Comments (14)
Arthfael
commented on September 27, 2024
2
Dear Tobi,
I just figured it out. All of the paths and sessionInfo details matched as
closely as possible, so I decided to think again from the start. If
readChromatogram worked for me in TIC/Base Peak mode, but not XIC mode,
then maybe my usage was wrong for that mode. Indeed, it turns out I had
misread the help file, I thought one needs to provide one tolerance value
for each mass, not a single one for all:
masses <- c(524, 670)
tols <- rep(100, length(masses)) # in ppm
XICs <- readChromatogram(Raws[1], masses, tols) # this fails
XICs <- readChromatogram(Raws[1], masses, tols[1]) # this works
My apologies for wasting your time. Maybe it would be a good idea to change
slightly the function so that if several tolerances are provided, it will
throw a more helpful error, as the error message which was printed now did
not actually relate to the cause of the error. Anyway, thank you for your
help!
All the best,
Armel
…On Thu, Feb 17, 2022 at 8:59 AM Tobias Kockmann ***@***.***> wrote:
That is all pretty wired. I meanwhile installed rawrr 1.2.0 using
BiocManager on a very similar system (Windows Server 2021):
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rawrr_1.2.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] magrittr_2.0.2 tidyselect_1.1.1 R6_2.5.1 rlang_1.0.1 fastmap_1.1.0 fansi_1.0.2
[7] dplyr_1.0.8 tools_4.1.0 DT_0.20 utf8_1.2.2 cli_3.2.0 DBI_1.1.2
[13] htmltools_0.5.2 ellipsis_0.3.2 yaml_2.2.2 assertthat_0.2.1 digest_0.6.29 tibble_3.1.6
[19] lifecycle_1.0.1 crayon_1.5.0 purrr_0.3.4 htmlwidgets_1.5.4 vctrs_0.3.8 glue_1.6.1
[25] compiler_4.1.0 pillar_1.7.0 generics_0.1.2 pkgconfig_2.0.3
What do you get when reading from the sample data that comes with the
package?
> rawfile <- sampleFilePath()
> Idx <- readIndex(rawfile)
> str(Idx)
'data.frame': 573 obs. of 8 variables:
$ scan : int 1 2 3 4 5 6 7 8 9 10 ...
$ scanType : chr "FTMS + c NSI Full ms [350.0000-1800.0000]" "FTMS + c NSI Full ms2 ***@***.*** [140.0000-1015.0000]" "FTMS + c NSI Full ms2 ***@***.*** [140.0000-1335.0000]" "FTMS + c NSI Full ms2 ***@***.*** [140.0000-1415.0000]" ...
$ rtinseconds : num 0.097 0.35 0.419 0.489 0.558 0.627 0.696 0.766 0.835 0.904 ...
$ precursorMass : num 1075 487 645 684 547 ...
$ MSOrder : chr "Ms" "Ms2" "Ms2" "Ms2" ...
$ charge : int 0 2 2 2 2 2 2 2 2 2 ...
$ masterScan : int NA NA NA NA NA NA NA NA NA NA ...
$ dependencyType: logi NA NA NA NA NA NA ...
My path to the sample data is:
> rawfile
[1] "X:/Rlibs/rawrr/extdata/sample.raw"
The rawrr assembly path (the path were the dll are placed) is
> rawrrAssemblyPath()
[1] "C:\\Users\\tobiasko.FGCZ-NET\\AppData\\Local/R/cache/R/rawrr/rawrrassembly"
as you can see, also here I am getting this strange mixture of \\ and /
in a single path. But that is obviously not a problem, since readIndex
works.
The exe and the dlls should be at the assembly path location together with
the EULA text:
> list.files(rawrrAssemblyPath())
[1] "eula.txt" "rawrr.exe"
[3] "ThermoFisher.CommonCore.Data.dll" "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[5] "ThermoFisher.CommonCore.RawFileReader.dll"
>
Could you just execute the same commands and upload the returns?
