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

[Marcel Ramos]

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.Ramos at roswellpark.org <mailto: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
>>     <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]]
>>
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>>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>
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