biobroom 1.8.0
John D. Storey and Andrew J. Bass
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/biobroom | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings biobroom_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/biobroom.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biobroom/DESCRIPTION’ ... OK
* this is package ‘biobroom’ version ‘1.8.0’
* 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 ‘biobroom’ 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 ‘DESeq2’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘dplyr::tbl_dt’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
finish: no visible global function definition for ‘tbl_dt’
glance.DGEExact: no visible global function definition for ‘p.adjust’
glance.GRanges: no visible binding for global variable ‘gr’
glance.GRangesList: no visible binding for global variable ‘gr’
makeExampleDataSet: no visible global function definition for
‘estimateSizeFactors’
makeExampleDataSet: no visible global function definition for ‘counts’
makeExampleDataSet: no visible global function definition for ‘colData’
makeExampleDataSet: no visible global function definition for
‘seqnames’
makeExampleDataSet: no visible global function definition for
‘rowRanges’
makeExampleDataSet: no visible global function definition for ‘start’
makeExampleDataSet: no visible global function definition for ‘end’
makeExampleDataSet: no visible global function definition for ‘DGEList’
makeExampleDataSet: no visible global function definition for
‘calcNormFactors’
makeExampleDataSet: no visible global function definition for
‘model.matrix’
makeExampleDataSet: no visible global function definition for ‘design’
makeExampleDataSet: no visible global function definition for
‘voomWithQualityWeights’
makeExampleDataSet: no visible global function definition for ‘voom’
makeExampleDataSet: no visible global function definition for ‘pData<-’
makeExampleDataSet: no visible global function definition for ‘fData<-’
makeExampleDataSet: no visible global function definition for ‘is’
tidy.DESeqDataSet: no visible binding for global variable ‘term’
tidy.DESeqDataSet: no visible binding for global variable ‘.’
tidy.DESeqDataSet: no visible global function definition for ‘counts’
tidy.DESeqDataSet: no visible binding for global variable ‘gene’
tidy.DGEList: no visible binding for global variable ‘gene’
tidy.EList: no visible global function definition for ‘setNames’
tidy.ExpressionSet: no visible binding for global variable ‘value’
tidy.ExpressionSet: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible global function definition for ‘pData’
tidy.MArrayLM: no visible binding for global variable ‘term’
tidy.MArrayLM: no visible binding for global variable ‘estimate’
tidy.MArrayLM: no visible binding for global variable ‘gene’
tidy.MSnSet: no visible binding for global variable ‘sample.id’
tidy.MSnSet: no visible binding for global variable ‘value’
tidy.MSnSet: no visible binding for global variable ‘protein’
tidy.MSnSet: no visible global function definition for ‘pData’
tidy.RangedSummarizedExperiment: no visible binding for global variable
‘value’
tidy.RangedSummarizedExperiment: no visible binding for global variable
‘gene’
tidy.RangedSummarizedExperiment: no visible global function definition
for ‘colData’
tidy.deSet: no visible global function definition for ‘exprs<-’
tidy.deSet: no visible binding for global variable ‘value’
tidy.deSet: no visible binding for global variable ‘gene’
tidy.deSet: no visible global function definition for ‘pData’
tidy.qvalue: no visible binding for global variable ‘smoothed’
tidy.qvalue: no visible binding for global variable ‘pi0’
tidy.qvalue: no visible binding for global variable ‘lambda’
tidy_matrix: no visible binding for global variable ‘value’
tidy_matrix: no visible binding for global variable ‘gene’
Undefined global functions or variables:
. DGEList calcNormFactors colData counts design end estimate
estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
setNames smoothed start tbl_dt term value voom voomWithQualityWeights
Consider adding
importFrom("methods", "is")
importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
"start")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
DESeq2_tidiers 9.924 0.084 10.052
edgeR_tidiers 4.868 0.040 5.145
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/biobroom.Rcheck/00check.log’
for details.