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Ampersands not escaped in xml export #234

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bokov opened this issue Oct 4, 2019 · 0 comments · Fixed by #249
Closed

Ampersands not escaped in xml export #234

bokov opened this issue Oct 4, 2019 · 0 comments · Fixed by #249
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bug help wanted

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@bokov
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@bokov bokov commented Oct 4, 2019

Please specify whether your issue is about:

  • a possible bug
  • a question about package functionality
  • a suggested code or documentation change, improvement to the code, or feature request

If you are reporting (1) a bug or (2) a question about code, please supply:

  • a fully reproducible example using a publicly available dataset (or provide your data)
  • if an error is occurring, include the output of traceback() run immediately after the error occurs
12: stop(list(message = "EntityRef: expecting ';' [23]", call = doc_parse_raw(x, 
        encoding = encoding, base_url = base_url, as_html = as_html, 
        options = options), cppstack = list(file = "", line = -1L, 
        stack = c("/home/a/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so(+0x18dcf) [0x7fa412210dcf]", 
        "/home/a/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so(+0x234c5) [0x7fa41221b4c5]", 
        "/home/a/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so(+0x22fe0) [0x7fa41221afe0]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(__xmlRaiseError+0x38b) [0x7fa411ec5fab]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(+0x38c27) [0x7fa411ec9c27]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlParseEntityRef+0x14f) [0x7fa411ed094f]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlParseReference+0x6f) [0x7fa411edc9ff]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlParseContent+0x170) [0x7fa411edd450]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlParseElement+0x153) [0x7fa411eddcc3]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(xmlParseDocument+0x2c2) [0x7fa411ede2f2]", 
        "/usr/lib/x86_64-linux-gnu/libxml2.so.2(+0x4d707) [0x7fa411ede707]", 
        "/home/a/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so(+0x2114b) [0x7fa41221914b]", 
        "/home/a/R/x86_64-pc-linux-gnu-library/3.4/xml2/libs/xml2.so(_xml2_doc_parse_raw+0x17e) [0x7fa41220fcae]", 
        "/usr/lib/R/lib/libR.so(+0xd6bdd) [0x7fa4374a2bdd]", "/usr/lib/R/lib/libR.so(Rf_eval+0x7b1) [0x7fa4374e7271]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(Rf_eval+0x32c) [0x7fa4374e6dec]", 
        "/usr/lib/R/lib/libR.so(+0x11ea3e) [0x7fa4374eaa3e]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(Rf_eval+0x32c) [0x7fa4374e6dec]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x151554) [0x7fa43751d554]", 
        "/usr/lib/R/lib/libR.so(+0x151990) [0x7fa43751d990]", "/usr/lib/R/lib/libR.so(+0x151cb4) [0x7fa43751dcb4]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x112d74) [0x7fa4374ded74]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x170) [0x7fa4374e6c30]", 
        "/usr/lib/R/lib/libR.so(+0x11b576) [0x7fa4374e7576]", "/usr/lib/R/lib/libR.so(Rf_eval+0x817) [0x7fa4374e72d7]", 
        "/usr/lib/R/lib/libR.so(+0x11b576) [0x7fa4374e7576]", "/usr/lib/R/lib/libR.so(+0x11955a) [0x7fa4374e555a]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x170) [0x7fa4374e6c30]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(Rf_eval+0x32c) [0x7fa4374e6dec]", 
        "/usr/lib/R/lib/libR.so(+0x11ea3e) [0x7fa4374eaa3e]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x151554) [0x7fa43751d554]", 
        "/usr/lib/R/lib/libR.so(+0x151990) [0x7fa43751d990]", "/usr/lib/R/lib/libR.so(+0x151cb4) [0x7fa43751dcb4]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x112d74) [0x7fa4374ded74]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x170) [0x7fa4374e6c30]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x151554) [0x7fa43751d554]", 
        "/usr/lib/R/lib/libR.so(+0x151990) [0x7fa43751d990]", "/usr/lib/R/lib/libR.so(+0x151cb4) [0x7fa43751dcb4]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11d94c) [0x7fa4374e994c]", "/usr/lib/R/lib/libR.so(Rf_eval+0x585) [0x7fa4374e7045]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(+0x112d74) [0x7fa4374ded74]", 
        "/usr/lib/R/lib/libR.so(Rf_eval+0x170) [0x7fa4374e6c30]", 
        "/usr/lib/R/lib/libR.so(+0x11cc2f) [0x7fa4374e8c2f]", "/usr/lib/R/lib/libR.so(Rf_eval+0x32c) [0x7fa4374e6dec]", 
        "/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x232) [0x7fa437510152]", 
        "/usr/lib/R/lib/libR.so(+0x144531) [0x7fa437510531]", "/usr/lib/R/lib/libR.so(run_Rmainloop+0x4f) [0x7fa4375105ef]", 
        "/usr/lib/rstudio/bin/rsession(rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*)+0x1b2) [0xec72f2]", 
        "/usr/lib/rstudio/bin/rsession(rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&)+0x252d) [0xea682d]", 
        "/usr/lib/rstudio/bin/rsession(main+0x33cf) [0x70645f]", 
        "/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fa435b72f45]", 
        "/usr/lib/rstudio/bin/rsession() [0x7173f5]"))))
11: .Call(`_xml2_doc_parse_raw`, x, encoding, base_url, as_html, 
        options)
10: doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, 
        options = options)
9: read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, 
       options = options)
8: read_xml.character(paste0(twrap(x[i, j, drop = TRUE], names(x)[j]), 
       "\n"))
7: xml2::read_xml(paste0(twrap(x[i, j, drop = TRUE], names(x)[j]), 
       "\n")) at export_methods.R#284
6: create_node(.value, .x, .copy = .copy, ...)
5: xml_add_child.xml_node(thisrow, xml2::read_xml(paste0(twrap(x[i, 
       j, drop = TRUE], names(x)[j]), "\n")))
4: xml2::xml_add_child(thisrow, xml2::read_xml(paste0(twrap(x[i, 
       j, drop = TRUE], names(x)[j]), "\n"))) at export_methods.R#284
3: .export.rio_xml(file = file, x = x, ...) at extensions.R#53
2: .export(file = file, x = x, ...) at export.R#147
1: export(bar, "bar.xml")
  • the output of sessionInfo()

