search

CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
42 stars 27 forks source link

`get.formula` fails if elements has length one #129

Open meowcat opened 2 years ago

meowcat commented 2 years ago

generate.formula gets an error if the specified element list has only one element specified. Inserting a dummy element with max count of zero circumvents the issue. Of course, I don't know if the actual root cause has anything to to with list length.

generate.formula(120, window = 0.0036, list(c("C", "0", "12")))
# Error in .jcall(mfTool, "Lorg/openscience/cdk/interfaces/IMolecularFormulaSet;",  : 
#  java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1

generate.formula(120, window = 0.0036, list(c("C", "0", "12"), c("H", "0", "0")))
# [[1]] cdkFormula:  C10 , mass =  120 , charge =  0

generate.formula(120, window = 0.0036, list(c("H", "0", "200")))
# Error in .jcall(mfTool, "Lorg/openscience/cdk/interfaces/IMolecularFormulaSet;",  : 
#  java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1

list(c("C", "0", "12")) is in fact a list of length one, so the issue isn't that it got converted to a list of length 3:

list(c("C", "0", "12"))
# [[1]]
# [1] "C"  "0"  "12"

(I am aware that the doc specifies c("C", 0, 50) but of course 0 and 50 get converted to character anyway.)

System (please complete the following information):

> session_info()
- Session info -------------------------------------------------------------------------------------------------------------------------------------------
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Windows 10 x64 (build 19042)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United States.1252
 ctype    English_United States.1252
 tz       Europe/Berlin
 date     2022-03-17
 rstudio  2021.09.0+351 Ghost Orchid (desktop)
 pandoc   2.14.0.3 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown)

