To avoid this unexpected warning and error, the dependence on shinythemes could be clarified in the README.

> RDML::rdmlEdit()
Loading required package: shiny

Listening on http://127.0.0.1:7933
Warning: Error in library: there is no package called ‘shinythemes’
  74: <Anonymous>

Dear kablag,

when I load RDML files on the RDMLedit web-server, I see the following log messages

target: Assertion on 'id' failed: Must be of type 'string', not 'NULL'.
run: Assertion on 'name' failed: Must be of type 'string', not 'NULL'.
react: Assertion on 'id' failed: Must be of type 'string', not 'NULL'.

However, when inspecting the files, they don't appear to be compromised.

Any ideas about these log messages?
Can I simply ignore/clear them?

Thanks in advance,
janstrauss1

Import fails, when the XML has a documentation element. My file has the following element and I receive the error message given in the title.

    <documentation id="Barcode">
        <text>1234567890</text>
    </documentation>

The link http://shtest.evrogen.net/rdmlEdit/ is broken.

Remove flat.table option from RDML function, because its functionality can be implemented by selectFData.

Dear kablag,

when I try to export a loaded RDML file from the RDMLedit web-server using Store RDML, I get the Firefox error message

File not found

Thus, I currently don't see a way how use the RDMLedit web-server to modify RDML files.

Any suggestions what could cause the error?

Many thanks in advance,
janstrauss1

library(devtools)
install_github("RDML", "kablag")
Downloading github repo kablag/RDML@master
Installing RDML
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore CMD INSTALL
'/private/var/folders/ps/4cns4xzn38z6f9xycv0r8mv00000gn/T/RtmpzlxO38/devtools14ea2dfa9693/kablag-RDML-c67d479'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library' --install-tests

• installing source package ‘RDML’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called ‘rlist’
  ERROR: lazy loading failed for package ‘RDML’
• removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RDML’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RDML’
  Error: Command failed (1)
  In addition: Warning message:
  Username parameter is deprecated. Please use kablag/RDML

I need to import uncorrected fluorescence data (no baseline subtraction and thus no software curve analysis) into R from an RDML file. When working in R with the RDML package and trying to import default RDML output from BioRad CFX Maestro v1.1 software I consistently run into the following error:

Error in (function (cq) : Assertion on 'cq' failed: May not be NA.

The import terminates at this error and no object is created. I understand that the function is unhappy about NA values in the cq but I don't know how to solve this issue to work with the data in R. This error also occurs when using RDMLedit online.

I am attaching an RDML output by Maestro (salmonid_ef1a.rdml) which fails with the above error. How can I get these Maestro files into R to work with the fluorescence data?

salmonid_ef1a.zip

I am getting the same assertion violation as described in #28:

Error in (function (cq)  : Assertion on 'cq' failed: May not be NA.

The RDML should parse OK. As you can see below, the <cq>NaN</cq> tag appears legitimately when a reaction did not amplify at all (e.g. a negative test).

[...]
            <react id="1">
                <sample id="mysample1"/>
                <data>
                    <tar id="the_target"/>
                    <cq>NaN</cq>
                    <adp>
                        <cyc>1.0</cyc>
                        <fluor>0.045274403</fluor>
                    </adp>                    
[...]
                    <adp>
                        <cyc>45.0</cyc>
                        <fluor>-0.013826137</fluor>
                    </adp>
[...]
            <react id="86">
                <sample id="mysample1"/>
                <data>
                    <tar id="the_positive_control"/>
                    <cq>26.96937</cq>
                    <adp>
                        <cyc>1.0</cyc>
                        <fluor>0.01319422</fluor>
                    </adp>
[...]
                    <adp>
                        <cyc>25.0</cyc>
                        <fluor>0.090496756</fluor>
                    </adp>
                    <adp>
                        <cyc>26.0</cyc>
                        <fluor>0.13862325</fluor>
                    </adp>

Do it after removing flat.table option from RDML function

Dear kablag,

I am trying to run the command RDMLedit() locally from a RStudio session.

However, I receive the error

Listening on http://127.0.0.1:7366
Warning: Error in library: there is no package called ‘dpcR’
52: stop
51: library
Error in library(dpcR) : there is no package called ‘dpcR’

Clearly, I don't have dpcR installed but install.packages("dpcR") gives me

Warning in install.packages :
package ‘dpcR’ is not available (for R version 3.5.1)

It appears that the ‘dpcR’ package has been removed from the CRAN repository and I wonder if you really need it to run RDMLedit() locally?

