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

6 messages · Maarten van Iterson, Marcel Ramos

Original
Maarten van Iterson
# 
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
Marcel Ramos
# 
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
On 12/13/2017 02:09 PM, Maarten van Iterson wrote:
This email message may contain legally privileged and/or...{{dropped:4}}
Marcel Ramos
# 
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:
This email message may contain legally privileged and/or...{{dropped:4}}
Maarten van Iterson
# 
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:
Loading required package: MASS
in method for ?coerce? with signature
?"RangedRaggedAssay","RaggedExperiment"?: no definition for class
?RaggedExperiment?
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:

  
  


  


      

    

    

      
      

        


  

        

      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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
This email message may contain legally privileged and/or...{{dropped:4}}

  
  


  


      

    

    

      
      

        


  

        

      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: