Wentao Yang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ABSSeq |
| Branch: RELEASE_3_7 |
| Last Commit: 0c3a251 |
| Last Changed Date: 2018-06-28 13:58:45 -0400 (Thu, 28 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:52:45 -0400 (Wed, 17 Oct 2018).
| Package 9/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ABSSeq 1.34.1 Wentao Yang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ABSSeq |
| Version: 1.34.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABSSeq_1.34.1.tar.gz |
| StartedAt: 2018-10-16 19:46:55 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:50:03 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 187.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ABSSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ABSSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ABSSeq_1.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ABSSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ABSSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ABSSeq’ version ‘1.34.1’
* 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 ‘ABSSeq’ 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘edgeR’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for ‘new’
ABSSeqlm: no visible global function definition for ‘pnorm’
ABSSeqlm: no visible global function definition for ‘p.adjust’
ReplaceOutliersByMAD: no visible global function definition for ‘is’
ReplaceOutliersByMAD: no visible global function definition for
‘model.matrix’
ReplaceOutliersByMAD: no visible global function definition for
‘predict’
aFoldcomplexDesign: no visible binding for global variable ‘sd’
aFoldcomplexDesign: no visible binding for global variable ‘var’
aFoldcomplexDesign: no visible global function definition for ‘sd’
callDEs: no visible global function definition for ‘is’
callDEs: no visible binding for global variable ‘p.adjust.methods’
callDEs: no visible global function definition for ‘pnorm’
callDEs: no visible global function definition for ‘pnbinom’
callDEs: no visible global function definition for ‘p.adjust’
callParameter: no visible global function definition for ‘is’
callParameter: no visible binding for global variable ‘var’
callParameter: no visible global function definition for ‘quantile’
callParameter: no visible global function definition for ‘predict’
callParameter: no visible global function definition for ‘model.matrix’
callParameterwithoutReplicates: no visible global function definition
for ‘is’
callParameterwithoutReplicates: no visible binding for global variable
‘sd’
callParameterwithoutReplicates: no visible global function definition
for ‘predict’
callParameterwithoutReplicates: no visible binding for global variable
‘var’
callParameterwithoutReplicates: no visible global function definition
for ‘quantile’
callParameterwithoutReplicates: no visible global function definition
for ‘model.matrix’
callPergroup: no visible binding for global variable ‘var’
estimateSizeFactorsForMatrix: no visible binding for global variable
‘median’
genAFold: no visible binding for global variable ‘var’
genAFold: no visible binding for global variable ‘sd’
genAFold: no visible global function definition for ‘sd’
normalFactors: no visible global function definition for ‘is’
normalFactors: no visible global function definition for ‘validObject’
normalFactors : rowQuar: no visible global function definition for
‘quantile’
normalFactors: no visible global function definition for
‘calcNormFactors’
plotDifftoBase: no visible global function definition for ‘is’
plotDifftoBase: no visible global function definition for ‘plot’
preAFold: no visible global function definition for ‘quantile’
preAFold: no visible global function definition for ‘var’
preAFold: no visible global function definition for ‘predict’
preAFoldComplex: no visible global function definition for ‘quantile’
preAFoldComplex: no visible global function definition for ‘var’
preAFoldComplex: no visible global function definition for ‘predict’
qtotalNormalized : rowQuar: no visible global function definition for
‘quantile’
qtotalNormalized : rowQuar: no visible global function definition for
‘sd’
qtotalNormalized : rowQuar: no visible global function definition for
‘median’
qtotalNormalized : rowQuar : <anonymous>: no visible global function
definition for ‘median’
replaceByrow: no visible global function definition for ‘median’
replaceByrow: no visible global function definition for ‘mad’
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
definition for ‘validObject’
[[<-,SumInfo-character-missing: no visible global function definition
for ‘as’
counts<-,ABSDataSet-matrix: no visible global function definition for
‘validObject’
excounts<-,ABSDataSet-matrix: no visible global function definition for
‘validObject’
groups<-,ABSDataSet-factor: no visible global function definition for
‘validObject’
maxRates<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
minRates<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
minimalDispersion<-,ABSDataSet-numeric: no visible global function
definition for ‘validObject’
normMethod<-,ABSDataSet-character: no visible global function
definition for ‘validObject’
paired<-,ABSDataSet-logical: no visible global function definition for
‘validObject’
sFactors<-,ABSDataSet-numeric: no visible global function definition
for ‘validObject’
Undefined global functions or variables:
as calcNormFactors is mad median model.matrix new p.adjust
p.adjust.methods plot pnbinom pnorm predict quantile sd validObject
var
Consider adding
importFrom("graphics", "plot")
importFrom("methods", "as", "is", "new", "validObject")
importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
"p.adjust.methods", "pnbinom", "pnorm", "predict",
"quantile", "sd", "var")
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
Examples with CPU or elapsed time > 5s
user system elapsed
results 19.337 0.864 21.628
plotDifftoBase 17.013 0.762 17.884
ABSSeq 16.695 0.810 17.612
callDEs 15.822 0.762 16.679
callParameter 14.923 0.816 15.812
ABSSeqlm 10.291 0.632 11.021
ReplaceOutliersByMAD 9.486 0.706 10.276
excounts 9.448 0.718 10.256
genAFold 7.851 0.377 8.297
aFoldcomplexDesign 6.963 0.331 7.344
* 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-3.7-bioc/meat/ABSSeq.Rcheck/00check.log’
for details.
ABSSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ABSSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ABSSeq’ ... ** 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 * DONE (ABSSeq)
ABSSeq.Rcheck/ABSSeq-Ex.timings
| name | user | system | elapsed | |
| ABSDataSet | 0.075 | 0.001 | 0.078 | |
| ABSSeq | 16.695 | 0.810 | 17.612 | |
| ABSSeqlm | 10.291 | 0.632 | 11.021 | |
| LevelstoNormFC | 0.053 | 0.006 | 0.060 | |
| ReplaceOutliersByMAD | 9.486 | 0.706 | 10.276 | |
| aFoldcomplexDesign | 6.963 | 0.331 | 7.344 | |
| callDEs | 15.822 | 0.762 | 16.679 | |
| callParameter | 14.923 | 0.816 | 15.812 | |
| callParameterwithoutReplicates | 3.549 | 0.090 | 3.681 | |
| counts | 0.043 | 0.005 | 0.049 | |
| estimateSizeFactorsForMatrix | 0.061 | 0.004 | 0.066 | |
| excounts | 9.448 | 0.718 | 10.256 | |
| genAFold | 7.851 | 0.377 | 8.297 | |
| groups | 0.047 | 0.004 | 0.051 | |
| maxRates | 0.048 | 0.004 | 0.051 | |
| minRates | 0.043 | 0.004 | 0.048 | |
| minimalDispersion | 0.047 | 0.004 | 0.051 | |
| normMethod | 0.053 | 0.004 | 0.057 | |
| normalFactors | 2.663 | 0.363 | 3.039 | |
| paired | 0.050 | 0.005 | 0.055 | |
| plotDifftoBase | 17.013 | 0.762 | 17.884 | |
| qtotalNormalized | 3.289 | 0.393 | 3.707 | |
| results | 19.337 | 0.864 | 21.628 | |
| sFactors | 3.135 | 0.353 | 3.539 | |
| simuN5 | 0.043 | 0.004 | 0.046 | |