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tobiasko
commented on September 27, 2024
1
Hi @Arthfael
since release 3.13 rawrr is a Bioconductor package, see
https://bioconductor.org/packages/release/bioc/html/rawrr.html
I would recommend to use the latest BioC release 3.14 to install rawrr with the help of the BiocManager:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rawrr")
I am honestly not sure what you get when installing from GitHub directly using devtools::. Version 0.2.1 is stone age. Please don't use it.
from rawrr.
tobiasko
commented on September 27, 2024
Hi @Arthfael
That is indeed a bit strange! Could you please upload your sessionInfo? Do you get the same error when reading from a single file (outside of the lapply function)? Are other reading functions of the package also affected (readIndex)?
Best,
Tobi
from rawrr.
Arthfael
commented on September 27, 2024
Dear Tobi,
Yes, same error if I run on a single file, regardless of whether I use
forward or backwards slashes:
Raws[1]
[1] "Q:\\MS\\Acquired data\\test_QC02_25ng_20210727161519.raw"
Both
XICs <- readChromatogram(Raws[1], masses, tols)
and
XICs <- readChromatogram(normalizePath(Raws[1], winslash = "/"), masses,
tols)
produce the error.
(*NB:*
I get the same result whether I install the package with >
devtools::install_github("cpanse/rawrr") or >
devtools::install_github("fgcz/rawrr")
However, if I do it with > install.packages('
http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.2.1.tar.gz', repo = NULL) I instead
get this error:
XICs <- readChromatogram(Raws[1], masses, tols)
Error in !silent : invalid argument type
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file
'C:\Users\MyUser\AppData\Local\Temp\2\Rtmp29h2p2\file31187bb1737': No such
file or directory
But this is an older version I think?)
Here it my sessionInfo output:
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats4 grid parallel compiler stats graphics grDevices
utils datasets methods base
other attached packages:
[1] rawrr_1.3.3 aRmel_2.0.1.15 DEP_1.14.0
MSnbase_2.18.0 ProtGenerics_1.24.0
[6] mzR_2.26.1 Rcpp_1.0.7 qvalue_2.24.0
sva_3.40.0 BiocParallel_1.26.1
[11] genefilter_1.74.0 mgcv_1.8-35 nlme_3.1-152
limma_3.48.1 UniProt.ws_2.32.0
[16] RCurl_1.98-1.3 RSQLite_2.2.7 GO.db_3.13.0
AnnotationDbi_1.54.1 IRanges_2.26.0
[21] S4Vectors_0.30.0 Biobase_2.52.0 BiocGenerics_0.38.0
biomaRt_2.48.2 fs_1.5.0
[26] tibble_3.1.3 magrittr_2.0.1 htmlwidgets_1.5.3
svDialogs_1.0.3 gridExtra_2.3
[31] VennDiagram_1.6.20 futile.logger_1.4.3 statmod_1.4.36
pdftools_3.0.1 xml2_1.3.2
[36] Peptides_2.4.4 plotly_4.9.4.1 openxlsx_4.2.4.9000
coin_1.4-1 survival_3.2-11
[41] snow_0.4-3 minpack.lm_1.2-1 modeest_2.4.0
rstudioapi_0.13 ggrepel_0.9.1
[46] rgl_0.107.10 reshape2_1.4.4 reshape_0.8.8
gtools_3.9.2 ggpubr_0.4.0
[51] ggplot2_3.3.5 gplots_3.1.1 stringr_1.4.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 tidyr_1.1.3 bit64_4.0.5