Many thanks in advance,
janstrauss1

Below my output from sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools stats graphics grDevices utils datasets methods base

other attached packages:
[1] MBmca_0.0.3-5 plotly_4.8.0 ggvis_0.4.3 dplyr_0.7.6 labeling_0.3 ggplot2_3.0.0
[7] withr_2.1.2 crayon_1.3.4 chipPCR_0.0.8-10 RDML_0.9-9 backports_1.1.2 robustbase_0.93-2
[13] pipeR_0.6.1.3 markdown_0.8 yaml_2.2.0 V8_1.5 shinyjs_1.0 shinythemes_1.1.1
[19] shiny_1.1.0

loaded via a namespace (and not attached):
[1] httr_1.3.1 tidyr_0.8.1 jsonlite_1.5 viridisLite_0.3.0 assertthat_0.2.0 Rfit_0.23.0
[7] cellranger_1.1.0 outliers_0.14 pillar_1.3.0 lattice_0.20-35 quantreg_5.36 glue_1.3.0
[13] rlist_0.4.6.1 digest_0.6.16 promises_1.0.1 checkmate_1.8.5 colorspace_1.3-2 htmltools_0.3.6
[19] httpuv_1.4.5 Matrix_1.2-14 plyr_1.8.4 pkgconfig_2.0.2 SparseM_1.77 purrr_0.2.5
[25] xtable_1.8-2 ptw_1.9-13 scales_1.0.0 later_0.7.3 MatrixModels_0.4-1 tibble_1.4.2
[31] lazyeval_0.2.1 magrittr_1.5 readxl_1.1.0 mime_0.5 MASS_7.3-50 xml2_1.2.0
[37] data.table_1.11.4 stringr_1.3.1 munsell_0.5.0 bindrcpp_0.2.2 compiler_3.5.1 signal_0.7-6
[43] rlang_0.2.2 grid_3.5.1 nloptr_1.0.4 htmlwidgets_1.2 gtable_0.2.0 curl_3.2
[49] R6_2.2.2 zoo_1.8-3 lubridate_1.7.4 bindr_0.1.1 stringi_1.2.4 parallel_3.5.1
[55] Rcpp_0.12.18 DEoptimR_1.0-8 tidyselect_0.2.4 lmtest_0.9-36

This issue was observed on a linux Mint R 3.6.3 and R 4.1.2 Version.

   shinyjs: extendShinyjs: `functions` argument must be provided. See the documentation for `?extendShinyjs` for more details.

In my humble tries to solve this: the Shiny UI.R may be changed to solve this issue:

    extendShinyjs(script = "www/js/my_shinyjs_scripts.js",
                  functions = c("winprint"))

Do it after removing flat.table option from RDML function

Hi
I am working with Roche Lightcycler 96 files. When I open lc96p files straight from the thermal cycler there is no problem importing these files. However, when opening in lightcycler software and saving files either, as lc96p or rdml files, I get an error when importing this files with rdmlEdit(). Browser suddenly closes and R terminal says:

Listening on http://127.0.0.1:5267
Warning: Error in : Some prefixes [d2, d3] don't already exist.
Stack trace (innermost first):
    72: xml_ns_rename
    71: GetDilutionsRoche
    70: fromRDML
    69: .subset2(public_bind_env, "initialize")
    68: RDML$new
    67: eval [/home/galo/R/x86_64-pc-linux-gnu-library/3.3/RDML/RDMLedit/server.R#62]
    66: eval
    65: withProgress
    58: isolate
    57: observerFunc [/home/galo/R/x86_64-pc-linux-gnu-library/3.3/RDML/RDMLedit/server.R#54]
     2: shiny::runApp
     1: rdmlEdit

Bests

Dear kablag,

I am generating individual RDML files for different qPCR runs (e.g. run1, run2).
The different runs contain samples from the same experiment (e.g. exp1) and I would like to merge individual files by exp.id?

I noticed, however, that RDML currently add's a suffix to the exp.id like in my toy example below instead of merging by identical exp.id

Is there a way how I could merge by identical exp.id?

Many thanks in advance,
Jan

Create structure view prettier than str ().
Maybe table

Hi,

I would like to inspect some lightcycler 96 files (*.lc96p ) and came along your nice shiny app.

