Error during Reference database searching - DDA MS/MS data processing

MetaboAnalyst
1

Error during Reference database searching - DDA MS/MS data processing

Hello,

I am trying to use “PerformDBSearchingBatch” in MetaboAnalystR searching MS/MS reference library, however, I consistently get the error below, please help to check it, Tx

Error in checkForRemoteErrors(val) :
6 nodes produced errors; first error: Expecting a single string value: [type=NULL; extent=0].

PerformDBSearchingBatch is used to searching MS/MS reference library

Results will be scored based on the similarity rules above

Parallel computing is allowed. CPU cores used are controlled by argument “ncores”.

mSet ←

  • PerformDBSearchingBatch(
  • mSet,
  • ppm1 = 5,
  • ppm2 = 15,
  • rt_tol = 15,
  • database_path = “ms2_db/MS2ID_Bio.sqlite”,
  • use_rt = FALSE,
  • enableNL = FALSE,
  • NLdatabase_path = NULL,
  • ncores = 6L,
  • useEntropy = FALSE
  • )
    ==== Database searching against MS2ID_Bio.sqlite started ====
    Error in checkForRemoteErrors(val) :
    6 nodes produced errors; first error: Expecting a single string value: [type=NULL; extent=0].

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale:

time zone:
tzcode source: internal

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] OptiLCMS_1.1.0 MSnbase_2.26.0 ProtGenerics_1.32.0 S4Vectors_0.38.1 mzR_2.34.1 Rcpp_1.0.11 BiocParallel_1.34.2
[8] Biobase_2.60.0 BiocGenerics_0.46.0 MetaboAnalystR_4.0.0

loaded via a namespace (and not attached):
[1] later_1.3.1 splines_4.3.1 bitops_1.0-7 tibble_3.2.1 hardhat_1.3.0 preprocessCore_1.62.1
[7] graph_1.78.0 pROC_1.18.4 XML_3.99-0.14 rpart_4.1.19 lifecycle_1.0.3 edgeR_3.42.4
[13] doParallel_1.0.17 processx_3.8.2 globals_0.16.2 lattice_0.21-8 MASS_7.3-60 scrime_1.3.5
[19] backports_1.4.1 magrittr_2.0.3 limma_3.56.2 Hmisc_5.1-1 plotly_4.10.2 rmarkdown_2.25
[25] remotes_2.4.2.1 yaml_2.3.7 httpuv_1.6.11 sessioninfo_1.2.2 pkgbuild_1.4.2 cowplot_1.1.1
[31] MsCoreUtils_1.12.0 DBI_1.1.3 RColorBrewer_1.1-3 lubridate_1.9.3 pkgload_1.3.3 multcomp_1.4-25
[37] zlibbioc_1.46.0 purrr_1.0.2 nnet_7.3-19 TH.data_1.1-2 sandwich_3.0-2 ipred_0.9-14
[43] lava_1.7.2.1 IRanges_2.34.1 ggrepel_0.9.3 listenv_0.9.0 parallelly_1.36.0 ncdf4_1.21
[49] codetools_0.2-19 RApiSerialize_0.1.2 tidyselect_1.2.0 base64enc_0.1-3 jsonlite_1.8.7 caret_6.0-94
[55] multtest_2.56.0 ellipsis_0.3.2 Formula_1.2-5 survival_3.5-7 iterators_1.0.14 emmeans_1.8.8
[61] foreach_1.5.2 rsm_2.10.4 tools_4.3.1 progress_1.2.2 glue_1.6.2 prodlim_2023.08.28
[67] gridExtra_2.3 xfun_0.40 usethis_2.2.2 crmn_0.0.21 dplyr_1.1.3 withr_2.5.1
[73] BiocManager_1.30.22 fastmap_1.1.1 fansi_1.0.4 callr_3.7.3 entropy_1.3.1 caTools_1.18.2
[79] digest_0.6.33 mime_0.12 timechange_0.2.0 R6_2.5.1 estimability_1.4.1 colorspace_2.1-0
[85] Cairo_1.6-1 gtools_3.9.4 RSQLite_2.3.1 utf8_1.2.3 tidyr_1.3.0 generics_0.1.3
[91] data.table_1.14.8 recipes_1.0.8 class_7.3-22 prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.2
[97] RJSONIO_1.3-1.8 ModelMetrics_1.2.2.2 pkgconfig_2.0.3 gtable_0.3.4 timeDate_4022.108 blob_1.2.4
[103] siggenes_1.74.0 impute_1.74.1 htmltools_0.5.6 profvis_0.3.8 fgsea_1.26.0 RBGL_1.76.0
[109] MALDIquant_1.22.1 clue_0.3-65 scales_1.2.1 gower_1.0.1 knitr_1.44 rstudioapi_0.15.0
[115] reshape2_1.4.4 curl_5.0.2 coda_0.19-4 checkmate_2.2.0 nlme_3.1-163 cachem_1.0.8
[121] zoo_1.8-12 stringr_1.5.0 KernSmooth_2.23-22 miniUI_0.1.1.1 foreign_0.8-85 mzID_1.38.0
[127] vsn_3.68.0 pillar_1.9.0 grid_4.3.1 vctrs_0.6.3 gplots_3.1.3 pcaMethods_1.92.0
[133] urlchecker_1.0.1 promises_1.2.1 stringfish_0.15.8 xtable_1.8-4 cluster_2.1.4 htmlTable_2.4.1
[139] evaluate_0.22 mvtnorm_1.2-3 cli_3.6.1 locfit_1.5-9.8 compiler_4.3.1 rlang_1.1.1
[145] crayon_1.5.2 future.apply_1.11.0 ps_1.7.5 fs_1.6.3 affy_1.78.2 plyr_1.8.8
[151] stringi_1.7.12 viridisLite_0.4.2 munsell_0.5.0 lazyeval_0.2.2 devtools_2.4.5 Matrix_1.6-1.1
[157] hms_1.1.3 glasso_1.11 bit64_4.0.5 future_1.33.0 ggplot2_3.4.3 shiny_1.7.5
[163] qs_0.25.5 igraph_1.5.1 memoise_2.0.1 RcppParallel_5.1.7 affyio_1.70.0 fastmatch_1.1-4
[169] bit_4.0.5

2

Hi,
Thanks for reporting this issue. We have validated this issue and fixed it. Please try to re-install OptiLCMS and try it again. Let us know if you have other comments!

Zhiqiang

3

Hello,

I also try to use “PerformDBSearchingBatch” in MetaboAnalystR searching MS/MS reference library and show the same error:6 nodes produced errors; first error: Expecting a single string value: [type=NULL; extent=0].
Then I re-install OptiLCMS and try it again,but it happens again.

4

The same error occurred for me as well when I was trying to use the following code:

mSet ← PerformDBSearchingBatch (mSet,
ppm1 = 10,
ppm2 = 25,
rt_tol = 5,
database_path = “ms2_db/MS2ID_Bio_v09102023.sqlite”,
use_rt = FALSE,
enableNL = FALSE,
ncores = 6L)

==== Database searching against MS2ID_Bio_v09102023.sqlite started ====
Error in checkForRemoteErrors(val) :
6 nodes produced errors; first error: Expecting a single string value: [type=NULL; extent=0].

Please let me know how to resolve the issue. I already tried reinstalling OptiLCMS but the same error was raised.