knitr_1.33
[5] multcomp_1.4-17 DelayedArray_0.18.0
data.table_1.14.0 rpart_4.1-15
[9] KEGGREST_1.32.0 doParallel_1.0.16
generics_0.1.0 preprocessCore_1.54.0
[13] callr_3.7.0 lambda.r_1.2.4
TH.data_1.0-10 usethis_2.0.1
[17] timeSeries_3062.100 bit_4.0.4 tzdb_0.1.2
httpuv_1.6.1
[21] SummarizedExperiment_1.22.0 assertthat_0.2.1 xfun_0.24
fBasics_3042.89.1
[25] hms_1.1.0 promises_1.2.0.1 fansi_0.5.0
progress_1.2.2
[29] caTools_1.18.2 dbplyr_2.1.1 readxl_1.3.1
DBI_1.1.1
[33] purrr_0.3.4 ellipsis_0.3.2
crosstalk_1.1.1 dplyr_1.0.7
[37] backports_1.2.1 annotate_1.70.0 libcoin_1.0-8
MatrixGenerics_1.4.0
[41] vctrs_0.3.8 remotes_2.4.0
imputeLCMD_2.0 Cairo_1.5-12.2
[45] abind_1.4-5 cachem_1.0.5 withr_2.4.2
prettyunits_1.1.1
[49] cluster_2.1.2 lazyeval_0.2.2 crayon_1.4.1
labeling_0.4.2
[53] edgeR_3.34.0 pkgconfig_2.0.3
GenomeInfoDb_1.28.1 pkgload_1.2.1
[57] devtools_2.4.2 rlang_0.4.11
spatial_7.3-14 lifecycle_1.0.0
[61] sandwich_3.0-1 filelock_1.0.2 affyio_1.62.0
BiocFileCache_2.0.0
[65] rprojroot_2.0.2 cellranger_1.1.0
matrixStats_0.59.0 Matrix_1.3-3
[69] carData_3.0-4 zoo_1.8-9
processx_3.5.2 GlobalOptions_0.1.2
[73] png_0.1-7 viridisLite_0.4.0 rjson_0.2.20
stabledist_0.7-1
[77] bitops_1.0-7 shinydashboard_0.7.1
KernSmooth_2.23-20 Biostrings_2.60.1
[81] blob_1.2.2 shape_1.4.6 qpdf_1.1
NbClust_3.0
[85] readr_2.0.0 rstatix_0.7.0
tmvtnorm_1.4-10 ggsignif_0.6.2
[89] scales_1.1.1 memoise_2.0.0 plyr_1.8.6
zlibbioc_1.38.0
[93] RColorBrewer_1.1-2 pcaMethods_1.84.0 clue_0.3-59
cli_3.0.1
[97] affy_1.70.0 XVector_0.32.0 ps_1.6.0
formatR_1.11
[101] MASS_7.3-54 tidyselect_1.1.1 vsn_3.60.0
stringi_1.7.4
[105] forcats_0.5.1 askpass_1.1
locfit_1.5-9.4 norm_1.0-9.5
[109] MALDIquant_1.19.3 tools_4.1.0 rio_0.5.27
circlize_0.4.13
[113] MsCoreUtils_1.4.0 foreach_1.5.1
foreign_0.8-81 statip_0.2.3
[117] farver_2.1.0 mzID_1.30.0 stable_1.1.4
digest_0.6.27
[121] BiocManager_1.30.16 shiny_1.6.0
GenomicRanges_1.44.0 car_3.0-11
[125] broom_0.7.8 later_1.2.0 ncdf4_1.17
httr_1.4.2
[129] ComplexHeatmap_2.8.0 colorspace_2.0-2 XML_3.99-0.6
splines_4.1.0
[133] rmutil_1.1.5 gmm_1.6-6
sessioninfo_1.1.1 xtable_1.8-4
[137] jsonlite_1.7.2 futile.options_1.0.1
timeDate_3043.102 testthat_3.0.4
[141] modeltools_0.2-23 R6_2.5.0 mime_0.11
pillar_1.6.1
[145] htmltools_0.5.1.1 svGUI_1.0.1 glue_1.4.2
fastmap_1.1.0
[149] DT_0.18 codetools_0.2-18
pkgbuild_1.2.0 mvtnorm_1.1-2
[153] utf8_1.2.1 lattice_0.20-44 curl_4.3.2
zip_2.2.0
[157] desc_1.3.0 munsell_0.5.0
GetoptLong_1.0.5 GenomeInfoDbData_1.2.6
[161] iterators_1.0.13 impute_1.66.0 haven_2.4.1
gtable_0.3.0
…On Mon, Feb 14, 2022 at 11:25 AM Tobias Kockmann ***@***.***> wrote:
Hi @Arthfael <https://github.com/Arthfael>
That is indeed a bit strange! Could you please upload your sessionInfo?
Do you get the same error when reading from a single file (outside of the
lapply function)? Are other reading functions of the package also
affected (readIndex)?
Best,
Tobi
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Arthfael
commented on September 27, 2024
(I also tried the two branches, e.g. >
***@***.***_3_13", force = TRUE), but get
the same error as with the master.)
On Wed, Feb 16, 2022 at 10:53 AM Armel Nicolas ***@***.***>
wrote:
… Dear Tobi,
Yes, same error if I run on a single file, regardless of whether I use
forward or backwards slashes:
> Raws[1]
[1] "Q:\\MS\\Acquired data\\test_QC02_25ng_20210727161519.raw"
Both
> XICs <- readChromatogram(Raws[1], masses, tols)
and
> XICs <- readChromatogram(normalizePath(Raws[1], winslash = "/"),
masses, tols)
produce the error.
(*NB:*
I get the same result whether I install the package with >
devtools::install_github("cpanse/rawrr") or >
devtools::install_github("fgcz/rawrr")
However, if I do it with > install.packages('
http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.2.1.tar.gz', repo = NULL) I instead
get this error:
> XICs <- readChromatogram(Raws[1], masses, tols)
Error in !silent : invalid argument type
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file
'C:\Users\MyUser\AppData\Local\Temp\2\Rtmp29h2p2\file31187bb1737': No such
file or directory
But this is an older version I think?)
Here it my sessionInfo output:
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats4 grid parallel compiler stats graphics grDevices
utils datasets methods base
other attached packages:
[1] rawrr_1.3.3 aRmel_2.0.1.15 DEP_1.14.0
MSnbase_2.18.0 ProtGenerics_1.24.0
[6] mzR_2.26.1 Rcpp_1.0.7 qvalue_2.24.0
sva_3.40.0 BiocParallel_1.26.1
[11] genefilter_1.74.0 mgcv_1.8-35 nlme_3.1-152
limma_3.48.1 UniProt.ws_2.32.0
[16] RCurl_1.98-1.3 RSQLite_2.2.7 GO.db_3.13.0
AnnotationDbi_1.54.1 IRanges_2.26.0
[21] S4Vectors_0.30.0 Biobase_2.52.0 BiocGenerics_0.38.0
biomaRt_2.48.2 fs_1.5.0
[26] tibble_3.1.3 magrittr_2.0.1 htmlwidgets_1.5.3
svDialogs_1.0.3 gridExtra_2.3
[31] VennDiagram_1.6.20 futile.logger_1.4.3 statmod_1.4.36
pdftools_3.0.1 xml2_1.3.2
[36] Peptides_2.4.4 plotly_4.9.4.1 openxlsx_4.2.4.9000
coin_1.4-1 survival_3.2-11
[41] snow_0.4-3 minpack.lm_1.2-1 modeest_2.4.0
rstudioapi_0.13 ggrepel_0.9.1
[46] rgl_0.107.10 reshape2_1.4.4 reshape_0.8.8
gtools_3.9.2 ggpubr_0.4.0
[51] ggplot2_3.3.5 gplots_3.1.1 stringr_1.4.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 tidyr_1.1.3 bit64_4.0.5
knitr_1.33
[5] multcomp_1.4-17 DelayedArray_0.18.0
data.table_1.14.0 rpart_4.1-15
[9] KEGGREST_1.32.0 doParallel_1.0.16
generics_0.1.0 preprocessCore_1.54.0
[13] callr_3.7.0 lambda.r_1.2.4
TH.data_1.0-10 usethis_2.0.1
[17] timeSeries_3062.100 bit_4.0.4 tzdb_0.1.2
httpuv_1.6.1
[21] SummarizedExperiment_1.22.0 assertthat_0.2.1 xfun_0.24
fBasics_3042.89.1
[25] hms_1.1.0 promises_1.2.0.1 fansi_0.5.0
progress_1.2.2
[29] caTools_1.18.2 dbplyr_2.1.1 readxl_1.3.1
DBI_1.1.1
[33] purrr_0.3.4 ellipsis_0.3.2
crosstalk_1.1.1 dplyr_1.0.7
[37] backports_1.2.1 annotate_1.70.0
libcoin_1.0-8 MatrixGenerics_1.4.0
[41] vctrs_0.3.8 remotes_2.4.0
imputeLCMD_2.0 Cairo_1.5-12.2
[45] abind_1.4-5 cachem_1.0.5 withr_2.4.2
prettyunits_1.1.1
[49] cluster_2.1.2 lazyeval_0.2.2 crayon_1.4.1
labeling_0.4.2
[53] edgeR_3.34.0 pkgconfig_2.0.3
GenomeInfoDb_1.28.1 pkgload_1.2.1
[57] devtools_2.4.2 rlang_0.4.11
spatial_7.3-14 lifecycle_1.0.0
[61] sandwich_3.0-1 filelock_1.0.2
affyio_1.62.0 BiocFileCache_2.0.0
[65] rprojroot_2.0.2 cellranger_1.1.0
matrixStats_0.59.0 Matrix_1.3-3
[69] carData_3.0-4 zoo_1.8-9
processx_3.5.2 GlobalOptions_0.1.2
[73] png_0.1-7 viridisLite_0.4.0 rjson_0.2.20
stabledist_0.7-1
[77] bitops_1.0-7 shinydashboard_0.7.1
KernSmooth_2.23-20 Biostrings_2.60.1
[81] blob_1.2.2 shape_1.4.6 qpdf_1.1
NbClust_3.0
[85] readr_2.0.0 rstatix_0.7.0
tmvtnorm_1.4-10 ggsignif_0.6.2
[89] scales_1.1.1 memoise_2.0.0 plyr_1.8.6
zlibbioc_1.38.0
[93] RColorBrewer_1.1-2 pcaMethods_1.84.0 clue_0.3-59
cli_3.0.1
[97] affy_1.70.0 XVector_0.32.0 ps_1.6.0
formatR_1.11
[101] MASS_7.3-54 tidyselect_1.1.1 vsn_3.60.0
stringi_1.7.4
[105] forcats_0.5.1 askpass_1.1
locfit_1.5-9.4 norm_1.0-9.5
[109] MALDIquant_1.19.3 tools_4.1.0 rio_0.5.27
circlize_0.4.13
[113] MsCoreUtils_1.4.0 foreach_1.5.1
foreign_0.8-81 statip_0.2.3
[117] farver_2.1.0 mzID_1.30.0 stable_1.1.4
digest_0.6.27
[121] BiocManager_1.30.16 shiny_1.6.0
GenomicRanges_1.44.0 car_3.0-11
[125] broom_0.7.8 later_1.2.0 ncdf4_1.17
httr_1.4.2
[129] ComplexHeatmap_2.8.0 colorspace_2.0-2 XML_3.99-0.6
splines_4.1.0
[133] rmutil_1.1.5 gmm_1.6-6
sessioninfo_1.1.1 xtable_1.8-4
[137] jsonlite_1.7.2 futile.options_1.0.1
timeDate_3043.102 testthat_3.0.4
[141] modeltools_0.2-23 R6_2.5.0 mime_0.11
pillar_1.6.1
[145] htmltools_0.5.1.1 svGUI_1.0.1 glue_1.4.2
fastmap_1.1.0
[149] DT_0.18 codetools_0.2-18
pkgbuild_1.2.0 mvtnorm_1.1-2
[153] utf8_1.2.1 lattice_0.20-44 curl_4.3.2
zip_2.2.0
[157] desc_1.3.0 munsell_0.5.0
GetoptLong_1.0.5 GenomeInfoDbData_1.2.6
[161] iterators_1.0.13 impute_1.66.0 haven_2.4.1
gtable_0.3.0
On Mon, Feb 14, 2022 at 11:25 AM Tobias Kockmann ***@***.***>
wrote:
> Hi @Arthfael <https://github.com/Arthfael>
>
> That is indeed a bit strange! Could you please upload your sessionInfo?
> Do you get the same error when reading from a single file (outside of the
> lapply function)? Are other reading functions of the package also
> affected (readIndex)?
>
> Best,
> Tobi
>
> —
> Reply to this email directly, view it on GitHub
> <#47 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABSHV4NPRV2AIPTSL3UO2J3U3DG2BANCNFSM5NJC5MRA>
> .
