BioC experimental data: CHECK report for yeastExpData on malbec1

##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings yeastExpData_0.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/yeastExpData.Rcheck’
* using R version 3.3.3 (2017年03月06日)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yeastExpData/DESCRIPTION’ ... OK
* this is package ‘yeastExpData’ version ‘0.20.0’
* 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 ‘yeastExpData’ 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from documentation object 'gfp':
Variables in data frame 'gfp'
 Code: ER ER_to_Golgi GFP_tagged GFP_visualized Golgi TAP_visualized
 abundance actin ambiguous bud bud_neck cell_periphery cytoplasm
 early_Golgi endosome error gene_name late_Golgi lipid_particle
 localization_summary microtubule missingAbundance mitochondrion
 nuclear_periphery nucleolus nucleus orfid peroxisome
 punctate_composite spindle_pole vacuolar_membrane vacuole yORF
 Docs: GFP_tagged GFP_visualized TAP_visualized abundance error
 gene_name localization_summary orfid yORF
Data codoc mismatches from documentation object 'proteinProperties':
Variables in data frame 'proteinProperties'
 Code: ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER
 SGDID THR TRP TYR VAL aromaticity cai codonBias cterm fop gravy
 length molwt nterm pi type yORF
 Docs: SGDID cai codonBias cterm length molwt nterm pi yORF
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘lattice’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
 Warning: large data file saved inefficiently:
 size ASCII compress
 ccyclered.rda 364Kb FALSE none
 
 Note: significantly better compression could be obtained
 by using R CMD build --resave-data
 old_size new_size compress
 ccyclered.rda 364Kb 58Kb xz
 fcabundance.rda 110Kb 67Kb xz
 gfp.rda 118Kb 60Kb xz
 litG.rda 22Kb 8Kb xz
 proteinProperties.rda 488Kb 314Kb xz
 y2hG.rda 22Kb 9Kb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘Rgraphviz’
* 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: 3 WARNINGs, 1 NOTE
See
 ‘/home/biocbuild/bbs-3.4-data-experiment/meat/yeastExpData.Rcheck/00check.log’
for details.

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