diggit 1.5.2
Mariano J Alvarez
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/diggit | | Last Changed Rev: 120591 / Revision: 121152 | | Last Changed Date: 2016-08-30 13:33:12 -0700 (Tue, 30 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings diggit_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/diggit.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 ‘diggit/DESCRIPTION’ ... OK
* this is package ‘diggit’ version ‘1.5.2’
* 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 ... OK
* 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 eval(expr, envir, enclos): 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 : 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 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", "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 ... 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
marina-methods 95.088 5.732 37.017
diggit-plot 12.964 0.100 13.066
conditional-methods 12.608 0.208 12.817
aqtl-methods 11.936 0.252 12.233
diggit-methods 5.328 0.104 5.431
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/diggit.Rcheck/00check.log’
for details.
* installing *source* package ‘diggit’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘diggit’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘diggit’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘diggit’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘diggit’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diggit)