BioC 3.3: CHECK report for IMPCdata on zin2

Package: IMPCdata

Version: 1.6.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IMPCdata_1.6.0.tar.gz

StartedAt: 2016-10-13 03:22:01 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:25:17 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 195.8 seconds

RetCode: 0

Status:  OK

CheckDir: IMPCdata.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 IMPCdata_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/IMPCdata.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 ‘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
getIMPCDataset   0.309  0.008   6.711
getAlleles       0.156  0.020  30.629
printAlleles     0.145  0.016  29.575
getGenes         0.141  0.016  29.926
printGenes       0.131  0.023  29.697
getParameters    0.057  0.009   8.967
getProcedures    0.033  0.012   9.617
printProcedures  0.040  0.005   8.881
printParameters  0.031  0.009   7.872
printPhenCenters 0.019  0.006   7.964
* 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
  ‘/home/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	0.156	0.020	30.629
getGenes	0.141	0.016	29.926
getIMPCDataset	0.309	0.008	6.711
getIMPCTable	0.009	0.000	1.417
getName	0.002	0.000	0.366
getParameters	0.057	0.009	8.967
getPhenCenters	0.004	0.008	4.947
getPipelines	0.005	0.001	1.400
getProcedures	0.033	0.012	9.617
getStrains	0.005	0.004	2.434
getZygosities	0.002	0.000	0.291
printAlleles	0.145	0.016	29.575
printGenes	0.131	0.023	29.697
printParameters	0.031	0.009	7.872
printPhenCenters	0.019	0.006	7.964
printPipelines	0.005	0.000	1.365
printProcedures	0.040	0.005	8.881
printStrains	0.008	0.000	1.907