BioC 3.3: CHECK report for IMPCdata on oaxaca

Package: IMPCdata

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.6.0.tar.gz

StartedAt: 2016-10-13 02:51:42 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:55:06 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 204.2 seconds

RetCode: 0

Status:  OK

CheckDir: IMPCdata.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IMPCdata_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/IMPCdata.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IMPCdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IMPCdata’ version ‘1.6.0’
* 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 ‘IMPCdata’ 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 loading without being on the library search path ... 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
getAlleles: no visible global function definition for ‘URLencode’
getGenes: no visible global function definition for ‘URLencode’
getIMPCDataset: no visible global function definition for ‘URLencode’
getIMPCDataset: no visible global function definition for ‘read.csv’
getIMPCTable: no visible global function definition for ‘write.table’
getName: no visible global function definition for ‘URLencode’
getParameters: no visible global function definition for ‘URLencode’
getPipelines: no visible global function definition for ‘URLencode’
getProcedures: no visible global function definition for ‘URLencode’
getStrains: no visible global function definition for ‘URLencode’
getZygosities: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode read.csv write.table
Consider adding
  importFrom("utils", "URLencode", "read.csv", "write.table")
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
getAlleles       0.138  0.035  30.404
printAlleles     0.134  0.034  29.214
printGenes       0.131  0.031  30.459
getGenes         0.128  0.031  29.293
getParameters    0.061  0.009   8.701
printProcedures  0.039  0.009   8.879
getProcedures    0.038  0.009   9.708
printParameters  0.034  0.009   7.868
printPhenCenters 0.019  0.006   8.005
getPhenCenters   0.011  0.003   5.720
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/IMPCdata.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
getAlleles	0.138	0.035	30.404
getGenes	0.128	0.031	29.293
getIMPCDataset	0.478	0.014	4.021
getIMPCTable	0.009	0.001	1.413
getName	0.001	0.000	0.366
getParameters	0.061	0.009	8.701
getPhenCenters	0.011	0.003	5.720
getPipelines	0.005	0.002	1.535
getProcedures	0.038	0.009	9.708
getStrains	0.007	0.002	2.497
getZygosities	0.001	0.000	0.292
printAlleles	0.134	0.034	29.214
printGenes	0.131	0.031	30.459
printParameters	0.034	0.009	7.868
printPhenCenters	0.019	0.006	8.005
printPipelines	0.004	0.001	1.363
printProcedures	0.039	0.009	8.879
printStrains	0.007	0.002	1.902