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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:yeastExpData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings yeastExpData_0.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/yeastExpData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘yeastExpData/DESCRIPTION’ ... OK
* this is package ‘yeastExpData’ version ‘0.46.0’
* 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 loading without being on the library search path ... 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 59Kb xz
fcabundance.rda 110Kb 67Kb xz
gfp.rda 118Kb 60Kb xz
litG.rda 22Kb 8Kb xz
proteinProperties.rda 488Kb 312Kb xz
y2hG.rda 22Kb 9Kb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘yeastExample.Rnw’... OK
OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘yeastExample.Rnw’ using Sweave
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘Rgraphviz’
Error: processing vignette 'yeastExample.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'yeastExample.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file /home/biocbuild/bbs-3.17-data-experiment/meat/yea
stExpData.Rcheck/vign_test/yeastExpData/vignettes/yeastExample-subGraphs.pdf):
PDF inclusion: required page does not exist <0>
==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘yeastExample.Rnw’
SUMMARY: processing the following file failed:
‘yeastExample.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-data-experiment/meat/yeastExpData.Rcheck/00check.log’
for details.
