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3.6 years ago by
Guest User12k
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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/BS genome.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/njzgdjy14tj51zl3kl 8stdn40000gn/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 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 3.6 years ago by James W. MacDonald45k • written 3.6 years ago by Guest User12k
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gravatar for James W. MacDonald
3.6 years ago by
United States
James W. MacDonald45k wrote:
Hi Matt, On 5/26/2014 2:46 PM, Matt Paul [guest] wrote: > 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 I am taking you literally here; if you are trying to load your package using library(mypackage), that won't work. Below it looks like the installation went OK, and library(BSgenome.Scersk1MvOV1) should load the package. If not, what happens? Best, Jim > 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/njzgdjy14tj51zl3 kl8stdn40000gn/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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 3.6 years ago by James W. MacDonald45k
Hi James, That was not the literal input I'm afraid. I used: library(BSgenome.Scersk1MvOV1), as you suggest. When I do this I get this: Error in library(BSgenome.Scersk1MvOV1) : there is no package called ‘BSgenome.Scersk1MvOV1’. I have talked to some people in my lab and they said that the comp is running two versions of R. I'm trying to run this all through R studio so perhaps the command line R and Rstudio version are not matching up. I don't have a clue if they're right, but I'm going to try on a different computer and see. Thanks for your speedy response, Matt [[alternative HTML version deleted]]
ADD REPLYlink written 3.6 years ago by Matthew Robert Paul20
since R CMD INSTALL indicated success installing to ˜/Library/Frameworks/R.framework/Versions/3.1/Resources/library why don't you set that in your .libPaths() before running library() again On Tue, May 27, 2014 at 10:58 AM, Matthew Robert Paul <mattpaul@nyu.edu>wrote: > Hi James, > > That was not the literal input I'm afraid. I used: > library(BSgenome.Scersk1MvOV1), > as you suggest. When I do this I get this: > > Error in library(BSgenome.Scersk1MvOV1) : > there is no package called ‘BSgenome.Scersk1MvOV1’. > > I have talked to some people in my lab and they said that the comp is > running two versions of R. I'm trying to run this all through R studio so > perhaps the command line R and Rstudio version are not matching up. I don't > have a clue if they're right, but I'm going to try on a different computer > and see. > > Thanks for your speedy response, > Matt > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 3.6 years ago by Vincent J. Carey, Jr.6.2k
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