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

[Maarten van Iterson]

Hi Marcel,

Thanks for looking into this. I fixed it and pushed. Lets see if the
package is building without errors now!

Cheers,
Maarten

On Wed, Dec 13, 2017 at 9:53 PM, Marcel Ramos <Marcel.Ramos at roswellpark.org>
wrote:

> 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> 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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