"Error: line 1 did not have 9 elements" for readIndex() and readChromatogram() + "Error : No scan vector is provided"for readSpectrum

[candidaorelmex]

Hi,

I tried to use your package for the first time and ran into some error. It also schows up for the sample file provided by the package, so I am fairly certain that it's not an issue caused by the raw file. Here the code with the errors (placed in quotes below the code that I ran:

rawf = file.path(path.package(package = 'rawrr'), 'extdata', 'sample.raw')

readIndex(rawf) "Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 9 elements"

readSpectrum(rawf) "Error in readSpectrum(rawf) : No scan vector is provided."

readChromatogram(rawf) "Error in readChromatogram(rawf) : No mass vector is provided."`

How can I resolve these issues? I also tried these functions with a path to one of my own raw files, it didnt work either.

Thanks a lot for your help, I cant wait to inspect my raw files with a rawrr!

[cpanse]

If you use Windows, please check #54 and https://github.com/fgcz/rawDiag/issues/33 Otherwise, please post the output of sessionInfo(). C

[cpanse]

rawrr::readChromatogram requires a raw file and a vector of masses.

[candidaorelmex]

the windows decimal operator wasnt the issue, I have it set as described in #33/#54.

my sessionInfo() output is:

loaded via a namespace (and not attached): [1] rgl_1.2.1 ps_1.7.5 class_7.3-20 crayon_1.5.2 nlme_3.1-163 backports_1.4.1 ellipse_0.5.0
[8] GOSemSim_2.22.0 rlang_1.1.1 SparseM_1.81 filelock_1.0.2 rjson_0.2.21 bit64_4.0.5 glue_1.6.2
[15] processx_3.8.2 parallel_4.2.2 DOSE_3.22.1 tidyselect_1.2.0 XML_3.99-0.14 xtable_1.8-4 MatrixModels_0.5-2
[22] magrittr_2.0.3 evaluate_0.21 cli_3.6.1 zlibbioc_1.44.0 rstudioapi_0.15.0 miniUI_0.1.1.1 rpart_4.1.19
[29] fastmatch_1.1-4 polynom_1.4-1 treeio_1.20.2 xfun_0.40 askpass_1.1 parameters_0.21.1 cluster_2.1.4
[36] caTools_1.18.2 tidygraph_1.2.3 KEGGREST_1.38.0 quantreg_5.97 ape_5.7-1 listenv_0.9.0 reshape_0.8.9
[43] png_0.1-8 future_1.33.0 ipred_0.9-14 zeallot_0.1.0 withr_2.5.0 bitops_1.0-7 cellranger_1.1.0
[50] e1071_1.7-13 coda_0.19-4 pillar_1.9.0 GlobalOptions_0.1.2 cachem_1.0.8 multcomp_1.4-25 GetoptLong_1.0.5
[57] paletteer_1.5.0 vctrs_0.6.3 ellipsis_0.3.2 generics_0.1.3 lava_1.7.2.1 tools_4.2.2 foreign_0.8-83
[64] munsell_0.5.0 tweenr_2.0.2 fgsea_1.22.0 emmeans_1.8.8 proxy_0.4-27 fastmap_1.1.1 compiler_4.2.2
[71] abind_1.4-5 httpuv_1.6.11 GenomeInfoDbData_1.2.9 prodlim_2023.03.31 lattice_0.20-45 visNetwork_2.1.2 utf8_1.2.3
[78] later_1.3.1 BiocFileCache_2.6.1 Quandl_2.11.0 jsonlite_1.8.7 ada_2.0-5 tidytree_0.4.5 carData_3.0-5
[85] estimability_1.4.1 lazyeval_0.2.2 promises_1.2.1 car_3.1-2 R.utils_2.12.2 checkmate_2.2.0 rmarkdown_2.24
[92] sandwich_3.0-2 textshaping_0.3.6 downloader_0.4 igraph_1.5.1 survival_3.4-0 systemfonts_1.0.4 htmltools_0.5.6
[99] memoise_2.0.1 graphlayouts_1.0.0 quadprog_1.5-8 viridisLite_0.4.2 assertthat_0.2.1 digest_0.6.33 mime_0.12
[106] rappdirs_0.3.3 bayestestR_0.13.1 yulab.utils_0.0.8 future.apply_1.11.0 blob_1.2.4 R.oo_1.25.0 ragg_1.2.5
[113] Formula_1.2-5 splines_4.2.2 rematch2_2.1.2 RCurl_1.98-1.12 broom_1.0.5 hms_1.1.3 colorspace_2.1-0
[120] base64enc_0.1-3 shape_1.4.6 aplot_0.2.0 websocket_1.4.1 nnet_7.3-18 Rcpp_1.0.11 mvtnorm_1.2-2
[127] enrichplot_1.16.2 fansi_1.0.4 tzdb_0.4.0 parallelly_1.36.0 svGUI_1.0.1 R6_2.5.1 lifecycle_1.0.3
[134] statsExpressions_1.5.1 zip_2.3.0 datawizard_0.8.0 curl_5.0.2 ggsignif_0.6.4 snakecase_0.11.0 DO.db_2.9
[141] Matrix_1.6-1 qvalue_2.28.0 TH.data_1.1-2 RColorBrewer_1.1-3 htmlwidgets_1.6.2 polyclip_1.10-4 shadowtext_0.1.2
[148] chromote_0.1.2 timechange_0.2.0 gridGraphics_0.5-1 globals_0.16.2 openssl_2.1.0 insight_0.19.3 htmlTable_2.4.1
[155] patchwork_1.1.3 codetools_0.2-18 GO.db_3.15.0 gtools_3.9.4 prettyunits_1.1.1 dbplyr_2.3.3 gridBase_0.4-7
[162] R.methodsS3_1.8.2 correlation_0.8.4 gtable_0.3.4 ggfun_0.1.2 httr_1.4.7 KernSmooth_2.23-20 stringi_1.7.12
[169] progress_1.2.2 reshape2_1.4.4 farver_2.1.1 uuid_1.1-1 viridis_0.6.4 ggtree_3.4.4 xml2_1.3.5
[176] ade4_1.7-22 ggplotify_0.1.2 scatterpie_0.2.1 ggraph_2.1.0 janitor_2.2.0 pkgconfig_2.0.3 rstatix_0.7.2
[183] evd_2.3-6.1 knitr_1.43

[cpanse]

Thanks; interesting; I need the R, rawrr, and Windows OS versions. Also, have you tried the rawrr::readChromatogram command with the correct arguments? Also, when you changed the sep. setting, have you rebooted the OS and restarted R? C

[candidaorelmex]

Sure: R -> 4.2.2 rawrr -> 1.4.0 WindowsOS -> Windows 10, Version 22H2 (OS build 19045.3086)

readChromatogram works!

regarding the sep. settings: yes I have, it didn't help.

Thank you for your assistance!

[cpanse]

OK; I see the problem. your rawrr version is out of date. current version is 1.8.1.

please update.

https://bioconductor.org/packages/rawrr/

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rawrr")

the mono assembly is mismatching with the Rcode.

[candidaorelmex]

I updated rawrr to 1.8.1, yet the same error messages persist.

[cpanse]

@candidaorelmex and run rawrr::installRawrrExe() .

[candidaorelmex]

It works! thanks a lot for your help:)