SomatiCA 1.4.0
Mengjie Chen
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/SomatiCA | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SomatiCA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomatiCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomatiCA’ version ‘1.4.0’
* 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 ‘SomatiCA’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘foreach’ ‘lars’ ‘DNAcopy’ ‘methods’ ‘rebmix’ ‘GenomicRanges’ ‘IRanges’ ‘sn’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... NOTE
The following files look like leftovers:
‘SomatiCA/NEWS.Rd’
Please remove them from your package.
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in bibentry(bibtype = entry, textVersion = textVersion, header = header, footer = footer, ...): argument "textVersion" is missing, with no default
* 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 ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
‘DNAcopy’ ‘doParallel’ ‘foreach’ ‘lars’ ‘rebmix’
Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
refineSegment: no visible global function definition for ‘sn.mle’
somaticRatio: no visible global function definition for ‘sn.mle’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘SomatiCA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [172s/176s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
SomatiCApipe 63.655 14.196 79.321
admixtureRate 54.000 12.214 68.611
GCbiasRemoval 8.287 0.166 8.547
* 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
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/SomatiCA.Rcheck/00check.log’
for details.