> Triage notifications on the go with GitHub Mobile for iOS
> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
> or Android
> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
>
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
from rawrr.
Arthfael
commented on September 27, 2024
Dear Tobi,
Thank you, I now remember discovering and also trying the Bioconductor
version when I originally encountered the problem. Unfortunately I also get
the same error with it.
Kind regards,
Armel
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…On Wed, Feb 16, 2022 at 11:46 AM Tobias Kockmann ***@***.***> wrote:
Hi @Arthfael <https://github.com/Arthfael>
since release 3.13 rawrr is a Bioconductor package, see
https://bioconductor.org/packages/release/bioc/html/rawrr.html
I would recommend to use the latest BioC release 3.14 to install rawrr
with the help of the BiocManager:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rawrr")
I am honestly not sure what you get when installing from GitHub directly
using devtools::. Version 0.2.1 is stone age. Please don't use it.
—
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Arthfael
commented on September 27, 2024
Updated sessionInfo:
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] coin_1.4-2 codetools_0.2-18 lattice_0.20-44
matrixStats_0.61.0 mvtnorm_1.1-3 zoo_1.8-9
[7] MASS_7.3-54 NbClust_3.0 grid_4.1.0 stats4_4.1.0
magrittr_2.0.2 multcomp_1.4-18
[13] fs_1.5.2 rstudioapi_0.13 Matrix_1.3-3
sandwich_3.0-1 TH.data_1.1-0 splines_4.1.0
[19] tools_4.1.0 survival_3.2-11 parallel_4.1.0
compiler_4.1.0 cluster_2.1.2 libcoin_1.0-9
[25] modeltools_0.2-23
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On Wed, Feb 16, 2022 at 1:01 PM Armel Nicolas ***@***.***>
wrote:
…
Dear Tobi,
Thank you, I now remember discovering and also trying the Bioconductor
version when I originally encountered the problem. Unfortunately I also get
the same error with it.
Kind regards,
Armel
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<#m_7244262636551291840_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Wed, Feb 16, 2022 at 11:46 AM Tobias Kockmann ***@***.***>
wrote:
> Hi @Arthfael <https://github.com/Arthfael>
>
> since release 3.13 rawrr is a Bioconductor package, see
>
> https://bioconductor.org/packages/release/bioc/html/rawrr.html
>
> I would recommend to use the latest BioC release 3.14 to install rawrr
> with the help of the BiocManager:
>
> if (!require("BiocManager", quietly = TRUE))
> install.packages("BiocManager")
>
> BiocManager::install("rawrr")
>
> I am honestly not sure what you get when installing from GitHub directly
> using devtools::. Version 0.2.1 is stone age. Please don't use it.
>
> —
> Reply to this email directly, view it on GitHub
> <#47 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABSHV4NO5KEASYG5DHBPVRTU3N6B7ANCNFSM5NJC5MRA>
> .
> Triage notifications on the go with GitHub Mobile for iOS
> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
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from rawrr.
tobiasko
commented on September 27, 2024
Did you follow this
https://bioconductor.org/packages/release/bioc/install/rawrr/INSTALL
or specifically did you install the RawFileReader DLLs and rawrr exe on your system:
> installRawFileReaderDLLs()
Do you accept the Thermo License agreement 'X:/Rlibs/rawrr/rawrrassembly/RawFileReaderLicense.txt'? [Y/n]: Y
trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.Data.dll'
Content type 'application/octet-stream' length 360448 bytes (352 KB)
downloaded 352 KB
trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.MassPrecisionEstimator.dll'
Content type 'application/octet-stream' length 11264 bytes (11 KB)
downloaded 11 KB
trying URL 'https://github.com/thermofisherlsms/ThermoRawFileParser/raw/master/packages/ThermoFisher.CommonCore.RawFileReader.4.0.26/lib//ThermoFisher.CommonCore.RawFileReader.dll'
Content type 'application/octet-stream' length 620544 bytes (606 KB)
downloaded 606 KB
ThermoFisher.CommonCore.Data.dll ThermoFisher.CommonCore.MassPrecisionEstimator.dll
0 0
ThermoFisher.CommonCore.RawFileReader.dll
0
> installRawrrExe()
trying URL 'http://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr.1.1.12.exe'
Content type 'application/x-msdos-program' length 26624 bytes (26 KB)
downloaded 26 KB
MD5 6d5f6d19512eaba73e92d2bfb474e6f2 C:\Users\tobiasko.FGCZ-NET\AppData\Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe
[1] 0
>
from rawrr.
