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BioC 3.2: CHECK report for cnvGSA on zin1

This page was generated on 2016-04-23 10:12:25 -0700 (Sat, 23 Apr 2016).

Package 200/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cnvGSA 1.14.0
Joseph Lugo
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/cnvGSA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cnvGSA
Version: 1.14.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cnvGSA_1.14.0.tar.gz
StartedAt: 2016-04-22 23:21:34 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:22:39 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cnvGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cnvGSA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cnvGSA.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 ‘cnvGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cnvGSA’ version ‘1.14.0’
* 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 ‘cnvGSA’ can be installed ... [6s/6s] 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘brglm’ ‘doParallel’ ‘foreach’ ‘splitstackshape’
  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
cnvGSAgsTables: no visible global function definition for ‘detectCores’
cnvGSAgsTables: no visible binding for global variable ‘SID’
cnvGSAgsTables: no visible binding for global variable ‘geneID_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘SubjCnvKey’
cnvGSAgsTables: no visible global function definition for
  ‘registerDoParallel’
cnvGSAgsTables: no visible global function definition for ‘%dopar%’
cnvGSAgsTables: no visible global function definition for ‘foreach’
cnvGSAgsTables: no visible binding for global variable ‘i’
cnvGSAgsTables: no visible binding for global variable ‘CHR’
cnvGSAgsTables: no visible binding for global variable ‘BP1’
cnvGSAgsTables: no visible binding for global variable ‘BP2’
cnvGSAgsTables: no visible binding for global variable ‘TYPE’
cnvGSAgsTables: no visible binding for global variable ‘geneID’
cnvGSAgsTables: no visible binding for global variable ‘Symbol’
cnvGSAgsTables: no visible binding for global variable ‘Symbol_TYPE’
cnvGSAgsTables: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘GsID’
cnvGSAlogRegTest: no visible binding for global variable ‘GsKey’
cnvGSAlogRegTest: no visible binding for global variable ‘OlpKL_SID’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘Condition’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘detectCores’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘registerDoParallel’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘%dopar%’
cnvGSAlogRegTest : f.testGLM_wrap: no visible global function
  definition for ‘foreach’
cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global
  variable ‘i’
f.readData: no visible binding for global variable ‘IID’
f.readData: no visible binding for global variable ‘FID’
f.readData: no visible binding for global variable ‘AFF’
f.readData: no visible binding for global variable ‘SID’
f.readData: no visible binding for global variable ‘gs_all.ls’
f.readData: no visible binding for global variable ‘gsid2name.chv’
f.readData: no visible global function definition for ‘GRanges’
f.readData: no visible global function definition for ‘Rle’
f.readData: no visible global function definition for ‘IRanges’
f.readData: no visible global function definition for ‘strand’
f.readData: no visible global function definition for ‘ranges’
f.readData: no visible global function definition for ‘mcols’
f.readData: no visible binding for global variable ‘OlpKL_CNV’
f.readData: no visible binding for global variable ‘geneID_type’
f.readData: no visible binding for global variable ‘CnvKey’
f.readData: no visible binding for global variable ‘OlpKL_SID’
f.readData: no visible binding for global variable ‘geneID_TYPE’
f.readData: no visible binding for global variable ‘SubjCnvKey’
f.readData: no visible binding for global variable ‘GsKey’
f.readData: no visible binding for global variable ‘GsID’
f.readData: no visible binding for global variable ‘GsName’
f.readData: no visible global function definition for ‘cSplit’
f.readData: no visible binding for global variable ‘Symbol’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] 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-bioc/meat/cnvGSA.Rcheck/00check.log’
for details.


cnvGSA.Rcheck/00install.out:

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

cnvGSA.Rcheck/cnvGSA-Ex.timings:

nameusersystemelapsed
CnvGSAInput-class0.0010.0000.001
CnvGSAOutput-class000
cnvGSAIn0.6780.0190.735
cnvGSAgsTables0.5140.0040.531
cnvGSAlogRegTest0.4800.0030.484
f.enrFiles0.0010.0010.000
f.makeViz0.0000.0000.001
f.readConfig0.3620.0000.362