In serialize(data, node$con)
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@thomasboegl-23807
Last seen 14 months ago

Hello everyone!

I recently started with trying to evaluate my data with xcms. I downloaded all packages and started with the "LCMS data preprocessing and analysis with xcms" (https://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html) Tutorial.

But there occurs this Warning: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading

What does it mean? Does it have any influence? It seems like that it the output is generated correclty..


> library(faahKO)
> library(RColorBrewer)
> library(pander)
> library(magrittr)
> library(pheatmap)
> library(SummarizedExperiment)
Loading required package: GenomicRanges
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:xcms’:

    distance

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

> cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE, recursive = TRUE)
> pd <- data.frame(sample_name = sub(basename(cdfs), pattern = ".CDF", replacement = "", fixed = TRUE), sample_group = c(rep("KO", 6), rep("WT", 6)), stringsAsFactors = FALSE)
> raw_data <- readMSData(files = cdfs, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
> raw_data
MSn experiment data ("OnDiskMSnExp")
Object size in memory: 4.56 Mb
- - - Spectra data - - -
 MS level(s): 1 
 Number of spectra: 15336 
 MSn retention times: 41:41 - 74:60 minutes
- - - Processing information - - -
Data loaded [Mon Jul 06 15:19:12 2020] 
 MSnbase version: 2.14.2 
- - - Meta data  - - -
phenoData
  rowNames: 1 2 ... 12 (12 total)
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] ko15.CDF...  [12] wt22.CDF
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F01.S0001 F01.S0002 ... F12.S1278 (15336 total)
  fvarLabels: fileIdx spIdx ... spectrum (33 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
> mzs <- mz(raw_data)
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
...


> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] SummarizedExperiment_1.18.1 DelayedArray_0.14.0         matrixStats_0.56.0         
 [4] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         IRanges_2.22.2             
 [7] pheatmap_1.0.12             magrittr_1.5                pander_0.6.3               
[10] RColorBrewer_1.1-2          xcms_3.9.1                  MSnbase_2.14.2             
[13] ProtGenerics_1.20.0         S4Vectors_0.26.1            mzR_2.22.0                 
[16] Rcpp_1.0.4.6                BiocParallel_1.22.0         Biobase_2.48.0             
[19] BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] splines_4.0.2          lattice_0.20-41        colorspace_1.4-1       vctrs_0.3.1           
 [5] snow_0.4-3             vsn_3.56.0             XML_3.99-0.4           survival_3.2-3        
 [9] rlang_0.4.6            pillar_1.4.4           glue_1.4.1             affy_1.66.0           
[13] GenomeInfoDbData_1.2.3 affyio_1.58.0          foreach_1.5.0          lifecycle_0.2.0       
[17] plyr_1.8.6             mzID_1.26.0            robustbase_0.93-6      zlibbioc_1.34.0       
[21] munsell_0.5.0          pcaMethods_1.80.0      gtable_0.3.0           codetools_0.2-16      
[25] doParallel_1.0.15      MassSpecWavelet_1.54.0 preprocessCore_1.50.0  DEoptimR_1.0-8        
[29] scales_1.1.1           BiocManager_1.30.10    limma_3.44.3           XVector_0.28.0        
[33] farver_2.0.3           RANN_2.6.1             impute_1.62.0          ggplot2_3.3.2         
[37] digest_0.6.25          ncdf4_1.17             grid_4.0.2             bitops_1.0-6          
[41] tools_4.0.2            RCurl_1.98-1.2         tibble_3.0.1           crayon_1.3.4          
[45] pkgconfig_2.0.3        MASS_7.3-51.6          ellipsis_0.3.1         Matrix_1.2-18         
[49] rstudioapi_0.11        iterators_1.0.12       R6_2.4.1               MALDIquant_1.19.3     
[53] multtest_2.44.0        compiler_4.0.2   

software error • 153 views
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