msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spectra available
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hp71727 ▴ 10
Last seen 3 months ago
ETH Zurich

Dear Bioconductor team

When I try to run the "spectralMatching" function from the msPurity package on R I run into the following error:

q_dbPth <-
        createDatabase(pa = pa,
                       xcmsObj = xcmsObj,
                       dbName = 'test-mspurity-vignette.sqlite')

result <- spectralMatching(
        cores = 1

Error in getSmeta(con, pids) : No meta data for spectra available

I tried assigning a metadata list when I create the database with the function "msPurity::createDatabase", but this does not solve the issue.

q_dbPth <- createDatabase(pa, xcmsObj, metadata=list('polarity'='positive','instrument'='Q-Exactive'))

Here is also the session info

> sessionInfo("msPurity")
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 14393)

Matrix products: default

[1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252    LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C                        LC_TIME=German_Switzerland.1252    

attached base packages:

other attached packages:
[1] msPurity_1.22.0

loaded via a namespace (and not attached):
  [1] utils_4.2.0                 ProtGenerics_1.28.0         bitops_1.0-7                matrixStats_0.62.0          doParallel_1.0.17           RColorBrewer_1.1-3          GenomeInfoDb_1.32.4         backports_1.4.1            
  [9] MSnbase_2.22.0              tools_4.2.0                 utf8_1.2.2                  R6_2.5.1                    affyio_1.66.0               rpart_4.1.16                Hmisc_4.7-1                 DBI_1.1.3                  
 [17] BiocGenerics_0.42.0         colorspace_2.0-3            nnet_7.3-17                 withr_2.5.0                 gridExtra_2.3               tidyselect_1.2.0            compiler_4.2.0              MassSpecWavelet_1.62.0     
 [25] preprocessCore_1.58.0       graph_1.74.0                cli_3.4.1                   Biobase_2.56.0              htmlTable_2.4.1             datasets_4.2.0              DelayedArray_0.22.0         base_4.2.0                 
 [33] checkmate_2.1.0             scales_1.2.1                DEoptimR_1.0-11             robustbase_0.95-0           affy_1.74.0                 RBGL_1.72.0                 stringr_1.4.1               digest_0.6.29              
 [41] foreign_0.8-82              XVector_0.36.0              htmltools_0.5.3             jpeg_0.1-9                  base64enc_0.1-3             pkgconfig_2.0.3             MatrixGenerics_1.8.1        fastmap_1.1.0              
 [49] dbplyr_2.2.1                limma_3.52.4                grDevices_4.2.0             htmlwidgets_1.5.4           rlang_1.0.6                 rstudioapi_0.14             impute_1.70.0               generics_0.1.3             
 [57] mzID_1.34.0                 BiocParallel_1.30.4         dplyr_1.0.10                RCurl_1.98-1.9              magrittr_2.0.3              GenomeInfoDbData_1.2.8      Formula_1.2-4               interp_1.1-3               
 [65] MALDIquant_1.21             Matrix_1.4-1                Rcpp_1.0.9                  munsell_0.5.0               S4Vectors_0.34.0            fansi_1.0.3                 MsCoreUtils_1.8.0           lifecycle_1.0.3            
 [73] vsn_3.64.0                  stringi_1.7.8               MASS_7.3-56                 SummarizedExperiment_1.26.1 zlibbioc_1.42.0             plyr_1.8.7                  grid_4.2.0                  parallel_4.2.0             
 [81] doSNOW_1.0.20               deldir_1.0-6                methods_4.2.0               lattice_0.20-45             MsFeatures_1.4.0            splines_4.2.0               mzR_2.30.0                  knitr_1.40                 
 [89] xcms_3.18.0                 pillar_1.8.1                igraph_1.3.5                fastcluster_1.2.3           GenomicRanges_1.48.0        reshape2_1.4.4              codetools_0.2-18            stats4_4.2.0               
 [97] XML_3.99-0.11               glue_1.6.2                  latticeExtra_0.6-30         data.table_1.14.2           pcaMethods_1.88.0           BiocManager_1.30.18         CAMERA_1.52.0               vctrs_0.4.2                
[105] png_0.1-7                   foreach_1.5.2               graphics_4.2.0              gtable_0.3.1                RANN_2.6.1                  clue_0.3-61                 assertthat_0.2.1            ggplot2_3.3.6              
[113] xfun_0.33                   ncdf4_1.19                  survival_3.3-1              tibble_3.1.8                snow_0.4-4                  iterators_1.0.14            stats_4.2.0                 IRanges_2.30.1             
[121] cluster_2.1.3

Has anyone encountered this issue before or know how to circumvent it or solve it?

msPurity Metabolomics Bioconductor xcms spectralMatching • 164 views
Entering edit mode
Last seen 6 weeks ago
United Kingdom

This has been resolved (Windows Firewall issue) - see github issue


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