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

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
?RaggedExperiment?
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

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=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>
wrote:
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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[Bioc-devel] unknown build error novel bioc. package

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