BioC experimental data: CHECK report for ChAMPdata on perceval

Package: ChAMPdata

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMPdata_1.7.0.tar.gz

StartedAt: 2015-08-22 08:54:02 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 08:57:15 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 192.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ChAMPdata.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMPdata_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘1.7.0’
* 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 ‘ChAMPdata’ can be installed ... [3s/7s] OK
* checking installed package size ... NOTE
  installed size is 245.6Mb
  sub-directories of 1Mb or more:
    data     121.9Mb
    extdata  123.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 Rd files ... NOTE
prepare_Rd: bloodCtl.Rd:162-164: Dropping empty section \details
prepare_Rd: bloodCtl.Rd:165-167: Dropping empty section \source
prepare_Rd: bloodCtl.Rd:168-170: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘multi.hit’ ‘snp.hit’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from documentation object 'probe.features':
Variables in data frame 'probe.features'
  Code: arm cgi CHR conserved_tfbs distancetoGene feat.cgi feature gene
        MAPINFO
  Docs: arm cgi CHR feat.cgi feature feature.1 feature.2 feature.3
        feature.4 gene.1 gene.2 gene.3 gene.4 MAPINFO

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [47s/57s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChAMPdata-package 29.052  0.985  36.515
testDataSet       12.819  0.432  15.512
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.

* installing *source* package ‘ChAMPdata’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ChAMPdata)

name	user	system	elapsed
ChAMPdata-package	29.052	0.985	36.515
bloodCtl	0.004	0.002	0.226
probe.features	2.040	0.262	2.673
probeInfoALL.lv	0.655	0.042	0.823
testDataSet	12.819	0.432	15.512