Hi Maarten, Sorry about the confusion. The link you provided pointed to errors in *omicRexposome*.
It appears that the errors you're getting for *omicsPrint* have to do with the `getGEO` call on line #261 in the vignette. It can be fixed if you introduce a `fileext` argument to `tempfile()`. Please see pull request # 3. Regards, Marcel On 12/13/2017 03:25 PM, Maarten van Iterson wrote: > 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 <mailto: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 >> >> <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-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://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. > > This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
