conumee 1.5.2
Volker Hovestadt
| Snapshot Date: 2016-06-16 16:20:05 -0700 (Thu, 16 Jun 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/conumee | | Last Changed Rev: 117512 / Revision: 118696 | | Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| 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 conumee_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/conumee.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conumee/DESCRIPTION’ ... OK
* this is package ‘conumee’ 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘conumee’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘conumee’ for: ‘plot’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
.cumsum0: no visible global function definition for ‘head’
.curl: no visible global function definition for ‘tail’
CNV.bin,CNV.analysis: no visible global function definition for ‘optim’
CNV.detailplot,CNV.analysis: no visible global function definition for
‘par’
CNV.detailplot,CNV.analysis: no visible global function definition for
‘plot’
CNV.detailplot,CNV.analysis: no visible global function definition for
‘axis’
CNV.detailplot,CNV.analysis: no visible global function definition for
‘colorRamp’
CNV.detailplot,CNV.analysis : <anonymous>: no visible global function
definition for ‘rgb’
CNV.detailplot,CNV.analysis: no visible global function definition for
‘lines’
CNV.detailplot_wrap,CNV.analysis: no visible global function definition
for ‘par’
CNV.detailplot_wrap,CNV.analysis: no visible global function definition
for ‘frame’
CNV.detailplot_wrap,CNV.analysis: no visible global function definition
for ‘title’
CNV.fit,CNV.data-CNV.data-CNV.anno: no visible global function
definition for ‘lm’
CNV.fit,CNV.data-CNV.data-CNV.anno: no visible global function
definition for ‘predict’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘par’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘plot’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘abline’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘axis’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘colorRamp’
CNV.genomeplot,CNV.analysis : <anonymous>: no visible global function
definition for ‘rgb’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘lines’
CNV.genomeplot,CNV.analysis: no visible global function definition for
‘text’
CNV.load,matrix: no visible binding for global variable ‘anno’
CNV.write,CNV.analysis: no visible global function definition for
‘write.table’
Undefined global functions or variables:
abline anno axis colorRamp frame head lines lm optim par plot predict
rgb tail text title write.table
Consider adding
importFrom("grDevices", "colorRamp", "rgb")
importFrom("graphics", "abline", "axis", "frame", "lines", "par",
"plot", "text", "title")
importFrom("stats", "lm", "optim", "predict")
importFrom("utils", "head", "tail", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'CNV.data,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'read.450k.exp' is deprecated.
Warning: 'read.450k' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
CNV.detailplot_wrap 114.480 0.340 114.860
CNV.analysis-class 113.100 1.320 115.224
CNV.write 113.656 0.444 114.127
CNV.detailplot 111.492 0.496 113.008
CNV.genomeplot 108.968 0.372 109.420
CNV.segment 99.916 0.072 100.001
CNV.fit 44.968 2.192 47.212
CNV.anno-class 39.088 0.020 39.126
CNV.detail 38.532 0.164 39.085
CNV.bin 36.596 0.136 36.744
CNV.create_anno 33.236 0.012 33.267
read.450k.url 4.420 0.072 12.728
* 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 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/conumee.Rcheck/00check.log’
for details.