- Packages -----------------------------------------------------------------------------------------------------------------------------------------------
 ! package        * version  date (UTC) lib source
   affy             1.72.0   2021-10-26 [1] Bioconductor
   affyio           1.64.0   2021-10-26 [1] Bioconductor
   assertthat       0.2.1    2019-03-21 [1] CRAN (R 4.1.1)
   backports        1.4.1    2021-12-13 [1] CRAN (R 4.1.2)
   base64enc        0.1-3    2015-07-28 [1] CRAN (R 4.1.1)
   Biobase          2.54.0   2021-10-26 [1] Bioconductor
   BiocGenerics   * 0.40.0   2021-10-26 [1] Bioconductor
   BiocManager      1.30.16  2021-06-15 [1] CRAN (R 4.1.1)
   BiocParallel     1.28.3   2021-12-09 [1] Bioconductor
   bitops           1.0-7    2021-04-24 [1] CRAN (R 4.1.1)
   brio             1.1.3    2021-11-30 [1] CRAN (R 4.1.2)
   broom            0.7.12   2022-01-28 [1] CRAN (R 4.1.2)
   cachem           1.0.6    2021-08-19 [1] CRAN (R 4.1.1)
   callr            3.7.0    2021-04-20 [1] CRAN (R 4.1.1)
   caTools          1.18.2   2021-03-28 [1] CRAN (R 4.1.2)
   cellranger       1.1.0    2016-07-27 [1] CRAN (R 4.1.1)
   ChemmineOB       1.32.0   2021-10-26 [1] Bioconductor
   ChemmineR        3.46.0   2021-10-26 [1] Bioconductor
   cli              3.2.0    2022-02-14 [1] CRAN (R 4.1.2)
   clue             0.3-60   2021-10-11 [1] CRAN (R 4.1.1)
   cluster          2.1.2    2021-04-17 [2] CRAN (R 4.1.2)
   codetools        0.2-18   2020-11-04 [2] CRAN (R 4.1.2)
   colorspace       2.0-3    2022-02-21 [1] CRAN (R 4.1.2)
   crayon           1.5.0    2022-02-14 [1] CRAN (R 4.1.2)
   data.table       1.14.2   2021-09-27 [1] CRAN (R 4.1.1)
   data.tree        1.0.0    2020-08-03 [1] CRAN (R 4.1.2)
   DBI              1.1.2    2021-12-20 [1] CRAN (R 4.1.2)
   dbplyr           2.1.1    2021-04-06 [1] CRAN (R 4.1.1)
   desc             1.4.1    2022-03-06 [1] CRAN (R 4.1.2)
   devtools       * 2.4.3    2021-11-30 [1] CRAN (R 4.1.2)
   digest           0.6.29   2021-12-01 [1] CRAN (R 4.1.2)
   doParallel       1.0.17   2022-02-07 [1] CRAN (R 4.1.2)
   dplyr          * 1.0.8    2022-02-08 [1] CRAN (R 4.1.2)
   DT               0.21     2022-02-26 [1] CRAN (R 4.1.2)
   ellipsis         0.3.2    2021-04-29 [1] CRAN (R 4.1.1)
   enviPat          2.4      2019-04-07 [1] CRAN (R 4.1.1)
   evaluate         0.15     2022-02-18 [1] CRAN (R 4.1.2)
   fansi            1.0.2    2022-01-14 [1] CRAN (R 4.1.2)
   fastmap          1.1.0    2021-01-25 [1] CRAN (R 4.1.1)
   fingerprint      3.5.7    2018-01-07 [1] CRAN (R 4.1.1)
   forcats        * 0.5.1    2021-01-27 [1] CRAN (R 4.1.1)
   foreach          1.5.2    2022-02-02 [1] CRAN (R 4.1.2)
   Formula          1.2-4    2020-10-16 [1] CRAN (R 4.1.1)
   fs               1.5.2    2021-12-08 [1] CRAN (R 4.1.2)
   generics         0.1.2    2022-01-31 [1] CRAN (R 4.1.2)
   ggplot2        * 3.3.5    2021-06-25 [1] CRAN (R 4.1.1)
   glue             1.6.2    2022-02-24 [1] CRAN (R 4.1.2)
   gplots         * 3.1.1    2020-11-28 [1] CRAN (R 4.1.2)
   gridExtra        2.3      2017-09-09 [1] CRAN (R 4.1.1)
   gtable           0.3.0    2019-03-25 [1] CRAN (R 4.1.1)
   gtools           3.9.2    2021-06-06 [1] CRAN (R 4.1.2)
   haven            2.4.3    2021-08-04 [1] CRAN (R 4.1.1)
   hms              1.1.1    2021-09-26 [1] CRAN (R 4.1.1)
   htmltools        0.5.2    2021-08-25 [1] CRAN (R 4.1.1)
   htmlwidgets      1.5.4    2021-09-08 [1] CRAN (R 4.1.1)
   httr             1.4.2    2020-07-20 [1] CRAN (R 4.1.1)
   impute           1.68.0   2021-10-26 [1] Bioconductor
   IRanges          2.28.0   2021-10-26 [1] Bioconductor
   iterators        1.0.14   2022-02-05 [1] CRAN (R 4.1.2)
   itertools        0.1-3    2014-03-12 [1] CRAN (R 4.1.1)
   jsonlite         1.8.0    2022-02-22 [1] CRAN (R 4.1.2)
   KernSmooth       2.23-20  2021-05-03 [2] CRAN (R 4.1.2)
   knitr            1.37     2021-12-16 [1] CRAN (R 4.1.2)
   lattice          0.20-45  2021-09-22 [2] CRAN (R 4.1.2)
   lifecycle        1.0.1    2021-09-24 [1] CRAN (R 4.1.1)
   limma            3.50.1   2022-02-17 [1] Bioconductor