tobiasko
commented on September 27, 2024
The problem is:
Bioc was not willing to host the binary rawrr.x.exe as part of the package. So it is downloaded on demand after the package installation through BiocManager. Same-same for the RawFileReader dlls. They are fetched from a Thermo GitHub Repo. I know this is kind of annoying, but it was the only option.
from rawrr.
Arthfael
commented on September 27, 2024
Dear Tobi,
Thanks, but unfortunately this still doesn't fix it: even after a fresh
install from Bioconductor, running both installRawrrExe() and
installRawFileReaderDLLs(), and restarting my R session, I still get the
same error.
NB: I had run both lines originally before reporting my issue here, and can
confirm that all 3 dlls and the rawrr.exe were already and are still
present at the location (hence why I assumed the issue was with the slash
orientation in the path causing it to somehow not be read properly.)
Best regards,
Armel
…On Wed, Feb 16, 2022 at 3:39 PM Tobias Kockmann ***@***.***> wrote:
The problem is:
Bioc was not willing to host the binary rawrr.x.exe as part of the
package. So it is downloaded on demand after the package installation
through BiocManager. Same-same for the RawFileReader dlls. They are
fetched from a Thermo GitHub Repo. I know this is kind of annoying, but it
was the only option.
—
Reply to this email directly, view it on GitHub
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Arthfael
commented on September 27, 2024
If that helps:
The debug files referred by the error message do not exist. But at the
debug location, there is a txt file with a similar name (and an empty
rs-graphics-someweirdcode folder) containing what looks like two error
codes: 524 and 670. (I tried searching what they mean but not sure they are
the same respectively CloudFlare- and Silverlight-related codes I found
through google?)
Best,
Armel
On Wed, Feb 16, 2022 at 9:08 PM Armel Nicolas ***@***.***>
wrote:
…
Dear Tobi,
Thanks, but unfortunately this still doesn't fix it: even after a fresh
install from Bioconductor, running both installRawrrExe() and
installRawFileReaderDLLs(), and restarting my R session, I still get the
same error.
NB: I had run both lines originally before reporting my issue here, and
can confirm that all 3 dlls and the rawrr.exe were already and are still
present at the location (hence why I assumed the issue was with the slash
orientation in the path causing it to somehow not be read properly.)
Best regards,
Armel
On Wed, Feb 16, 2022 at 3:39 PM Tobias Kockmann ***@***.***>
wrote:
> The problem is:
>
> Bioc was not willing to host the binary rawrr.x.exe as part of the
> package. So it is downloaded on demand after the package installation
> through BiocManager. Same-same for the RawFileReader dlls. They are
> fetched from a Thermo GitHub Repo. I know this is kind of annoying, but it
> was the only option.
>
> —
> Reply to this email directly, view it on GitHub
> <#47 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABSHV4IUSX4OPVPOMS4VJ7DU3OZIXANCNFSM5NJC5MRA>
> .
> Triage notifications on the go with GitHub Mobile for iOS
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tobiasko
commented on September 27, 2024
That is all pretty wired. I meanwhile installed rawrr 1.2.0 using BiocManager on a very similar system (Windows Server 2021):
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rawrr_1.2.0 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] magrittr_2.0.2 tidyselect_1.1.1 R6_2.5.1 rlang_1.0.1 fastmap_1.1.0 fansi_1.0.2
[7] dplyr_1.0.8 tools_4.1.0 DT_0.20 utf8_1.2.2 cli_3.2.0 DBI_1.1.2
[13] htmltools_0.5.2 ellipsis_0.3.2 yaml_2.2.2 assertthat_0.2.1 digest_0.6.29 tibble_3.1.6
[19] lifecycle_1.0.1 crayon_1.5.0 purrr_0.3.4 htmlwidgets_1.5.4 vctrs_0.3.8 glue_1.6.1
[25] compiler_4.1.0 pillar_1.7.0 generics_0.1.2 pkgconfig_2.0.3
What do you get when reading from the sample data that comes with the package?
