I recently updated my R packages and some code that I used to run with rtracklayer started failing. In particular, laying a new track was failing silently. I found that the same bug is reproducible in the vignette, but eval=FALSE for the code chunk in question and thus the vignette compiles to PDF as normal. Can anyone else reproduce this bug? Code and session info below. # This code chunk fails without an error. ################################################### ### code chunk number 15: layTrack (eval = FALSE) ################################################### ## track(session, "targets") <- targetTrack # We know the code is failing due to the below code and output table(trackNames(session)=="targets") FALSE 223 R version 2.15.1 (2012-06-22) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 [2] BSgenome_1.26.0 [3] Biostrings_2.26.0 [4] rtracklayer_1.18.0 [5] GenomicRanges_1.10.0 [[alternative HTML version deleted]]

Just a note: this is a long-standing bug. I'll try to look into it soon. Michael On Mon, Oct 22, 2012 at 12:29 PM, J.T. Poirier <poirier@jhmi.edu> wrote: > I recently updated my R packages and some code that I used to run with > rtracklayer started failing. In particular, laying a new track was failing > silently. I found that the same bug is reproducible in the vignette, but > eval=FALSE for the code chunk in question and thus the vignette compiles to > PDF as normal. Can anyone else reproduce this bug? Code and session info > below. > > # This code chunk fails without an error. > > ################################################### > ### code chunk number 15: layTrack (eval = FALSE) > ################################################### > ## track(session, "targets") <- targetTrack > > # We know the code is failing due to the below code and output > table(trackNames(session)=="targets") > > FALSE > 223 > > > R version 2.15.1 (2012-06-22) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > > locale: > [1] C/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII > > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 > [2] BSgenome_1.26.0 > [3] Biostrings_2.26.0 > [4] rtracklayer_1.18.0 > [5] GenomicRanges_1.10.0 > > > [[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]]