I am fairly new to R and to Bioconductor and have been running some code (previously written by another member of our cohort) to analyze our mass spec data. I've run into a couple of issues which I now can't seem to fix.
1) Our peak picking code loops through large numbers of files, nearly 1500 in this most recent project, so we often run into an issue of running out of memory. For instance, today we were able to get through about 300 files before it errored out with the message:
Biocparallel error: cannot allocate vector of size 1.2 mb
To tackle this issue, I tried restarting our Windows computer to give the R session a clean slate of memory and begin where we left off. After restarting the computer, the code ran into a new issue. mzR will not open or read our mzXML files. I've isolated the source of the error in our code, which reads as follows:
files_1 <- list.files(paste(mzxml_location, sites[i], "/",species[j],sep=""), recursive = TRUE, full.names = TRUE) files <- files_1[endsWith(files_1, "mzXML")] raw_data <- readMSData(files, msLevel. = 1, mode="onDisk")
The function finding the files works perfectly fine, but the last line results in the error message:
Error in pwizModule$open(filename) : [MSDataFile::readFile()] Unsupported file format.
along with warning messages stating that the directory names for each file are invalid. The files all exist at the specified directories, are uncorrupted, and in .mzXML format. This code also worked without running into this error message before I restarted the computer, so I'm not sure what could have changed or how to proceed. Not sure if it's important, but I did receive this warning message when loading mzR after the computer restart:
In fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.0) than is installed on your system (1.0.1). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc support forum at https://support.bioconductor.org/. For details see also https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
For additional information, here is the output of the sessionInfo():
R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252  LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  reshape2_1.4.3 CAMERA_1.38.1 splitstackshape_1.4.6 vegan_2.5-4 lattice_0.20-38  permute_0.9-5 pvclust_2.0-0 muma_1.4 rrcov_1.4-7 pcaPP_1.9-73  caTools_22.214.171.124 bitops_1.0-6 gtools_3.8.1 robustbase_0.93-4 mvtnorm_1.0-10  gplots_3.0.3 pls_2.7-1 pdist_1.2 car_3.0-3 carData_3.0-2  snow_0.4-3 xcms_3.4.4 MSnbase_2.8.3 ProtGenerics_1.14.0 S4Vectors_0.20.1  mzR_2.16.2 Rcpp_1.0.1 BiocParallel_1.16.6 multtest_2.38.0 Biobase_2.42.0  BiocGenerics_0.28.0 loaded via a namespace (and not attached):  nlme_3.1-137 doParallel_1.0.14 RColorBrewer_1.1-2 backports_1.1.3 tools_3.5.2  affyio_1.52.0 rpart_4.1-13 KernSmooth_2.23-15 Hmisc_4.2-0 lazyeval_0.2.2  mgcv_1.8-28 colorspace_1.4-1 nnet_7.3-12 gridExtra_2.3 curl_3.3  compiler_3.5.2 MassSpecWavelet_1.48.1 preprocessCore_1.44.0 graph_1.60.0 htmlTable_1.13.1  checkmate_1.9.1 scales_1.0.0 DEoptimR_1.0-8 affy_1.60.0 RBGL_1.58.2  stringr_1.4.0 digest_0.6.18 foreign_0.8-71 rio_0.5.16 htmltools_0.3.6  base64enc_0.1-4 pkgconfig_2.0.2 limma_3.38.3 htmlwidgets_1.3 rlang_0.3.2  readxl_1.3.1 rstudioapi_0.10 impute_1.56.0 BiocInstaller_1.32.1 mzID_1.20.1  acepack_1.4.1 zip_2.0.1 magrittr_1.5 Formula_1.2-3 MALDIquant_1.19.2  Matrix_1.2-15 munsell_0.5.0 abind_1.4-7 vsn_3.50.0 stringi_1.4.3  MASS_7.3-51.1 zlibbioc_1.28.0 plyr_1.8.4 grid_3.5.2 gdata_2.18.0  forcats_0.4.0 crayon_1.3.4 haven_2.1.0 splines_3.5.2 hms_0.4.2  knitr_1.22 pillar_1.3.1 igraph_1.2.4 codetools_0.2-16 XML_4.0-0  latticeExtra_0.6-28 pcaMethods_1.74.0 data.table_1.12.0 BiocManager_1.30.4 foreach_1.5.1  cellranger_1.1.0 gtable_0.3.0 RANN_2.6.1 ggplot2_3.1.0 xfun_0.5  openxlsx_4.1.0 ncdf4_1.16.1 survival_2.43-3 tibble_2.1.1 iterators_1.0.11  IRanges_2.16.0 cluster_2.0.7-1
Any help or advice would be greatly appreciated!