SomatiCA 2.1.2
Mengjie Chen
| Snapshot Date: 2016-05-01 16:20:05 -0700 (Sun, 01 May 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SomatiCA | | Last Changed Rev: 116523 / Revision: 116959 | | Last Changed Date: 2016-04-18 21:25:17 -0700 (Mon, 18 Apr 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 | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SomatiCA_2.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SomatiCA.Rcheck’
* using R version 3.3.0 RC (2016-04-28 r70561)
* using platform: x86_64-pc-linux-gnu (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 ‘2.1.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘SomatiCAData’
Depends: includes the non-default packages:
‘lars’ ‘DNAcopy’ ‘foreach’ ‘rebmix’ ‘GenomicRanges’ ‘IRanges’
‘doParallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [6s/6s] WARNING
Found the following significant warnings:
Warning: Package 'SomatiCA' is deprecated and will be removed from Bioconductor
Warning: replacing previous import ‘sn::coef’ by ‘rebmix::coef’ when loading ‘SomatiCA’
Warning: replacing previous import ‘sn::sd’ by ‘IRanges::sd’ when loading ‘SomatiCA’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/SomatiCA.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 loading without being on the library search path ... 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.
'library' or 'require' call to ‘sn’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.larsCBS: no visible global function definition for ‘rnorm’
GCbiasRemoval: no visible global function definition for ‘lm’
GCcount: no visible global function definition for ‘download.file’
admixtureRate : rdirichlet: no visible global function definition for
‘rgamma’
admixtureRate: no visible global function definition for ‘runif’
admixtureRate: no visible global function definition for ‘dnorm’
admixtureRate: no visible global function definition for ‘optimize’
plotSegment: no visible global function definition for ‘axis’
plotSegment: no visible global function definition for ‘lines’
plotSubclonality: no visible global function definition for
‘colorRampPalette’
plotSubclonality: no visible global function definition for ‘par’
plotSubclonality: no visible global function definition for ‘axis’
plotSubclonality: no visible global function definition for ‘lines’
plotSubclonality: no visible global function definition for ‘abline’
plotSubclonality: no visible global function definition for ‘text’
plotSubclonality: no visible global function definition for ‘legend’
refineSegment: no visible global function definition for ‘sn.mle’
refineSegment: no visible global function definition for ‘optimize’
somaticRatio: no visible global function definition for ‘sn.mle’
somaticRatio: no visible global function definition for ‘optimize’
subclonality: no visible global function definition for ‘pnorm’
SomatiCAFormat,character: no visible global function definition for
‘read.table’
Undefined global functions or variables:
abline axis colorRampPalette dnorm download.file legend lines lm
optimize par pnorm read.table rgamma rnorm runif sn.mle text
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("graphics", "abline", "axis", "legend", "lines", "par",
"text")
importFrom("stats", "dnorm", "lm", "optimize", "pnorm", "rgamma",
"rnorm", "runif")
importFrom("utils", "download.file", "read.table")
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 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 files in ‘vignettes’ ... OK
* checking examples ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
admixtureRate 16.340 0.008 16.601
SomatiCApipe 15.948 0.012 16.179
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/SomatiCA.Rcheck/00check.log’
for details.
* installing *source* package ‘SomatiCA’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘sn::coef’ by ‘rebmix::coef’ when loading ‘SomatiCA’
Warning: replacing previous import ‘sn::sd’ by ‘IRanges::sd’ when loading ‘SomatiCA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘sn::coef’ by ‘rebmix::coef’ when loading ‘SomatiCA’
Warning: replacing previous import ‘sn::sd’ by ‘IRanges::sd’ when loading ‘SomatiCA’
Warning: Package 'SomatiCA' is deprecated and will be removed from Bioconductor
version 3.3
* DONE (SomatiCA)