09:37 -0400 (Wed, 18 Oct 2017) |
| EndedAt: 2017-10-18 03:19:14 -0400 (Wed, 18 Oct 2017) |
| EllapsedTime: 576.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: XBSeq.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings XBSeq_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/XBSeq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 loading without being on the library search path ... 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 : <anonymous>: no visible global function definition for
‘ddelap’
Loglikhood : <anonymous>: no visible global function definition for
‘dpois’
Loglikhood_NB : <anonymous>: 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 : <anonymous>: 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 : <anonymous> : <anonymous>: 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 77.732 1.180 78.990
XBSeq 74.276 0.012 74.369
XBSeqTest 70.436 0.632 71.153
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Welcome to 'XBSeq'.
>
> test_check("XBSeq")
estimating parameters using MLE for group one
estimating parameters using MLE for group two
Error: XBplot(XB, Samplenum = "Sample_54_WT") did not throw an error.
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/XBSeq.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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(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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Welcome to 'XBSeq'.
>
> test_check("XBSeq")
estimating parameters using MLE for group one
estimating parameters using MLE for group two
Error: XBplot(XB, Samplenum = "Sample_54_WT") did not throw an error.
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
XBSeq.Rcheck/00install.out:
* installing *source* package ‘XBSeq’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (XBSeq)
XBSeq.Rcheck/XBSeq-Ex.timings:
| name | user | system | elapsed | |
| MAplot | 77.732 | 1.180 | 78.990 | |
| XBSeq | 74.276 | 0.012 | 74.369 | |
| XBSeqDataSet-class | 0.128 | 0.004 | 0.131 | |
| XBSeqTest | 70.436 | 0.632 | 71.153 | |
| XBplot | 0.844 | 0.000 | 0.845 | |
| conditions | 0.080 | 0.000 | 0.083 | |
| counts | 0.08 | 0.00 | 0.08 | |
| dispEst | 2.372 | 0.008 | 2.383 | |
| dispTable | 2.384 | 0.008 | 2.395 | |
| estimateRealCount | 0.092 | 0.000 | 0.092 | |
| estimateSCV | 2.428 | 0.000 | 2.438 | |
| fitInfo | 2.164 | 0.004 | 2.168 | |
| getSignalVars | 1.980 | 0.000 | 1.982 | |
| plotSCVEsts | 2.616 | 0.004 | 2.623 | |