Entering edit mode
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(
q_dbPth,
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
locale:
[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:
character(0)
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?