Put your code here:

## load package
library("rio")

## code goes here
# set up example data frames
bar <- foo <- as.data.frame(matrix(letters[1:24],nrow=6),stringsAsFactors = F);
# into the second one introduce an ampersand
bar[6,3] <- "r&d";
# foo saves successfully
export(foo,"foo.xml");
# bar, which differs from foo only by an embedded ampersand, errors
export(bar,"bar.xml");
# remove the ampersand and it works again
export(bar[-6,],"bar1.xml");
export(bar[,-3],"bar2.xml");


## session info for your system
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.6 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] 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] rio_0.5.20     testthat_2.2.1

loaded via a namespace (and not attached):
 [1] zip_2.0.4           Rcpp_1.0.2          compiler_3.4.4      pillar_1.4.2       
 [5] cellranger_1.1.0    prettyunits_1.0.2   forcats_0.3.0       remotes_2.1.0      
 [9] tools_3.4.4         digest_0.6.21       pkgbuild_1.0.5      pkgload_1.0.2      
[13] memoise_1.1.0       tibble_2.1.3        pkgconfig_2.0.3     rlang_0.4.0        
[17] openxlsx_4.1.0.1    cli_1.1.0           rstudioapi_0.10     curl_4.2           
[21] yaml_2.2.0          haven_2.1.1         xml2_1.2.2          withr_2.1.2        
[25] desc_1.2.0          fs_1.3.1            devtools_2.2.1.9000 hms_0.4.2          
[29] rprojroot_1.3-2     glue_1.3.1          data.table_1.12.4   R6_2.4.0           
[33] processx_3.4.1      readxl_1.3.1        foreign_0.8-70      sessioninfo_1.1.1  
[37] callr_3.3.2         magrittr_1.5        backports_1.1.2     ps_1.3.0           
[41] ellipsis_0.3.0      usethis_1.5.1       assertthat_0.2.1    crayon_1.3.4
bokov added a commit to bokov/rio that referenced this issue Dec 3, 2019
@bokov
Replace '&' with '&amp;' when exporting to HTML or XML, except column…
Loading status checks…
b9c11fc 
… headers for XML where '&' and ' ' both get replaced by '.'. Fixes leeper#234
@bokov bokov mentioned this issue Dec 4, 2019
Merged
5 of 6 tasks complete
@leeper leeper closed this in #249 Dec 17, 2019
leeper added a commit that referenced this issue Dec 17, 2019
@bokov @leeper
Replace '&' with '&amp;' when exporting to HTML or XML, except column…
3fba17b 
… headers for XML where '&' and ' ' both get replaced by '.'. Fixes #234
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