Error running example

[bru-dot-edu]

Hey, I'm trying to run the example in the readme. Let me know what info you need from me. I'm running on mac in Rstudio with R version 4.1.2. Here's the output:

18:32:48.170 [main] INFO de.ipbhalle.metfraglib.database.OnlinePubChemDatabase - Fetching candidates from PubChem 18:32:48.910 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Got 5 candidate(s) 18:32:48.942 [pool-5-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 20 % 18:32:48.955 [pool-5-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 40 % 18:32:48.966 [pool-5-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 60 % 18:32:48.976 [pool-5-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 80 % 18:32:48.987 [pool-5-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 100 % 18:32:49.929 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Processed 0 candidate(s) 18:32:49.930 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) were discarded before processing due to pre-filtering 18:32:49.930 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 5 candidate(s) discarded during processing due to errors 18:32:49.931 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded after processing due to post-filtering 18:32:49.931 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Stored 0 candidate(s)

[bru-dot-edu]

FYI I got it working using an older version of R (3.6.3), so it seems like it's a version issue.

[AharoniLab]

Hi,

I was also unable to run the package example

1) On Windows, running metfRag_2.4.2 I simply get an empty data frame after running: scored.candidates<-run.metfrag(settingsObject)

sessionInfo() _R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1255 LC_CTYPE=English_United States.1255 LC_MONETARY=English_United States.1255 LC_NUMERIC=C
[5] LC_TIME=English_United States.1255

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

other attached packages: [1] devtools_2.4.5 usethis_2.1.6

loaded via a namespace (and not attached): [1] Rcpp_1.0.10 compiler_4.2.2 later_1.3.0 urlchecker_1.0.1 prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 tools_4.2.2 digest_0.6.31 pkgbuild_1.4.0
[11] pkgload_1.3.2 memoise_2.0.1 lifecycle_1.0.3 rlang_1.0.6 shiny_1.7.4 cli_3.6.0 rstudioapi_0.14 curl_5.0.0 xfun_0.37 fastmap_1.1.1
[21] withr_2.5.0 stringr_1.5.0 desc_1.4.2 fs_1.6.1 vctrs_0.5.2 htmlwidgets_1.6.1 rprojroot_2.0.3 glue_1.6.2 R6_2.5.1 processx_3.8.0
[31] sessioninfo_1.2.2 callr_3.7.3 purrr_1.0.1 magrittr_2.0.3 promises_1.2.0.1 ps_1.7.2 ellipsis_0.3.2 htmltools_0.5.4 mime_0.12 xtable_1.8-4
[41] httpuv_1.6.9 tinytex_0.44 stringi_1.7.12 miniUI_0.1.1.1 cachem_1.0.7 crayon1.5.2

2) On Linux, I run initially with metfRag_2.4.2 and again got an empty data frame - however this time the output more detailed: scored.candidates<-run.metfrag(settingsObject) 09:51:09.025 [main] INFO de.ipbhalle.metfraglib.database.OnlinePubChemDatabase - Fetching candidates from PubChem 09:51:10.992 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Got 5 candidate(s) 09:51:11.206 [pool-2-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 20 % 09:51:11.219 [pool-2-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 40 % 09:51:11.231 [pool-2-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 60 % 09:51:11.244 [pool-2-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 80 % 09:51:11.256 [pool-2-thread-1] INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 100 % 09:51:12.002 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Processed 0 candidate(s) 09:51:12.002 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) were discarded before processing due to pre-filtering 09:51:12.002 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 5 candidate(s) discarded during processing due to errors 09:51:12.002 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded after processing due to post-filtering 09:51:12.003 [main] INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Stored 0 candidate(s)

...so initial candidates were detected, but next discarded due to unspecified error on the IPB server

Still on Linux, I upgrade the package to the latest release, which is quite confusingly under the "ipb-halle/MetFragRelaunched" repository. Building and testing went well and the installer could send spectra and retrieve results. However, from R I got a system error:

scored.candidates<-run.metfrag(settingsObject) Error in run.metfrag(settingsObject) : java.lang.ClassNotFoundException

sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages: [1] metfRag_2.5.0 rjson_0.2.20 rcdk_3.7.0 rcdklibs_2.8 rJava_1.0-6

loaded via a namespace (and not attached): [1] compiler_3.6.3 squash_1.0.9 tools_3.6.3 parallel_3.6.3 [5] fingerprint_3.5.7 iterators_1.0.14 itertools_0.1-3 png_0.1-8