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Przemol / seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
http://przemol.github.io/seqplots
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Error while instilling the genome on GUI app under El Capitan #20

Closed js2264 closed 8 years ago

js2264 commented 8 years ago 
> BiocInstaller::biocLite("BSgenome.Scerevisiae.UCSC.sacCer1")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 Patched (2016-01-25
  r70000).
Installing package(s) ‘BSgenome.Scerevisiae.UCSC.sacCer1’
installing the source package ‘BSgenome.Scerevisiae.UCSC.sacCer1’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz'
Content type 'application/x-gzip' length 2967322 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'Europe/London'
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'GMT'
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  unknown timezone 'America/New_York'
* installing *source* package ‘BSgenome.Scerevisiae.UCSC.sacCer1’ ...
Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'America/New_York'
** R
** inst
** preparing package for lazy loading
Error in if (file.size(codeFile) == file.size(loaderFile)) warning("package seems to be using lazy loading already") else { : 
  missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘BSgenome.Scerevisiae.UCSC.sacCer1’
* removing ‘/Applications/SeqPlots.app/Contents/Resources/app/Rmac/Versions/3.2/Resources/library/BSgenome.Scerevisiae.UCSC.sacCer1’

The downloaded source packages are in...

sessionInfo()


R version 3.2.3 Patched (2016-01-25 r70000)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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

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

loaded via a namespace (and not attached): [1] BiocInstaller_1.20.3 tools_3.2.3

Przemol commented 7 years ago

The error is caused by trying to lazy load a package first from default R package installation directory, defined by .libPaths() and then from actual SeqPlots genome package installation directory in SeqPlots data folder Sys.getenv('root'), 'genomes'). It was fixed by giving a priority to SeqPlots data folder in 6345d2bd45329c24e43782e1783f561926dc8ca3.