diggit 1.7.0
Mariano J Alvarez
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/diggit | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diggit_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/diggit.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 ‘diggit/DESCRIPTION’ ... OK
* this is package ‘diggit’ version ‘1.7.0’
* 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 ‘diggit’ can be installed ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/diggit.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in citeEntry(entry = "article", author = c(person(c("Mariano", "J"), "Alvarez"), person(c("James", "C"), "Chen"), person("Andrea", "Califano")), title = "{DIGGIT}: a Bioconductor package to infer genetic variants driving cellular phenotypes", journal = "Bioinformatics", year = 2015, volume = 31, number = 24, pages = "4032--4", textVersion = "Alvarez, M.J., Chen, J.C., and Califano, A. (2015) DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics 31(24):4032--4."): could not find function "citeEntry"
* 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
aecdf: no visible global function definition for ‘quantile’
aecdf: no visible global function definition for ‘ecdf’
aecdf: no visible global function definition for ‘knots’
aecdf: no visible global function definition for ‘lm’
aecdf: no visible global function definition for ‘approxfun’
aecdf : dnull: no visible global function definition for ‘predict’
aecdf : dnull: no visible global function definition for ‘qnorm’
conditionalInternal: no visible global function definition for
‘p.adjust’
conditionalInternal : <anonymous>: no visible global function
definition for ‘fisher.test’
conditionalInternal: no visible global function definition for ‘hclust’
conditionalInternal: no visible global function definition for
‘as.dist’
conditionalInternal: no visible global function definition for ‘cutree’
conditionalInternal : <anonymous> : <anonymous> : <anonymous>: no
visible global function definition for ‘fisher.test’
conditionalInternal : <anonymous> : <anonymous>: no visible global
function definition for ‘fisher.test’
correlation : <anonymous>: no visible global function definition for
‘cor’
correlation: no visible global function definition for ‘cor’
cortest: no visible global function definition for ‘pnorm’
distMode: no visible global function definition for ‘density’
fet: no visible global function definition for ‘fisher.test’
internalMIfb: no visible global function definition for ‘dnorm’
mutualInfo: no visible global function definition for ‘qnorm’
mutualInfo: no visible global function definition for ‘combn’
mutualInfo: no visible global function definition for ‘txtProgressBar’
mutualInfo : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
plothm: no visible global function definition for ‘rgb2hsv’
plothm: no visible global function definition for ‘col2rgb’
plothm: no visible global function definition for ‘hsv’
plothm: no visible global function definition for ‘image’
plothm: no visible global function definition for ‘box’
aqtl,diggit: no visible global function definition for ‘p.adjust’
aqtl,diggit: no visible global function definition for ‘pnorm’
conditional,diggit: no visible global function definition for
‘p.adjust’
conditional,diggit: no visible global function definition for ‘pnorm’
conditional,diggit: no visible global function definition for
‘txtProgressBar’
conditional,diggit : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
marina,matrix: no visible global function definition for ‘qnorm’
mindyFiltering,diggit: no visible global function definition for
‘p.adjust’
plot,diggit: no visible global function definition for ‘abline’
plot,diggit: no visible global function definition for ‘text’
plot,diggit: no visible global function definition for ‘axis’
Undefined global functions or variables:
abline approxfun as.dist axis box col2rgb combn cor cutree density
dnorm ecdf fisher.test hclust hsv image knots lm p.adjust pnorm
predict qnorm quantile rgb2hsv setTxtProgressBar text txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
importFrom("graphics", "abline", "axis", "box", "image", "text")
importFrom("stats", "approxfun", "as.dist", "cor", "cutree", "density",
"dnorm", "ecdf", "fisher.test", "hclust", "knots", "lm",
"p.adjust", "pnorm", "predict", "qnorm", "quantile")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
Codoc mismatches from documentation object 'aecdf':
aecdf
Code: function(dnull, symmetric = FALSE, n = 100)
Docs: function(dnull, symmetric = FALSE)
Argument names in code not in docs:
n
* 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
marina-methods 142.092 29.327 62.159
conditional-methods 19.562 2.881 22.464
diggit-plot 17.132 2.481 19.622
aqtl-methods 16.135 2.667 19.257
diggit-methods 6.330 0.302 6.745
* 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: 3 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/diggit.Rcheck/00check.log’
for details.