BioC 3.5: CHECK report for InPAS on oaxaca

Package: InPAS

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings InPAS_1.7.1.tar.gz

StartedAt: 2017-03-04 04:33:55 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:39:56 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 361.2 seconds

RetCode: 0

Status:  OK

CheckDir: InPAS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings InPAS_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/InPAS.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InPAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘InPAS’ 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 ‘InPAS’ 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 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
coverageFromBedGraph : <anonymous>: no visible global function
  definition for 'read.delim'
fft.smooth: no visible global function definition for 'fft'
fisher.exact.test : <anonymous>: no visible global function definition
  for 'fisher.test'
fisher.exact.test: no visible global function definition for 'p.adjust'
getCov: no visible global function definition for 'read.delim'
getCov : summaryFunction: no visible global function definition for
  'read.table'
limmaAnalyze: no visible global function definition for 'pt'
limmaAnalyze: no visible global function definition for 'pf'
limmaAnalyze: no visible global function definition for 'p.adjust'
prepare4GSEA: no visible global function definition for 'write.table'
removeUTR3__UTR3: no visible global function definition for 't.test'
searchDistalCPs : <anonymous>: no visible global function definition
  for 'loess.smooth'
singleGroupAnalyze: no visible global function definition for
  'model.matrix'
singleGroupAnalyze: no visible global function definition for
  'p.adjust'
singleSampleAnalyze : phmm: no visible global function definition for
  'poisson'
singleSampleAnalyze : phmm: no visible global function definition for
  'BIC'
singleSampleAnalyze: no visible global function definition for
  'p.adjust'
utr3UsageEstimation : <anonymous>: no visible global function
  definition for 't.test'
utr3UsageEstimation : <anonymous>: no visible global function
  definition for 'fisher.test'
utr3UsageEstimation: no visible global function definition for
  'model.matrix'
utr3UsageEstimation: no visible global function definition for
  'p.adjust'
valley: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  BIC fft fisher.test loess.smooth model.matrix p.adjust pf pnorm
  poisson pt read.delim read.table t.test write.table
Consider adding
  importFrom("stats", "BIC", "fft", "fisher.test", "loess.smooth",
             "model.matrix", "p.adjust", "pf", "pnorm", "poisson", "pt",
             "t.test")
  importFrom("utils", "read.delim", "read.table", "write.table")
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
filterRes   9.833  0.139  10.308
getUTR3eSet 6.284  0.036   6.320
testUsage   6.257  0.046   6.305
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/InPAS.Rcheck/00check.log’
for details.

* installing *source* package ‘InPAS’ ...
** 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 (InPAS)

name	user	system	elapsed
CPsites	0.001	0.000	0.002
coverageFromBedGraph	0.002	0.000	0.001
coverageRate	0.003	0.000	0.003
filterRes	9.833	0.139	10.308
fisher.exact.test	0.067	0.006	0.073
getUTR3eSet	6.284	0.036	6.320
inPAS	0.003	0.000	0.003
limmaAnalyze	0.033	0.006	0.040
prepare4GSEA	0.199	0.006	0.206
singleGroupAnalyze	0.594	0.007	0.601
singleSampleAnalyze	0.005	0.008	0.013
testUsage	6.257	0.046	6.305
usage4plot	2.829	0.202	3.429
utr3.hg19	0.671	0.031	0.707
utr3.mm10	0.639	0.014	0.654
utr3Annotation	0.001	0.000	0.001
utr3UsageEstimation	0.002	0.001	0.002