BioC 3.3: CHECK report for PSICQUIC on zin2

Package: PSICQUIC

Version: 1.10.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PSICQUIC_1.10.0.tar.gz

StartedAt: 2016-10-13 05:29:14 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:32:05 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: PSICQUIC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PSICQUIC_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSICQUIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSICQUIC’ version ‘1.10.0’
* 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 ‘PSICQUIC’ 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 ... 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:
  ‘httr’ ‘plyr’
  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
.loadRegistry: no visible global function definition for ‘DataFrame’
.loadRegistry : <anonymous>: no visible global function definition for
  ‘str’
.retrieveData: no visible global function definition for ‘read.table’
.retrieveData : <anonymous>: no visible global function definition for
  ‘str’
.translate.uniprotkb: no visible binding for global variable ‘id’
detectionMethods: no visible global function definition for ‘browseURL’
interactionTypes: no visible global function definition for ‘browseURL’
speciesIDs: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  DataFrame browseURL id read.table str
Consider adding
  importFrom("utils", "browseURL", "read.table", "str")
to your NAMESPACE file.
* 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
Examples with CPU or elapsed time > 5s
                user system elapsed
PSICQUIC-class 0.825  0.045  28.599
interactions   0.379  0.004  11.180
IDMapper-class 0.113  0.016   5.616
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.3-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
IDMapper-class	0.113	0.016	5.616
PSICQUIC-class	0.825	0.045	28.599
interactions	0.379	0.004	11.180
providers	0.015	0.004	1.178
rawQuery	0.032	0.000	1.960
webBrowser-functions	0.001	0.000	0.000