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BioC 3.0: CHECK report for SRAdb on oaxaca

This page was generated on 2015-04-10 10:04:08 -0700 (Fri, 10 Apr 2015).

Package 857/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.20.13
Jack Zhu
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/SRAdb
Last Changed Rev: 101002 / Revision: 102249
Last Changed Date: 2015-03-22 16:27:17 -0700 (Sun, 22 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: SRAdb
Version: 1.20.13
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SRAdb_1.20.13.tar.gz
StartedAt: 2015-04-10 03:38:15 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:39:20 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 65.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SRAdb_1.20.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SRAdb.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SRAdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SRAdb’ version ‘1.20.13’
* 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 ‘SRAdb’ 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 ... NOTE
The following files look like leftovers:
  ‘SRAdb/SRAdb-package.Rd’
Please remove them from your package.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘graph’
  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
colDescriptions: no visible global function definition for ‘dbGetQuery’
entityGraph : <anonymous>: no visible global function definition for
  ‘addEdge’
getFASTQinfo: no visible binding for global variable ‘sra_con’
getFASTQinfo: no visible global function definition for ‘dbGetQuery’
getSRA: no visible global function definition for ‘dbGetQuery’
getSRAdbFile: no visible global function definition for ‘dbConnect’
getSRAdbFile: no visible global function definition for ‘SQLite’
getSRAdbFile: no visible global function definition for ‘dbGetQuery’
getSRAdbFile: no visible global function definition for ‘dbDisconnect’
sraConvert: no visible global function definition for ‘dbGetQuery’
* 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 ... [3s/3s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/SRAdb.Rcheck/00check.log’
for details.

SRAdb.Rcheck/00install.out:

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

SRAdb.Rcheck/SRAdb-Ex.timings:

nameusersystemelapsed
IGVclear0.0010.0000.001
IGVcollapse0.0000.0010.001
IGVgenome0.0000.0000.001
IGVgoto0.0010.0000.001
IGVload0.0010.0000.001
IGVsession0.0060.0020.007
IGVsnapshot0.0010.0000.000
IGVsocket0.0010.0010.001
IGVsort0.0010.0000.001
SRAdb-package0.0400.0010.043
ascpR0.0020.0000.004
ascpSRA0.0020.0000.002
colDescriptions0.0020.0000.002
entityGraph0.0040.0010.004
getFASTQfile0.0020.0000.002
getFASTQinfo0.0010.0000.002
getSRA0.0060.0000.007
getSRAdbFile0.0000.0000.001
getSRAfile0.0040.0000.004
getSRAinfo0.0020.0000.002
listSRAfile0.0010.0000.001
sraConvert0.0020.0000.002
sraGraph0.0040.0000.005
startIGV0.0010.0000.001