SomatiCA 2.1.0
Mengjie Chen
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SomatiCA | | Last Changed Rev: 116389 / Revision: 116712 | | Last Changed Date: 2016-04-15 20:06:28 -0700 (Fri, 15 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | 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 SomatiCA_2.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SomatiCA.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.1.0’
* 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’ ‘mvtnorm’
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 ... [9s/13s] WARNING
Found the following significant warnings:
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 ‘/Users/biocbuild/bbs-3.2-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
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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
GCcontent.rda 3.1Mb 616Kb xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
admixtureRate 22.959 0.181 23.165
SomatiCApipe 22.080 0.157 22.368
* 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.2-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’
* DONE (SomatiCA)