> rawfile <- sampleFilePath()
> Idx <- readIndex(rawfile)
> str(Idx)
'data.frame': 573 obs. of 8 variables:
$ scan : int 1 2 3 4 5 6 7 8 9 10 ...
$ scanType : chr "FTMS + c NSI Full ms [350.0000-1800.0000]" "FTMS + c NSI Full ms2 [email protected] [140.0000-1015.0000]" "FTMS + c NSI Full ms2 [email protected] [140.0000-1335.0000]" "FTMS + c NSI Full ms2 [email protected] [140.0000-1415.0000]" ...
$ rtinseconds : num 0.097 0.35 0.419 0.489 0.558 0.627 0.696 0.766 0.835 0.904 ...
$ precursorMass : num 1075 487 645 684 547 ...
$ MSOrder : chr "Ms" "Ms2" "Ms2" "Ms2" ...
$ charge : int 0 2 2 2 2 2 2 2 2 2 ...
$ masterScan : int NA NA NA NA NA NA NA NA NA NA ...
$ dependencyType: logi NA NA NA NA NA NA ...
My path to the sample data is:
> rawfile
[1] "X:/Rlibs/rawrr/extdata/sample.raw"
The rawrr assembly path (the path were the dll are placed) is
> rawrrAssemblyPath()
[1] "C:\\Users\\tobiasko.FGCZ-NET\\AppData\\Local/R/cache/R/rawrr/rawrrassembly"
as you can see, also here I am getting this strange mixture of \\ and / in a single path. But that is obviously not a problem, since readIndex works.
The exe and the dlls should be at the assembly path location together with the EULA text:
> list.files(rawrrAssemblyPath())
[1] "eula.txt" "rawrr.exe"
[3] "ThermoFisher.CommonCore.Data.dll" "ThermoFisher.CommonCore.MassPrecisionEstimator.dll"
[5] "ThermoFisher.CommonCore.RawFileReader.dll"
>
Could you just execute the same commands and upload the returns?
from rawrr.
tobiasko
commented on September 27, 2024
Puh! Yip, we need to check more carefully if the parameters are valid (length = 1) and raise an error right away. That could be avoided very easily by a stopifnot() statement at the start of readChromatogram.
from rawrr.
tobiasko
commented on September 27, 2024
We need to check this here:
readChromatogram <- function(rawfile,
mass = NULL,
tol = 10,
filter = "ms",
type = 'xic'){
.isAssemblyWorking()
.checkRawFile(rawfile)
stopifnot(type %in% c('xic', 'bpc', 'tic'))
from rawrr.
Related Issues (20)
- Get information on gradient HOT 1
- Enhancement - Complete readIndex() function HOT 9
- Peak charges for MS1 spectras HOT 4
- Spectrum scan centroid mZ, intensity and noises values do not match HOT 2
- Error in Example: Length of "x" and "y" are not matching HOT 3
- Read noise value for profile mode mass spectra HOT 4
- Read_Spectrum - Sum Spectra
- unit should be minute / auc computation in seconds HOT 24
- validate_rawrrSpectrum 'StartTime' HOT 4
- "Error: line 1 did not have 9 elements" for readIndex() and readChromatogram() + "Error : No scan vector is provided"for readSpectrum HOT 9
- Problem executing readChromatogram inside Singularity container HOT 5
- Add a check if `input` file exists and is not empty
- Error in if (rvs != "No RAW file specified!") { : the condition has length > 1 HOT 16
- Switch to RawFileReader 5.0.93 HOT 2
- different total number of Spectra in msconvert, compomics/ThermoRawFileParser and thermofisherlsms/RawFileReader HOT 2
- Request for auc.rawrrChromatogram HOT 3
- profile mode in readSpectrum HOT 11
- speed up readIndex/readSpectrum by base::textConnection HOT 14
- rawrr::buildRawrrExe() fails HOT 6
- auc.rawrrChromatogram question
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