[Bioc-devel] unknown build error novel bioc. package

Maarten van Iterson mviterson at gmail.com
Wed Dec 13 21:25:13 CET 2017

Hi Marcel,

Thanks for your help, do you mean I should add "bgredata" to our DESCR
file? omicsPrint should not depend on it?

This sessionInfo when omicsPrint is loaded:

> library(omicsPrint)
Loading required package: MASS
in method for ‘coerce’ with signature
‘"RangedRaggedAssay","RaggedExperiment"’: no definition for class
> sessionInfo()
R Under development (unstable) (2017-09-30 r73418)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] omicsPrint_0.99.30 MASS_7.3-47

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               compiler_3.5.0
 [3] GenomeInfoDb_1.12.3        plyr_1.8.4
 [5] XVector_0.16.0             bitops_1.0-6
 [7] tools_3.5.0                zlibbioc_1.22.0
 [9] digest_0.6.12              tibble_1.3.4
[11] gtable_0.2.0               lattice_0.20-35
[13] rlang_0.1.4                Matrix_1.2-12
[15] DelayedArray_0.2.7         shiny_1.0.5
[17] parallel_3.5.0             gridExtra_2.3
[19] GenomeInfoDbData_0.99.0    stringr_1.2.0
[21] UpSetR_1.3.3               S4Vectors_0.14.7
[23] IRanges_2.10.5             stats4_3.5.0
[25] MultiAssayExperiment_1.2.1 grid_3.5.0
[27] shinydashboard_0.6.1       glue_1.2.0
[29] Biobase_2.36.2             R6_2.2.2
[31] purrr_0.2.4                tidyr_0.7.2
[33] magrittr_1.5               reshape2_1.4.2
[35] ggplot2_2.2.1              scales_0.5.0
[37] matrixStats_0.52.2         htmltools_0.3.6
[39] BiocGenerics_0.22.1        GenomicRanges_1.28.6
[41] RaggedExperiment_1.0.0     SummarizedExperiment_1.6.5
[43] mime_0.5                   xtable_1.8-2
[45] colorspace_1.3-2           httpuv_1.3.5
[47] stringi_1.1.6              RCurl_1.95-4.8
[49] lazyeval_0.2.1             munsell_0.4.3

On Wed, Dec 13, 2017 at 8:52 PM, Marcel Ramos <Marcel.Ramos at roswellpark.org>

> Hi Maarten,
> It appears that your vignette is pointing to a package that doesn't exist
> in the build system.
> Please reference `package = "brgedata"` instead.
> Regards,
> Marcel
> *Note. Apologies if you've received this email twice.
> On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
> Dear all,
> Our new package, omicsPrint, has been accepted and added to the
> bioconductor build system but is not passing through on any system. Locally
> we are able to build install and execute the vignette. We have tried
> several things without success.
> The current error we got for version 0.99.29 on malbec2 is:
> Error: processing vignette 'omicsPrint.Rmd' failed with diagnostics:
> parsing failed--expected only one '!series_data_table_begin'
> (https://bioconductor.org/checkResults/3.7/bioc-LATEST/omicRexposome/malbec2-buildsrc.html
> )
> Anyone idea's or suggestions for debugging?
> Regards,
> Maarten and Davy
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