Closed Begotalavera closed 2 years ago
rickhelmus
commented
2 years ago Hello,
Thanks for reporting the issue.
This seems to be related to XCMS or BiocParallel. I cannot reproduce it with the same grouping parameters as you use. Can you try it again with parallelization disabled, e.g. by running the following before grouping:
BiocParallel::register(BiocParallel::SerialParam(), default = TRUE)This may also give you more clear error information.
Thanks, Rick
Begotalavera
commented
2 years ago Hello,
Thanks for reporting the issue.
This seems to be related to
XCMSorBiocParallel. I cannot reproduce it with the same grouping parameters as you use. Can you try it again with parallelization disabled, e.g. by running the following before grouping:BiocParallel::register(BiocParallel::SerialParam(), default = TRUE)This may also give you more clear error information.
Thanks, Rick
Hello Rick,
Many thanks for your quick reply.
I tried to run BiocParallel::register(BiocParallel::SerialParam(), default = TRUE)
as you suggested... and now I am not getting this error any more.
Thanks! Bego
Hi,
I am getting this error ,
Performing retention time alignment... Sample number 10 used as center sample. Aligning Blank1_HILIC_neg.mzML against 1093_neg.mzML ... Error: BiocParallel errors 1 remote errors, element index: 1 4 unevaluated and other errors first remote error: cannot open the connection In addition: Warning messages: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading 7: In serialize(data, node$con) : 'package:stats' may not be available when loading 8: stop worker failed: wrong args for environment subassignment
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 65001
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] xcms_3.16.1 MSnbase_2.20.1 ProtGenerics_1.26.0 S4Vectors_0.32.3 mzR_2.28.0 Rcpp_1.0.7 Biobase_2.54.0 BiocGenerics_0.40.0 [9] BiocParallel_1.28.2 patRoon_1.2.0
loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.61.0 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
[6] GenomeInfoDb_1.30.0 backports_1.4.0 tools_4.1.2 utf8_1.2.2 R6_2.5.1
[11] affyio_1.64.0 DBI_1.1.1 colorspace_2.0-2 withr_2.4.3 tidyselect_1.1.1
[16] bit_4.0.4 compiler_4.1.2 MassSpecWavelet_1.60.0 preprocessCore_1.56.0 DelayedArray_0.20.0
[21] checkmate_2.0.0 scales_1.1.1 DEoptimR_1.0-9 robustbase_0.93-9 affy_1.72.0
[26] digest_0.6.29 XVector_0.34.0 pkgconfig_2.0.3 htmltools_0.5.2 fst_0.9.4
[31] MatrixGenerics_1.6.0 fastmap_1.1.0 limma_3.50.0 rlang_0.4.12 RSQLite_2.2.9
[36] impute_1.68.0 shiny_1.7.1 generics_0.1.1 mzID_1.32.0 dplyr_1.0.7
[41] RCurl_1.98-1.5 magrittr_2.0.1 GenomeInfoDbData_1.2.7 MALDIquant_1.20 Matrix_1.3-4
[46] munsell_0.5.0 fansi_0.5.0 MsCoreUtils_1.6.0 lifecycle_1.0.1 vsn_3.62.0
[51] MASS_7.3-54 SummarizedExperiment_1.24.0 zlibbioc_1.40.0 plyr_1.8.6 blob_1.2.2
[56] grid_4.1.2 parallel_4.1.2 promises_1.2.0.1 crayon_1.4.2 lattice_0.20-45
[61] MsFeatures_1.2.0 pillar_1.6.4 GenomicRanges_1.46.1 codetools_0.2-18 XML_3.99-0.8
[66] glue_1.5.1 pcaMethods_1.86.0 data.table_1.14.2 BiocManager_1.30.16 vctrs_0.3.8
[71] httpuv_1.6.3 Rdpack_2.1.3 foreach_1.5.1 gtable_0.3.0 RANN_2.6.1
[76] purrr_0.3.4 clue_0.3-60 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5
[81] mime_0.12 rbibutils_2.2.5 xtable_1.8-4 later_1.3.0 ncdf4_1.18
[86] snow_0.4-4 tibble_3.1.6 iterators_1.0.13 memoise_2.0.1 IRanges_2.28.0
[91] cluster_2.1.2 ellipsis_0.3.2