Error if too many scans are selected about rawrr

[rokaempf]

Thanks @cpanse and @tobiasko

The new version works fine and divide-and-conquer also helped!
Thanks for all your work on this package!

[tobiasko]

Hi @rokaempf

could you please post the content of path and scans and your session info?

[rokaempf]

Hi @tobiasko

Thanks for you quick answer! Hope that helps. Let me know if you need anything else!

> path
[1] "data/Orbitrap/130_00021_NP10_long.raw"

> scans
   [1]    1    2    3    4    5    6    7    8    9
  [10]   10   11   12   13   14   15   16   17   18
  [19]   19   20   21   22   23   24   25   26   27
  [28]   28   29   30   31   32   33   34   35   36
  [37]   37   38   39   40   41   42   43   44   45
  [46]   46   47   48   49   50   51   52   53   54
  [55]   55   56   57   58   59   60   61   62   63
  [64]   64   65   66   67   68   69   70   71   72
  [73]   73   74   75   76   77   78   79   80   81
  [82]   82   83   84   85   86   87   88   89   90
  [91]   91   92   93   94   95   96   97   98   99
 [100]  100  101  102  103  104  105  106  107  108
 [109]  109  110  111  112  113  114  115  116  117
 [118]  118  119  120  121  122  123  124  125  126
 [127]  127  128  129  130  131  132  133  134  135
 [136]  136  137  138  139  140  141  142  143  144
 [145]  145  146  147  148  149  150  151  152  153
 [154]  154  155  156  157  158  159  160  161  162
 [163]  163  164  165  166  167  168  169  170  171
 [172]  172  173  174  175  176  177  178  179  180
 [181]  181  182  183  184  185  186  187  188  189
 [190]  190  191  192  193  194  195  196  197  198
 [199]  199  200  201  202  203  204  205  206  207
 [208]  208  209  210  211  212  213  214  215  216
 [217]  217  218  219  220  221  222  223  224  225
 [226]  226  227  228  229  230  231  232  233  234
 [235]  235  236  237  238  239  240  241  242  243
 [244]  244  245  246  247  248  249  250  251  252
 [253]  253  254  255  256  257  258  259  260  261
 [262]  262  263  264  265  266  267  268  269  270
 [271]  271  272  273  274  275  276  277  278  279
 [280]  280  281  282  283  284  285  286  287  288
 [289]  294  300  306  312  318  324  330  336  342
 [298]  348  354  360  366  372  378  384  390  396
 [307]  402  408  414  420  426  432  438  444  450
 [316]  456  462  468  474  480  486  492  498  504
 [325]  510  516  522  528  534  540  546  552  558
 [334]  564  570  576  582  588  594  600  606  612
 [343]  618  624  630  636  642  648  654  660  666
 [352]  672  678  684  690  696  702  708  714  720
 [361]  726  732  738  744  750  756  762  768  774
 [370]  780  786  792  798  804  810  816  822  828
 [379]  834  840  846  852  858  864  870  876  882
 [388]  888  894  900  906  912  918  924  930  936
 [397]  942  948  954  960  966  972  978  984  990
 [406]  996 1002 1008 1014 1020 1026 1032 1038 1044
 [415] 1050 1056 1062 1068 1074 1080 1086 1092 1098
 [424] 1104 1110 1116 1122 1128 1134 1140 1146 1152
 [433] 1158 1164 1170 1176 1182 1188 1194 1200 1206
 [442] 1212 1218 1224 1230 1236 1242 1248 1254 1260
 [451] 1266 1272 1278 1284 1290 1296 1302 1308 1314
 [460] 1320 1326 1332 1338 1344 1350 1356 1362 1368
