[BioC] Creating a package

Matt Paul [guest] guest at bioconductor.org
Mon May 26 20:46:44 CEST 2014


Hi there,

I am trying to create one of the genome packages for the SK1 strain of S. cerevisiae. I thought it was going okay and the guide is very clear. When it comes to checking the package there were a few error messages. In the guide it said ignore messages so I plugged on and the installation went through okay. I cannot load up the package now though. 
Im using library(mypackage). This past few months have been a steep learning curve so I am not sure if I am missing something very basic or it's something beyond me. I have searched high and low. Below are the commands I ran to build and install. I also have the seedfile further down.

Thanks very much. I appreciate the help a lot. 

ercan1:SK1_MvO_V1 sevincercan$ R CMD build BSgenome.Scersk1MvOV1
* checking for file ‘BSgenome.Scersk1MvOV1/DESCRIPTION’ ... OK
* preparing ‘BSgenome.Scersk1MvOV1’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘BSgenome.Scersk1MvOV1_1.00.tar.gz’

ercan1:SK1_MvO_V1 sevincercan$ R CMD check BSgenome.Scersk1MvOV1_1.00.tar.gz 
* using log directory ‘/Users/sevincercan/Matt/Dropbox/SK1_MvO_V1/BSgenome.Scersk1MvOV1.Rcheck’
* using R version 3.1.0 (2014-04-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘BSgenome.Scersk1MvOV1/DESCRIPTION’ ... OK
* this is package ‘BSgenome.Scersk1MvOV1’ version ‘1.00’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome.Scersk1MvOV1’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BSgenome’
A package should be listed in only one of these fields.
* 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 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
.onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae SK1",
  species = "Yeast", provider = "Hochwagen Lab", provider_version =
  "1.00", release_date = "Unsure. Obtained in early 2014", release_name
  = "NULL", source_url = "NULL", seqnames = .seqnames, circ_seqs =
  .circ_seqs, mseqnames = .mseqnames, seqs_pkgname = pkgname, seqs_dir
  = extdata_dir, nmask_per_seq = .nmask_per_seq, masks_pkgname =
  pkgname, masks_dir = extdata_dir): partial argument match of
  'seqs_dir' to 'seqs_dirpath'
.onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae SK1",
  species = "Yeast", provider = "Hochwagen Lab", provider_version =
  "1.00", release_date = "Unsure. Obtained in early 2014", release_name
  = "NULL", source_url = "NULL", seqnames = .seqnames, circ_seqs =
  .circ_seqs, mseqnames = .mseqnames, seqs_pkgname = pkgname, seqs_dir
  = extdata_dir, nmask_per_seq = .nmask_per_seq, masks_pkgname =
  pkgname, masks_dir = extdata_dir): partial argument match of
  'masks_dir' to 'masks_dirpath'
* checking Rd files ... NOTE
prepare_Rd: package.Rd:15-17: Dropping empty section details
* 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 examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -rf /var/folders/j9/njzgdjy14tj51zl3kl8stdn40000gn/T//RtmprmI80X/Rd2pdf3f9731ac7bf'
ercan1:SK1_MvO_V1 

sevincercan$ R CMD INSTALL BSgenome.Scersk1MvOV1_1.00.tar.gz 
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘BSgenome.Scersk1MvOV1’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BSgenome.Scersk1MvOV1)




SEED FILE

Package: BSgenome.Scersk1MvOV1
Title: Full genome sequences for S. cerevisiae SK1 strain
Description: Full genome sequences for S. cerevisiae SK1 strain as prepared by Hochwagen lab (unsure of build date. obtained in early 2014) and stored in Biostrings objects.
Version: 1.00
organism: Saccharomyces cerevisiae SK1
species: Yeast
provider: Hochwagen Lab
provider_version: 1.00
release_date: Unsure. Obtained in early 2014
release_name: NULL
source_url: NULL
organism_biocview: Saccharomyces cerevisiae
BSgenomeObjname: Scersk1MvOV1
seqnames: paste("chr", c(paste("0", c(1:9), sep=""), c(10:16)), sep="")
circ_seqs: NULL
mseqnames: NULL
SrcDataFiles1: sk1_MvO_V1.fasta
PkgExamples: NULL
seqs_srcdir: /Users/sevincercan/Matt/SK1_MvO_V1



 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] seqinr_3.0-7         BSgenome_1.32.0      Biostrings_2.32.0   
[4] XVector_0.4.0        GenomicRanges_1.16.3 GenomeInfoDb_1.0.2  
[7] IRanges_1.22.7       BiocGenerics_0.10.0 

loaded via a namespace (and not attached):
[1] bitops_1.0-6     Rsamtools_1.16.0 stats4_3.1.0    
[4] tools_3.1.0      zlibbioc_1.10.0 

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