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BioC experimental data: CHECK report for SomaticCancerAlterations on zin1

This page was generated on 2016-04-23 10:54:56 -0700 (Sat, 23 Apr 2016).

Package 230/257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticCancerAlterations 1.6.1
Julian Gehring
Snapshot Date: 2016-04-20 09:20:20 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/SomaticCancerAlterations
Last Changed Rev: 3709 / Revision: 3730
Last Changed Date: 2016-04-10 09:59:54 -0700 (Sun, 10 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]YES, new version is higher than in internal repository

Summary

Package: SomaticCancerAlterations
Version: 1.6.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.6.1.tar.gz
StartedAt: 2016-04-20 12:07:30 -0700 (Wed, 20 Apr 2016)
EndedAt: 2016-04-20 12:09:03 -0700 (Wed, 20 Apr 2016)
EllapsedTime: 92.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SomaticCancerAlterations.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/SomaticCancerAlterations.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomaticCancerAlterations/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticCancerAlterations’ version ‘1.6.1’
* package encoding: UTF-8
* 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 ‘SomaticCancerAlterations’ can be installed ... [8s/8s] 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 ... 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 ... OK
* checking whether the namespace can be unloaded cleanly ... 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
hg2ncbi: no visible global function definition for ‘seqnameStyle<-’
hg2ncbi: no visible global function definition for ‘genome<-’
mutationDensity: no visible global function definition for
  ‘keepSeqlevels’
ncbi2hg: no visible global function definition for ‘seqnameStyle<-’
ncbi2hg: no visible global function definition for ‘genome<-’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.R’ [11s/11s]
 [11s/12s] OK
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-data-experiment/meat/SomaticCancerAlterations.Rcheck/00check.log’
for details.


SomaticCancerAlterations.Rcheck/00install.out:

* installing *source* package ‘SomaticCancerAlterations’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SomaticCancerAlterations)

SomaticCancerAlterations.Rcheck/SomaticCancerAlterations-Ex.timings:

nameusersystemelapsed
all-data0.0480.0000.048
all-functions0.2770.0040.281