BioC experimental data: CHECK report for yeastExpData on perceval

Package: yeastExpData

Version: 0.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yeastExpData_0.15.0.tar.gz

StartedAt: 2015-08-22 10:08:53 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 10:09:22 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 29.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: yeastExpData.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings yeastExpData_0.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/yeastExpData.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 ‘yeastExpData/DESCRIPTION’ ... OK
* this is package ‘yeastExpData’ version ‘0.15.0’
* 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 ... [2s/2s] 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: abundance actin ambiguous bud bud_neck cell_periphery cytoplasm
        early_Golgi endosome ER ER_to_Golgi error gene_name GFP_tagged
        GFP_visualized Golgi late_Golgi lipid_particle
        localization_summary microtubule missingAbundance mitochondrion
        nuclear_periphery nucleolus nucleus orfid peroxisome
        punctate_composite spindle_pole TAP_visualized
        vacuolar_membrane vacuole yORF
  Docs: abundance error gene_name GFP_tagged GFP_visualized
        localization_summary orfid TAP_visualized yORF

Data codoc mismatches from documentation object 'proteinProperties':
Variables in data frame 'proteinProperties'
  Code: ALA ARG aromaticity ASN ASP cai codonBias cterm CYS fop GLN GLU
        GLY gravy HIS ILE length LEU LYS MET molwt nterm PHE pi PRO SER
        SGDID THR TRP type TYR VAL yORF
  Docs: cai codonBias cterm length molwt nterm pi SGDID 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     59Kb       xz
  fcabundance.rda          110Kb     67Kb       xz
  gfp.rda                  118Kb     60Kb       xz
  litG.rda                  22Kb      8Kb       xz
  proteinProperties.rda    488Kb    313Kb       xz
  y2hG.rda                  22Kb      9Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] 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
  ‘/Users/biocbuild/bbs-3.2-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)

name	user	system	elapsed
ccyclered	0.010	0.002	0.012
fcabundance	0.071	0.006	0.088
gfp	0.372	0.019	0.550
litG	0.024	0.002	0.048
nPdist	0.002	0.001	0.003
proteinProperties	0.492	0.033	0.694