   logger           0.2.2    2021-10-19 [1] CRAN (R 4.1.1)
   lubridate        1.8.0    2021-10-07 [1] CRAN (R 4.1.1)
   magrittr         2.0.2    2022-01-26 [1] CRAN (R 4.1.2)
   MALDIquant       1.21     2021-12-23 [1] CRAN (R 4.1.2)
   MASS             7.3-54   2021-05-03 [2] CRAN (R 4.1.2)
   memoise          2.0.1    2021-11-26 [1] CRAN (R 4.1.2)
   modelr           0.1.8    2020-05-19 [1] CRAN (R 4.1.1)
   MsCoreUtils      1.6.2    2022-02-24 [1] Bioconductor
   MSnbase          2.20.1   2021-11-14 [1] Bioconductor
   munsell          0.5.0    2018-06-12 [1] CRAN (R 4.1.1)
   mzID             1.32.0   2021-10-26 [1] Bioconductor
   mzR              2.28.0   2021-10-26 [1] Bioconductor
   ncdf4            1.19     2021-12-15 [1] CRAN (R 4.1.2)
   pcaMethods       1.86.0   2021-10-26 [1] Bioconductor
   pillar           1.7.0    2022-02-01 [1] CRAN (R 4.1.2)
   pkgbuild         1.3.1    2021-12-20 [1] CRAN (R 4.1.2)
   pkgconfig        2.0.3    2019-09-22 [1] CRAN (R 4.1.1)
   pkgload          1.2.4    2021-11-30 [1] CRAN (R 4.1.2)
   plyr             1.8.6    2020-03-03 [1] CRAN (R 4.1.1)
   png              0.1-7    2013-12-03 [1] CRAN (R 4.1.1)
   preprocessCore   1.56.0   2021-10-26 [1] Bioconductor
   prettyunits      1.1.1    2020-01-24 [1] CRAN (R 4.1.1)
   processx         3.5.2    2021-04-30 [1] CRAN (R 4.1.1)
   ProtGenerics     1.26.0   2021-10-26 [1] Bioconductor
   ps               1.6.0    2021-02-28 [1] CRAN (R 4.1.1)
   purrr          * 0.3.4    2020-04-17 [1] CRAN (R 4.1.1)
   R.methodsS3      1.8.1    2020-08-26 [1] CRAN (R 4.1.1)
   R.oo             1.24.0   2020-08-26 [1] CRAN (R 4.1.1)
   R.utils          2.11.0   2021-09-26 [1] CRAN (R 4.1.2)
   R6               2.5.1    2021-08-19 [1] CRAN (R 4.1.1)
   rcdk           * 3.6.0    2021-10-17 [1] CRAN (R 4.1.1)
   rcdklibs       * 2.3      2020-03-08 [1] CRAN (R 4.1.1)
   Rcpp           * 1.0.8    2022-01-13 [1] CRAN (R 4.1.2)
   RCurl            1.98-1.6 2022-02-08 [1] CRAN (R 4.1.2)
   readJDX          0.6.1    2021-09-20 [1] CRAN (R 4.1.2)
   readr          * 2.1.2    2022-01-30 [1] CRAN (R 4.1.2)
   readxl           1.3.1    2019-03-13 [1] CRAN (R 4.1.1)
   remotes          2.4.2    2021-11-30 [1] CRAN (R 4.1.2)
   reprex           2.0.1    2021-08-05 [1] CRAN (R 4.1.1)
 D rJava          * 1.0-6    2021-12-10 [1] CRAN (R 4.1.2)
   rjson            0.2.21   2022-01-09 [1] CRAN (R 4.1.2)
   rlang            1.0.2    2022-03-04 [1] CRAN (R 4.1.2)
   rmarkdown        2.12     2022-03-02 [1] CRAN (R 4.1.2)
 P RMassBank      * 3.5.2.1  2022-03-17 [?] Bioconductor
   rprojroot        2.0.2    2020-11-15 [1] CRAN (R 4.1.1)
   rstudioapi       0.13     2020-11-12 [1] CRAN (R 4.1.1)
   rsvg             2.2.0    2022-02-07 [1] CRAN (R 4.1.2)
   rvest            1.0.2    2021-10-16 [1] CRAN (R 4.1.1)
   S4Vectors      * 0.32.3   2021-11-21 [1] Bioconductor
   scales           1.1.1    2020-05-11 [1] CRAN (R 4.1.1)
   sessioninfo      1.2.2    2021-12-06 [1] CRAN (R 4.1.2)
   stringi          1.7.6    2021-11-29 [1] CRAN (R 4.1.2)
   stringr        * 1.4.0    2019-02-10 [1] CRAN (R 4.1.1)
   testthat         3.1.2    2022-01-20 [1] CRAN (R 4.1.2)
   tibble         * 3.1.6    2021-11-07 [1] CRAN (R 4.1.2)
   tidyr          * 1.2.0    2022-02-01 [1] CRAN (R 4.1.2)
   tidyselect       1.1.2    2022-02-21 [1] CRAN (R 4.1.2)
   tidyverse      * 1.3.1    2021-04-15 [1] CRAN (R 4.1.1)
   tzdb             0.2.0    2021-10-27 [1] CRAN (R 4.1.1)
   usethis        * 2.1.5    2021-12-09 [1] CRAN (R 4.1.2)
   utf8             1.2.2    2021-07-24 [1] CRAN (R 4.1.1)
   vctrs            0.3.8    2021-04-29 [1] CRAN (R 4.1.1)
   vsn              3.62.0   2021-10-26 [1] Bioconductor
   webchem          1.1.2    2021-12-06 [1] CRAN (R 4.1.2)
   withr            2.5.0    2022-03-03 [1] CRAN (R 4.1.2)
   xfun             0.30     2022-03-02 [1] CRAN (R 4.1.2)
   XML              3.99-0.9 2022-02-24 [1] CRAN (R 4.1.2)
   xml2             1.3.3    2021-11-30 [1] CRAN (R 4.1.2)
   yaml             2.3.5    2022-02-21 [1] CRAN (R 4.1.2)
   zlibbioc         1.40.0   2021-10-26 [1] Bioconductor