 [469] 1374 1380 1386 1392 1398 1404 1410 1416 1422
 [478] 1428 1434 1440 1446 1452 1458 1464 1470 1476
 [487] 1482 1488 1494 1500 1506 1512 1518 1524 1530
 [496] 1536 1542 1548 1554 1560 1566 1572 1578 1584
 [505] 1590 1596 1602 1608 1614 1620 1626 1632 1638
 [514] 1644 1650 1656 1662 1668 1674 1680 1686 1692
 [523] 1698 1704 1710 1716 1722 1728 1734 1740 1746
 [532] 1752 1758 1764 1770 1776 1782 1788 1794 1800
 [541] 1806 1812 1818 1824 1830 1836 1842 1848 1854
 [550] 1860 1866 1872 1878 1884 1890 1896 1902 1908
 [559] 1914 1920 1926 1932 1938 1944 1950 1956 1962
 [568] 1968 1974 1980 1986 1992 1998 2004 2010 2016
 [577] 2022 2028 2034 2040 2045 2051 2057 2063 2069
 [586] 2075 2081 2087 2093 2099 2105 2111 2117 2123
 [595] 2129 2135 2141 2147 2153 2159 2165 2171 2177
 [604] 2183 2189 2195 2201 2207 2213 2219 2225 2231
 [613] 2237 2243 2249 2255 2261 2267 2273 2279 2285
 [622] 2291 2297 2303 2309 2315 2321 2327 2333 2339
 [631] 2345 2351 2357 2363 2369 2375 2381 2387 2393
 [640] 2399 2405 2411 2417 2423 2429 2435 2441 2447
 [649] 2453 2459 2465 2471 2477 2483 2489 2495 2501
 [658] 2507 2513 2519 2525 2531 2537 2543 2549 2555
 [667] 2561 2567 2573 2579 2585 2591 2597 2603 2609
 [676] 2615 2621 2627 2633 2639 2645 2651 2657 2663
 [685] 2669 2675 2681 2687 2693 2699 2705 2711 2717
 [694] 2723 2729 2735 2741 2747 2753 2759 2765 2771
 [703] 2777 2783 2789 2795 2801 2807 2813 2819 2825
 [712] 2831 2837 2843 2849 2855 2861 2867 2873 2879
 [721] 2885 2891 2897 2903 2909 2915 2921 2927 2933
 [730] 2939 2945 2951 2957 2963 2969 2975 2981 2987
 [739] 2993 2999 3005 3011 3017 3023 3029 3035 3041
 [748] 3047 3053 3059 3065 3071 3077 3083 3089 3095
 [757] 3101 3107 3113 3119 3125 3131 3137 3143 3149
 [766] 3155 3161 3167 3173 3179 3185 3191 3197 3203
 [775] 3209 3215 3221 3227 3233 3239 3245 3251 3257
 [784] 3263 3269 3275 3281 3287 3293 3299 3305 3311
 [793] 3317 3323 3329 3335 3341 3347 3353 3359 3365
 [802] 3371 3377 3383 3389 3395 3401 3407 3413 3419
 [811] 3425 3431 3437 3443 3449 3455 3461 3467 3473
 [820] 3479 3485 3491 3497 3503 3509 3515 3521 3527
 [829] 3533 3539 3545 3551 3557 3563 3569 3575 3581
 [838] 3587 3593 3599 3605 3611 3617 3623 3629 3635
 [847] 3641 3647 3653 3659 3665 3671 3677 3683 3689
 [856] 3695 3701 3707 3713 3719 3725 3731 3737 3743
 [865] 3749 3755 3761 3767 3773 3779 3785 3791 3797
 [874] 3803 3809 3815 3821 3827 3833 3839 3845 3851
 [883] 3857 3863 3869 3875 3881 3887 3893 3899 3905
 [892] 3911 3917 3923 3929 3935 3941 3947 3953 3959
 [901] 3965 3971 3977 3983 3989 3995 4001 4007 4013
 [910] 4019 4025 4031 4037 4043 4049 4055 4061 4067
 [919] 4073 4079 4085 4091 4097 4103 4109 4115 4121
 [928] 4127 4133 4139 4145 4151 4157 4163 4169 4175
 [937] 4181 4187 4193 4199 4205 4211 4217 4223 4229
 [946] 4235 4241 4247 4253 4259 4265 4271 4277 4283
 [955] 4289 4295 4301 4307 4313 4319 4325 4331 4337
 [964] 4343 4349 4355 4361 4367 4373 4379 4385 4391
 [973] 4397 4403 4409 4415 4421 4427 4433 4439 4445
 [982] 4451 4457 4463 4469 4475 4481 4487 4493 4499
 [991] 4505 4511 4517 4523 4529 4535 4541 4547 4553
[1000] 4559
 [ reached getOption("max.print") -- omitted 1107 entries ]

