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Hi, I'm having problems loading ChemmineOB and would be grateful for any help.
library(ChemmineOB)
gives
Error: package or namespace load failed for ‘ChemmineOB’:
.onLoad failed in loadNamespace() for 'ChemmineOB', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ChemmineOB/libs/ChemmineOB.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/ChemmineOB/libs/ChemmineOB.so, 10): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.7.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ChemmineOB/libs/ChemmineOB.so
Reason: image not found
From this error message, it looks like ChemmineOB.so is trying to load libopenbabel.7.dylib.
However, the latest OpenBabel 2.4.1 does not contain this dylib, but only libopenbabel.5.dylib.
(I downloaded Open Babel 2.4.1 per Dan Tenenbaum's instructions and successfully installed as instructed here (including sudo make install
). Tested OpenBabel and it works fine.
Does anyone have any ideas?
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] ChemmineR_3.44.0 Rcpp_1.0.7
loaded via a namespace (and not attached):
[1] pillar_1.6.2 compiler_4.1.0 BiocManager_1.30.16 bitops_1.0-7
[5] base64enc_0.1-3 tools_4.1.0 zlibbioc_1.38.0 digest_0.6.27
[9] lifecycle_1.0.0 tibble_3.1.3 gtable_0.3.0 pkgconfig_2.0.3
[13] png_0.1-7 rlang_0.4.11 DBI_1.1.1 gridExtra_2.3
[17] vctrs_0.3.8 htmlwidgets_1.5.3 grid_4.1.0 DT_0.18
[21] glue_1.4.2 R6_2.5.0 fansi_0.5.0 ggplot2_3.3.5
[25] magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.2 htmltools_0.5.1.1
[29] colorspace_2.0-2 rsvg_2.1.2 utf8_1.2.2 RCurl_1.98-1.3
[33] munsell_0.5.0 crayon_1.4.1 rjson_0.2.20
Just realised that OpenBabel moved from Sourceforge to Github, and the latest version is in fact 3.1.1.
Going to install that now..