clipper 1.12.0 Paolo Martini
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/clipper | Last Changed Rev: 117079 / Revision: 122332 | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings clipper_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/clipper.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.12.0’
* 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 ‘clipper’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cliqueMeanTest : <anonymous>: no visible global function definition for
‘t.test’
cliqueMixedTest : <anonymous>: no visible global function definition
for ‘t.test’
cliquePairedTest : <anonymous>: no visible global function definition
for ‘t.test’
cliquePairedTest : <anonymous>: no visible global function definition
for ‘pf’
cliqueParamTest: no visible global function definition for ‘pchisq’
estimateExprCov: no visible global function definition for ‘cov’
hote4mean: no visible global function definition for ‘cov’
hote4mean: no visible global function definition for ‘pf’
prunePaths: no visible global function definition for ‘hclust’
prunePaths: no visible global function definition for ‘as.dist’
prunePaths: no visible global function definition for ‘pdf’
prunePaths: no visible global function definition for ‘dev.off’
prunePaths: no visible global function definition for ‘cutree’
runPathwayVar: no visible global function definition for ‘qchisq’
runPathwayVar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
as.dist cov cutree dev.off hclust pchisq pdf pf qchisq t.test
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("stats", "as.dist", "cov", "cutree", "hclust", "pchisq",
"pf", "qchisq", "t.test")
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 sizes of PDF files under ‘inst/doc’ ... 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
clipperAllRoots 10.610 0.047 10.794
pathwayTest 10.032 0.019 10.272
clipper 5.295 0.088 5.651
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/clipper.Rcheck/00check.log’
for details.