When i try to load a file into the app, it unfortunately crashes with following error/warning:
"Warning: Error in <-: attempt to set an attribute on NULL"

I looked at server.R but could not spot an obvious bug.
Could you help me resolve this issue?

Thank you,
Michel

Error log:

rdmlEdit()

Listening on http://127.0.0.1:3839
Warning: Error in <-: attempt to set an attribute on NULL
  65: GetDilutionsRoche
  64: fromRDML
  63: initialize
  62: RDML$new
  46: observe [C:\Users\michelmo\Documents\R\win-library\4.1\RDML\RDMLedit/server.R#57]
  45: <observer>
   2: shiny::runApp
   1: rdmlEdit

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_Switzerland.1252 
[2] LC_CTYPE=English_Switzerland.1252   
[3] LC_MONETARY=English_Switzerland.1252
[4] LC_NUMERIC=C                        
[5] LC_TIME=English_Switzerland.1252    

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] forcats_0.5.1      purrr_0.3.4        readr_1.4.0       
 [4] tidyr_1.2.0        tibble_3.1.8       tidyverse_1.3.1   
 [7] stringr_1.4.1      whisker_0.4        rlist_0.4.6.2     
[10] data.table_1.14.2  PCRedux_1.1-2      MBmca_1.0.1-3     
[13] robustbase_0.95-0  chipPCR_1.0-2      pipeR_0.6.1.3     
[16] shinyMolBio_0.2    plotly_4.10.0.9001 ggplot2_3.3.6     
[19] ggvis_0.4.7.9000   dplyr_1.0.9        shinyjs_2.1.0     
[22] shinythemes_1.2.0  shiny_1.7.1        RDML_1.2          

loaded via a namespace (and not attached):
  [1] readxl_1.4.1       changepoint_2.2.3  backports_1.4.1   
  [4] lazyeval_0.2.2     splines_4.1.0      fda_6.0.3         
  [7] usethis_2.0.1      digest_0.6.27      foreach_1.5.2     
 [10] htmltools_0.5.2    RcppDE_0.1.6       qpcR_1.4-1        
 [13] fansi_1.0.3        magrittr_2.0.3     checkmate_2.1.0   
 [16] memoise_2.0.0      Rfit_0.24.2        cluster_2.1.2     
 [19] doParallel_1.0.17  ks_1.13.5          hdrcde_3.4        
 [22] remotes_2.3.0      modelr_0.1.8       extrafont_0.18    
 [25] extrafontdb_1.0    fds_1.8            prettyunits_1.1.1 
 [28] colorspace_2.0-1   rvest_1.0.0        signal_0.7-7      
 [31] ecp_3.1.3          haven_2.5.0        xfun_0.31         
 [34] callr_3.7.0        crayon_1.5.2       RCurl_1.98-1.6    
 [37] jsonlite_1.8.0     survival_3.2-11    zoo_1.8-10        
 [40] iterators_1.0.14   glue_1.6.2         gtable_0.3.0      
 [43] MatrixModels_0.5-0 pkgbuild_1.2.0     Rttf2pt1_1.3.10   
 [46] DEoptimR_1.0-11    SparseM_1.81       scales_1.2.0      
 [49] mvtnorm_1.1-3      DBI_1.1.1          Rcpp_1.0.8.3      
 [52] viridisLite_0.4.0  xtable_1.8-4       mclust_5.4.10     
 [55] deSolve_1.32       htmlwidgets_1.5.3  httr_1.4.2        
 [58] RColorBrewer_1.1-2 ellipsis_0.3.2     rainbow_3.6       
 [61] pkgconfig_2.0.3    ptw_1.9-16         dbplyr_2.1.1      
 [64] sass_0.4.1         utf8_1.2.2         tidyselect_1.1.2  
 [67] rlang_1.0.6        later_1.2.0        munsell_0.5.0     
 [70] cellranger_1.1.0   cachem_1.0.5       cli_3.1.1         
 [73] generics_0.1.3     broom_0.8.0        devtools_2.4.3    
 [76] fastmap_1.1.0      yaml_2.3.5         knitr_1.39        
 [79] outliers_0.15      processx_3.5.2     fs_1.5.2          
 [82] rgl_0.108.3.2      pbapply_1.5-0      nlme_3.1-152      
 [85] mime_0.10          quantreg_5.93      pracma_2.3.8      
 [88] xml2_1.3.3         compiler_4.1.0     rstudioapi_0.13   
 [91] curl_4.3.1         testthat_3.0.2     bcp_4.0.3         
 [94] reprex_2.0.0       bslib_0.3.1        pcaPP_2.0-1       
 [97] stringi_1.7.6      ps_1.6.0           desc_1.3.0        
[100] lattice_0.20-44    Matrix_1.3-3       markdown_1.1      
[103] vctrs_0.4.1        pillar_1.8.1       lifecycle_1.0.2   
[106] lmtest_0.9-40      jquerylib_0.1.4    bitops_1.0-7      
[109] httpuv_1.6.5       R6_2.5.1           promises_1.2.0.1  
[112] KernSmooth_2.23-20 sessioninfo_1.1.1  codetools_0.2-18  
[115] MASS_7.3-54        assertthat_0.2.1   pkgload_1.2.1     
[118] fontawesome_0.2.2  rprojroot_2.0.2    minpack.lm_1.2-2  
[121] withr_2.4.2        hms_1.1.2          mgcv_1.8-35       
[124] parallel_4.1.0     grid_4.1.0         segmented_1.6-0   
[127] Cairo_1.5-15       lubridate_1.8.0    fda.usc_2.0.2    

