cbonnefoy
commented
1 year ago I have the same issue.
get molecule from smiles
smiles <- "CN(C)CC(C1=C=C(C=C1)OC)C2(CCCCC2)O" molecule<-parse.smiles(smiles)[[1]] fragments<-frag.generateFragments(molecule) Error in .jcall(obj, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", : java.lang.NoSuchMethodError: net.sf.jniinchi.INCHI_RET.getValue(I)Lnet/sf/jniinchi/INCHI_RET; str(smiles) chr "CN(C)CC(C1=C=C(C=C1)OC)C2(CCCCC2)O" sessionInfo() R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale: [1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8 LC_MONETARY=French_France.utf8 [4] LC_NUMERIC=C LC_TIME=French_France.utf8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] metfRag_2.4.2 fingerprint_3.5.7 rjson_0.2.21 rcdk_3.7.0 rcdklibs_2.8 rJava_1.0-6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 lattice_0.20-45 png_0.1-8 digest_0.6.31 foreach_1.5.2
[6] utf8_1.2.3 R6_2.5.1 plyr_1.8.8 mzID_1.36.0 stats4_4.2.2
[11] ggplot2_3.4.1 pillar_1.8.1 itertools_0.1-3 zlibbioc_1.44.0 rlang_1.0.6
[16] rstudioapi_0.14 S4Vectors_0.36.1 preprocessCore_1.60.2 mzR_2.32.0 BiocParallel_1.32.5
[21] Spectra_1.8.1 ProtGenerics_1.30.0 munsell_0.5.0 compiler_4.2.2 pkgconfig_2.0.3
[26] BiocGenerics_0.44.0 pcaMethods_1.90.0 tidyselect_1.2.0 tibble_3.1.8 IRanges_2.32.0
[31] codetools_0.2-18 XML_3.99-0.13 fansi_1.0.4 dplyr_1.1.0 MASS_7.3-58.1
[36] grid_4.2.2 gtable_0.3.1 lifecycle_1.0.3 affy_1.76.0 magrittr_2.0.3
[41] MsCoreUtils_1.10.0 scales_1.2.1 ncdf4_1.21 cli_3.4.1 impute_1.72.3
[46] fs_1.5.2 affyio_1.68.0 doParallel_1.0.17 limma_3.54.1 generics_0.1.3
[51] vctrs_0.5.2 squash_1.0.9 iterators_1.0.14 tools_4.2.2 Biobase_2.58.0
[56] MSnbase_2.24.2 glue_1.6.2 parallel_4.2.2 clue_0.3-64 colorspace_2.1-0
[61] cluster_2.1.4 BiocManager_1.30.20 vsn_3.66.0 MALDIquant_1.22
Hello When I run the sample code, the following error occurs, how to solve it?
** Examples
get molecule from smiles
smiles <- "CN(C)CC(C1=C=C(C=C1)OC)C2(CCCCC2)O" molecule<-parse.smiles(smiles)[[1]]
calculate the fragments
fragments<-frag.generateFragments(molecule) Error in .jcall(obj, [Lorg/openscience/cdk/interfaces/IAtomContainer;", :java.lang.NoSuchMethodError:net.sf.jniinchi.INCHI_RET.getValue(I)Lnet/sf/jniinchi/INCHI_RET