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BioC 3.5: CHECK report for SRAdb on toluca2

This page was generated on 2017-04-23 14:35:12 -0400 (Sun, 23 Apr 2017).

Package 1262/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.33.0
Jack Zhu
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb
Last Changed Rev: 127256 / Revision: 129046
Last Changed Date: 2017-03-08 15:23:27 -0500 (Wed, 08 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SRAdb
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SRAdb_1.33.0.tar.gz
StartedAt: 2017-04-23 10:23:13 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 10:24:08 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 55.2 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 SRAdb_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SRAdb.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.33.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SRAdb’ can be installed ... 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
.socketWrite: no visible global function definition for ‘write.socket’
.socketWrite: no visible global function definition for ‘read.socket’
IGVsocket: no visible global function definition for ‘make.socket’
colDescriptions: no visible global function definition for ‘dbGetQuery’
entityGraph: no visible global function definition for ‘na.omit’
entityGraph: no visible global function definition for ‘new’
entityGraph : <anonymous>: no visible global function definition for
  ‘addEdge’
getFASTQfile: no visible global function definition for ‘download.file’
getFASTQinfo: no visible global function definition for ‘dbGetQuery’
getSRA: no visible global function definition for ‘dbGetQuery’
getSRAdbFile: no visible global function definition for ‘download.file’
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’
getSRAfile: no visible global function definition for ‘download.file’
getSRAinfo: no visible global function definition for ‘na.omit’
sraConvert: no visible global function definition for ‘dbGetQuery’
startIGV: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  SQLite addEdge browseURL dbConnect dbDisconnect dbGetQuery
  download.file make.socket na.omit new read.socket write.socket
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "download.file", "make.socket",
             "read.socket", "write.socket")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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
IGVclear0.0010.0010.001
IGVcollapse0.0010.0000.001
IGVgenome0.0010.0010.001
IGVgoto0.0010.0000.001
IGVload0.0010.0000.001
IGVsession0.0020.0010.003
IGVsnapshot0.0000.0000.001
IGVsocket0.0000.0000.001
IGVsort0.0010.0000.001
SRAdb-package0.0360.0010.036
ascpR0.0020.0000.001
ascpSRA0.0010.0010.002
colDescriptions0.0020.0000.002
entityGraph0.0030.0000.003
getFASTQfile0.0020.0010.002
getFASTQinfo0.0010.0000.002
getSRA0.0070.0010.013
getSRAdbFile0.0010.0000.000
getSRAfile0.0030.0000.008
getSRAinfo0.0020.0000.002
listSRAfile0.0010.0000.002
sraConvert0.0020.0010.004
sraGraph0.0030.0000.004
startIGV0.0000.0000.001