We've got two qPCR instruments in our lab, one is CFX Connect and the computer has Bio-Rad CFX Manager 3.0 installed, the other is CFX96Touch and computer has CFX Maestro 1.1 software. Both software produces xxxxx.pcrd as results by default and support export to rdml v1.1 format. For data import and processing, I am following the supplements SI1.pdf of your paper (BTW, link in README here to https://kablag.github.io/RDML/ seems dead and I cannot find it anywhere else, donno if the manual has been updated and I was maybe following an outdated version or what).

Commands I used to import my results:

raw_data <- RDML$new("/path/to/rdml")
fdata <- raw_data$GetFData(dplyr::filter(raw_data_tab, sample.type == "unkn"), long.table = FALSE)

Problem is, if I'am importing a file exported from CFX Manager, I get the fdata with no error, while if the file was exported from CFX Maestro, the raw_data$GetFData() step always says:

Error: Assertion failed. One of the following must apply:
 * checkClass(out): Must inherit from class 'adpsType', but has class 'NULL'
 * checkClass(out): Must inherit from class 'mdpsType', but has class 'NULL'

I tried to export rdml v1.0 but in vain. Also, I noticed that CFX Manager failed to open results produced from CFX96Touch & CFX Maestro, while CFX Maestro was able to open files from
CFX96Touch & CFX Maestro and CFX Connect & CFX Manager, although they were all xxxx.pcrd files (maybe due to software compatibility issues?)

While running RDML::rdmlEdit() I get:

> RDML::rdmlEdit()
Loading required package: shiny

Listening on http://127.0.0.1:5756
Learn different usages for shinyjs and other Shiny tricks:
	https://deanattali.com/blog/advanced-shiny-tips

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

    runExample

The following objects are masked from ‘package:methods’:

    removeClass, show


Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: ‘ggplot2’

The following object is masked from ‘package:ggvis’:

    resolution


Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

The following objects are masked from ‘package:ggvis’:

    add_data, hide_legend

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout


Attaching package: ‘shinyMolBio’

The following object is masked from ‘package:shinyjs’:

    runExample

The following object is masked from ‘package:shiny’:

    runExample

Warning: Error in : shinyjs: extendShinyjs: `functions` argument must be provided. See the documentation for `?extendShinyjs` for more details.
  79: stop
  78: errMsg
  77: extendShinyjs

Session info

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libopenblasp-r0.3.18.so
LAPACK: /usr/lib/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shinyMolBio_0.2   plotly_4.10.0     ggplot2_3.3.5     ggvis_0.4.7       dplyr_1.0.7       shinyjs_2.1.0     shinythemes_1.2.0
[8] shiny_1.7.1      

