BiocParallel errors in label: unnamed-chunk-13

[kozo2]

I'm Kozo from Bioconductor's Multilingualization Working Group. (http://workinggroups.bioconductor.org/currently-active-working-groups-committees.html) I will translate this repository into Japanese as an activity of the working group.

So I tried to build this repository first, but it failed with the following error.

label: unnamed-chunk-9 (with options) 
List of 1
 $ message: logi FALSE

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label: spectradata1

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label: spectra1
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label: spectra2

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   inline R code fragments

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label: unnamed-chunk-11

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  ordinary text without R code

label: unnamed-chunk-13
Quitting from lines 513-517 (R4MS.Rmd) 
Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error:
Error in .local(object, ...): File(s) C:\Users\lab\AppData\Local\Temp\RtmpSIKOxV/20171016_POOL_POS_1_105-134.h5 does/do already exist

> 

Let me know if you have any ideas for resolving this error.

The sessionInfo() is

> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=Japanese_Japan.utf8  LC_CTYPE=Japanese_Japan.utf8    LC_MONETARY=Japanese_Japan.utf8
[4] LC_NUMERIC=C                    LC_TIME=Japanese_Japan.utf8    

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

other attached packages:
 [1] magrittr_2.0.3              msdata_0.36.0               rpx_2.4.0                  
 [4] MsCoreUtils_1.8.0           QFeatures_1.6.0             MultiAssayExperiment_1.22.0
 [7] SummarizedExperiment_1.26.1 Biobase_2.56.0              GenomicRanges_1.48.0       
[10] GenomeInfoDb_1.32.2         IRanges_2.30.0              MatrixGenerics_1.8.0       
[13] matrixStats_0.62.0          Spectra_1.6.0               ProtGenerics_1.28.0        
[16] BiocParallel_1.30.2         S4Vectors_0.34.0            BiocGenerics_0.42.0        
[19] mzR_2.30.0                  Rcpp_1.0.8.3                BiocStyle_2.24.0           
[22] BiocManager_1.30.18         devtools_2.4.3              usethis_2.1.5              

loaded via a namespace (and not attached):
 [1] bitops_1.0-7            fs_1.5.2                bit64_4.0.5            
 [4] filelock_1.0.2          httr_1.4.3              rprojroot_2.0.3        
 [7] tools_4.2.0             bslib_0.3.1             utf8_1.2.2             
[10] R6_2.5.1                DBI_1.1.2               lazyeval_0.2.2         
[13] rhdf5filters_1.8.0      withr_2.5.0             tidyselect_1.1.2       
[16] prettyunits_1.1.1       processx_3.5.3          bit_4.0.4              
[19] curl_4.3.2              compiler_4.2.0          cli_3.3.0              
[22] xml2_1.3.3              desc_1.4.1              DelayedArray_0.22.0    
[25] bookdown_0.26           sass_0.4.1              callr_3.7.0            
[28] rappdirs_0.3.3          stringr_1.4.0           digest_0.6.29          
[31] rmarkdown_2.14          XVector_0.36.0          pkgconfig_2.0.3        
[34] htmltools_0.5.2         sessioninfo_1.2.2       dbplyr_2.1.1           
[37] fastmap_1.1.0           highr_0.9               rlang_1.0.2            
[40] rstudioapi_0.13         RSQLite_2.2.14          generics_0.1.2         
[43] jquerylib_0.1.4         jsonlite_1.8.0          dplyr_1.0.9            
[46] RCurl_1.98-1.6          GenomeInfoDbData_1.2.8  Matrix_1.4-1           
[49] Rhdf5lib_1.18.2         fansi_1.0.3             lifecycle_1.0.1        
[52] stringi_1.7.6           yaml_2.3.5              MASS_7.3-56            
[55] zlibbioc_1.42.0         brio_1.1.3              rhdf5_2.40.0           
[58] pkgbuild_1.3.1          BiocFileCache_2.4.0     blob_1.2.3             
[61] grid_4.2.0              msmbstyle_0.0.22        parallel_4.2.0         
[64] crayon_1.5.1            lattice_0.20-45         pillar_1.7.0           
[67] knitr_1.39              ps_1.7.0                igraph_1.3.1           
[70] codetools_0.2-18        pkgload_1.2.4           glue_1.6.2             
[73] evaluate_0.15           remotes_2.4.2           vctrs_0.4.1            
[76] testthat_3.1.4          purrr_0.3.4             assertthat_0.2.1       
[79] clue_0.3-60             cachem_1.0.6            xfun_0.31              
[82] AnnotationFilter_1.20.0 ncdf4_1.19              snow_0.4-4             
[85] tibble_3.1.7            memoise_2.0.1           cluster_2.1.3          
[88] ellipsis_0.3.2         
> 

[lgatto]

Thank you Kozo, I'll look into it.

[lgatto]

The errors happens in

sp_hdf5 <- setBackend(sp_sciex, MsBackendHdf5Peaks(), hdf5path = tempdir())
sp_hdf5
table(sp_hdf5$dataOrigin)
table(sp_hdf5$dataStorage)

(which is now named sciex_hdf5 to make sure that's where the error happens)

It looks like the temp dir where the hdf5 files are created already contains these files. I don't have this issue on linux, although I'm not sure whether this is because a new tempdir() is used every time, or the old on is deleted.

[kozo2]

Thank you for the advice. First of all, I will try this on Linux instead of Windows.

[kozo2]

In the Linux environment, there was no error like the Windows environment. I close this issue.