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.ra...@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 > > [[alternative HTML version deleted]] > > _______________________________________________bioc-de...@r-project.org > mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