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.1   purrr_0.3.4        colorspace_2.0-2   vctrs_0.3.8        generics_0.1.1     viridisLite_0.4.0 
 [7] htmltools_0.5.2    utf8_1.2.2         rlang_1.0.2        later_1.3.0        pillar_1.6.4       glue_1.6.0        
[13] withr_2.4.2        DBI_1.1.1          RColorBrewer_1.1-3 readxl_1.3.1       lifecycle_1.0.1    stringr_1.4.0     
[19] munsell_0.5.0      gtable_0.3.0       cellranger_1.1.0   htmlwidgets_1.5.4  fastmap_1.1.0      httpuv_1.6.5      
[25] fansi_0.5.0        Rcpp_1.0.7         xtable_1.8-4       promises_1.2.0.1   backports_1.3.0    scales_1.1.1      
[31] checkmate_2.0.0    pipeR_0.6.1.3      cachem_1.0.6       jsonlite_1.7.2     mime_0.12          digest_0.6.28     
[37] stringi_1.7.6      rlist_0.4.6.2      grid_4.1.2         cli_3.1.0          tools_4.1.2        magrittr_2.0.1    
[43] lazyeval_0.2.2     tibble_3.1.6       RDML_1.0           whisker_0.4        tidyr_1.1.4        crayon_1.4.2      
[49] pkgconfig_2.0.3    ellipsis_0.3.2     data.table_1.14.2  xml2_1.3.2         lubridate_1.8.0    rstudioapi_0.13   
[55] assertthat_0.2.1   httr_1.4.2         R6_2.5.1           compiler_4.1.2    

Dear kablag,

I am creating a RDML file from my raw data that I can open and inspect in the RDMLedit web-server.

However, when I try to validate my RDML file using the RDML validator at rdml.org, I get the error message

The uploaded file is not an RDML file

Also when I use RDML-Ninja v0.9.3 to validate my RDML file, I receive an error message

Error: XML parse error at line 1, column 1: error occurred while parsing element

I tried with files generated from the RDML vignette and receive the same error messages.

Any ideas about the issue?

Thanks,
janstrauss1

Below is my output from sessionInfo() of my Rstudio session

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] labeling_0.3 ggplot2_3.0.0 withr_2.1.2 crayon_1.3.4 chipPCR_0.0.8-10 qpcR_1.4-1
[7] Matrix_1.2-14 robustbase_0.93-2 rgl_0.99.16 minpack.lm_1.2-1 MASS_7.3-50 magrittr_1.5
[13] RDML_0.9-9 backports_1.1.2

loaded via a namespace (and not attached):
[1] zoo_1.8-3 lattice_0.20-35 Rfit_0.23.0 colorspace_1.3-2
[5] miniUI_0.1.1.1 htmltools_0.3.6 rlang_0.2.2 pillar_1.3.0
[9] manipulateWidget_0.10.0 later_0.7.3 nloptr_1.0.4 readxl_1.1.0
[13] plyr_1.8.4 stringr_1.3.1 outliers_0.14 MatrixModels_0.4-1
[17] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0 htmlwidgets_1.2
[21] knitr_1.20 SparseM_1.77 httpuv_1.4.5 lmtest_0.9-36
[25] crosstalk_1.0.0 quantreg_5.36 parallel_3.5.1 DEoptimR_1.0-8
[29] Rcpp_0.12.18 xtable_1.8-2 promises_1.0.1 scales_1.0.0
[33] checkmate_1.8.5 pipeR_0.6.1.3 webshot_0.5.0 jsonlite_1.5
[37] mime_0.5 ptw_1.9-13 digest_0.6.16 stringi_1.2.4
[41] rlist_0.4.6.1 shiny_1.1.0 grid_3.5.1 tools_3.5.1
[45] tibble_1.4.2 lazyeval_0.2.1 data.table_1.11.4 xml2_1.2.0
[49] lubridate_1.7.4 R6_2.2.2 signal_0.7-6 compiler_3.5.1

Hi, we use this RDML package for qPCR analysis, but now we have encountered a file which I cannot open, as it has measurements for different dyes for different samples:
Samples 1-24 are measuring VIC dye, while samples 25-70 uses FAM. They are represented as separate runs in the file.

When I attempt to read in this file, I get this error:

my.rdml <- RDML$new("multidye_qPCR.rdml")
Unzipping multidye_qPCR.rdml...
Parsing data...
Getting dateMade
Getting dateUpdated
Getting id
Getting experementer
Getting documentation
Getting dye
Getting sample
Getting target
Getting thermalCyclingConditions
Getting experiment: All Wells
run: Amp Step 3_VIC
|============================================== | 50%
Error in UseMethod("xmlAttrs", node) :
no applicable method for 'xmlAttrs' applied to an object of class "NULL"

(The example file is attached)

Any suggestions how to address this issue?

problemrdml.zip