I just reinstalled but have the same error:

getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
Error in fromJSON(data) : no data to parse

But the URL created in the code should work:

SessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252

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

other attached packages:
[1] RMassBank_2.9.1 Rcpp_0.12.19 devtools_1.13.3

loaded via a namespace (and not attached):
[1] BiocInstaller_1.26.1 compiler_3.4.2 git2r_0.19.0 plyr_1.8.4 rcdklibs_2.2.1
[6] bitops_1.0-6 iterators_1.0.10 ProtGenerics_1.8.0 tools_3.4.2 zlibbioc_1.22.0
[11] MALDIquant_1.16.4 digest_0.6.18 memoise_1.1.0 tibble_1.3.4 preprocessCore_1.38.1
[16] gtable_0.2.0 lattice_0.20-35 png_0.1-7 rlang_0.1.2 foreach_1.4.3
[21] curl_3.2 yaml_2.2.0 parallel_3.4.2 rJava_0.9-10 withr_2.0.0
[26] httr_1.3.1 IRanges_2.10.5 S4Vectors_0.14.7 stats4_3.4.2 grid_3.4.2
[31] Biobase_2.36.2 impute_1.50.1 R6_2.2.2 rcdk_3.4.9 XML_3.98-1.16
[36] BiocParallel_1.10.1 limma_3.32.10 ggplot2_2.2.1 mzR_2.10.0 itertools_0.1-3
[41] scales_0.5.0 pcaMethods_1.68.0 codetools_0.2-15 BiocGenerics_0.22.1 fingerprint_3.5.7
[46] mzID_1.14.0 MSnbase_2.2.0 colorspace_1.3-2 affy_1.54.0 RCurl_1.95-4.11
[51] doParallel_1.0.11 lazyeval_0.2.0 munsell_0.4.3 rjson_0.2.20 vsn_3.44.0
[56] affyio_1.46.0

Same for me:

library(RMassBank)
data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
Error in fromJSON(data) : no data to parse

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252

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

other attached packages:
[1] RMassBank_2.9.1 Rcpp_0.12.16

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 purrr_0.2.5 rJava_0.9-10 lattice_0.20-35 colorspace_1.3-2
[6] stats4_3.5.1 yaml_2.2.0 fingerprint_3.5.7 vsn_3.48.1 XML_3.98-1.16
[11] rlang_0.2.2 pillar_1.3.0 glue_1.3.0 MSnbase_2.6.4 mzR_2.14.0
[16] BiocParallel_1.14.2 affy_1.58.0 BiocGenerics_0.26.0 bindrcpp_0.2.2 affyio_1.50.0
[21] foreach_1.4.4 bindr_0.1.1 plyr_1.8.4 mzID_1.18.0 ProtGenerics_1.12.0
[26] zlibbioc_1.26.0 munsell_0.5.0 pcaMethods_1.72.0 gtable_0.2.0 rcdklibs_2.0
[31] codetools_0.2-15 Biobase_2.40.0 IRanges_2.14.12 doParallel_1.0.14 BiocInstaller_1.30.0
[36] parallel_3.5.1 itertools_0.1-3 preprocessCore_1.42.0 scales_1.0.0 limma_3.36.5
[41] rcdk_3.4.7.1 S4Vectors_0.18.3 impute_1.54.0 rjson_0.2.20 ggplot2_3.0.0
[46] png_0.1-7 digest_0.6.18 dplyr_0.7.7 grid_3.5.1 tools_3.5.1
[51] bitops_1.0-6 magrittr_1.5 lazyeval_0.2.1 RCurl_1.95-4.11 tibble_1.4.2
[56] crayon_1.3.4 pkgconfig_2.0.2 MASS_7.3-51 assertthat_0.2.0 rstudioapi_0.8
[61] iterators_1.0.10 R6_2.3.0 MALDIquant_1.18 compiler_3.5.1

I just started a conversation with Duncan, the maintainer of RCurl, but this stucked somehow. We checked some things, but it did not change. I dunno if something happens with RCurl... I wrote a workaround using httr:

get_cactus <- function(identifier,representation){
ret <- tryCatch(GET(paste("https://cactus.nci.nih.gov/chemical/structure/",
URLencode(identifier), "/", representation, sep = "")),
error = function(e) NA)
if (is.na(ret))
return(NA)
if (ret[2] == 404)
return(NA)
ret <- content(ret)
return(unlist(strsplit(ret, "\n")))

}

In a pure R command line R --vanilla, I get the following:

library(RCurl)
getURL("http://cts.fiehnlab.ucdavis.edu/service/compound/UHOVQNZJYSORNB-UHFF
[1] ""

If I use the https URL, all seems to be fine:
getURL("https://cts.fiehnlab.ucdavis.edu/service/compound/UHOVQNZJYSORNB-UHFF
[1] ....

Here, the change to https may resolve the problem. The problem with CACTUS still persists:

getURL("https://cactus.nci.nih.gov/chemical/structure/LFTLOKWAGJYHHR-UHFFFAO$
Error in function (type, msg, asError = TRUE) :
Unknown SSL protocol error in connection to cactus.nci.nih.gov:443

Indeed ... this works:
https://cactus.nci.nih.gov/chemical/structure/UHOVQNZJYSORNB-UHFFFAOYSA-N/smiles

but not in R:

getURL("https://cactus.nci.nih.gov/chemical/structure/UHOVQNZJYSORNB-UHFFFAOYSA-N/smiles")
Error in function (type, msg, asError = TRUE) :
Unknown SSL protocol error in connection to cactus.nci.nih.gov:443

The issue started here was in particular on the CTS issue. Unfortunately
my patch #210 (merged by Emma, thanks!) fixed only one occurrence
of the baseURL , so I committed 1ce4d16 to fix the rest.

We still need someone (@meowcat ?) to push to BioC.

The Unknown SSL protocol error is a separate Windows / RCurl issue,
please use #208 to discuss that. Yours, Steffen

I can confirm that 1ce4d16 fixed this issue for me too, but I guess we can only resolve this once pushed to BioC @meowcat ?