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

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

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

other attached packages:
 [1] Matrix_1.3-4      plotly_4.9.4.1   
 [3] DescTools_0.99.42 baseline_1.3-1   
 [5] forcats_0.5.1     stringr_1.4.0    
 [7] dplyr_1.0.7       purrr_0.3.4      
 [9] readr_2.0.0       tidyr_1.1.3      
[11] tibble_3.1.2      ggplot2_3.3.5    
[13] tidyverse_1.3.1   rawrr_0.2.5      

loaded via a namespace (and not attached):
 [1] httr_1.4.2        viridisLite_0.4.0
 [3] bit64_4.0.5       vroom_1.5.3      
 [5] jsonlite_1.7.2    modelr_0.1.8     
 [7] assertthat_0.2.1  expm_0.999-6     
 [9] gld_2.6.2         lmom_2.8         
[11] cellranger_1.1.0  yaml_2.2.1       
[13] pillar_1.6.1      backports_1.2.1  
[15] lattice_0.20-44   glue_1.4.2       
[17] quadprog_1.5-8    digest_0.6.27    
[19] rvest_1.0.0       colorspace_2.0-2 
[21] htmltools_0.5.1.1 lpSolve_5.6.15   
[23] pkgconfig_2.0.3   broom_0.7.8      
[25] SparseM_1.81      haven_2.4.1      
[27] mvtnorm_1.1-2     scales_1.1.1     
[29] rootSolve_1.8.2.2 tzdb_0.1.2       
[31] proxy_0.4-26      farver_2.1.0     
[33] generics_0.1.0    ellipsis_0.3.2   
[35] withr_2.4.2       lazyeval_0.2.2   
[37] cli_3.0.1         magrittr_2.0.1   
[39] crayon_1.4.1      readxl_1.3.1     
[41] fs_1.5.0          fansi_0.5.0      
[43] MASS_7.3-54       xml2_1.3.2       
[45] class_7.3-19      tools_4.1.0      
[47] data.table_1.14.0 hms_1.1.0        
[49] lifecycle_1.0.0   Exact_2.1        
[51] munsell_0.5.0     reprex_2.0.0     
[53] limSolve_1.5.6    compiler_4.1.0   
[55] e1071_1.7-7       rlang_0.4.11     
[57] grid_4.1.0        rstudioapi_0.13  
[59] htmlwidgets_1.5.3 crosstalk_1.1.1  
[61] labeling_0.4.2    boot_1.3-28      
[63] gtable_0.3.0      DBI_1.1.1        
[65] R6_2.5.0          lubridate_1.7.10 
[67] bit_4.0.4         utf8_1.2.1       
[69] stringi_1.7.3     parallel_4.1.0   
[71] Rcpp_1.0.7        vctrs_0.3.8      
[73] dbplyr_2.1.1      tidyselect_1.1.1

[tobiasko]

hmmm. ok. Most likely it is connected to some sort of resource shortage. But just to make sure: Could you please move to the latest rawrr version? We have started using Bioconductor:

https://bioconductor.org/packages/release/bioc/html/rawrr.html

and pushed the version number to 1.0.X. We also recommend using the BiocManager for package installation:

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

BiocManager::install("rawrr")

[cpanse]

Hi @rokaempf

if you apply the divide-and-conquer paradigm it should work.

#R >= 4.1
(rawfile <- rawrr::sampleFilePath())
S <- (rawrr::readIndex(rawfile) |>
  subset (MSOrder == 'Ms'))$scan |>
  lapply(FUN=function(i){rawrr::readSpectrum(rawfile=rawfile,i)[[1]]})

or using BiocParallel::bplapply

#R >= 4.1
(rawfile <- rawrr::sampleFilePath())
S <- (rawrr::readIndex(rawfile) |>
  subset (MSOrder == 'Ms'))$scan |>
  BiocParallel::bplapply(FUN=function(i){rawrr::readSpectrum(rawfile=rawfile,i)[[1]]})

C

[rokaempf]

Hey @tobiasko and @cpanse
Perfect! Thanks for the update!
I'll try both and let you know!

Great support and thanks again for all you work!

[rokaempf]

Maybe not the right place to report this issue, but the Bioconductor installation does not work for me:

> rawrr::installRawrrExe()
Error: .onLoad failed in loadNamespace() for 'rawrr', details:
  call: buildRawrrExe()
  error: Could not find 'msbuild' or 'xbuild' in the path. Therefore, it is not possible to build the 'rawrr.exe' assembly from source code.
Try to run rawrr::installRawrrExe().

[cpanse]

Dear @rokaempf,

thanks for reporting.

can you please terminate R and restart with the install procedure.

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

BiocManager::install("rawrr")
rawrr::installRawFileReaderDLLs()
rawrr::installRawrrExe()

If it is not working. what OS are you running?

TNX
C

[rokaempf]

Dear @cpanse

I tried it, but still no success!
I'm running it on Windows 10 Education Version 2004 (see SessionInfo below)

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("rawrr", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for
details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'rawrr'
trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/rawrr_1.0.2.zip'
Content type 'application/zip' length 1398523 bytes (1.3 MB)
downloaded 1.3 MB

package ‘rawrr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\...\Local\Temp\RtmpMlMb3z\downloaded_packages
> rawrr::installRawFileReaderDLLs()
Error: .onLoad failed in loadNamespace() for 'rawrr', details:
  call: buildRawrrExe()
  error: Could not find 'msbuild' or 'xbuild' in the path. Therefore, it is not possible to build the 'rawrr.exe' assembly from source code.
Try to run rawrr::installRawrrExe().
> rawrr::installRawrrExe()
Error: .onLoad failed in loadNamespace() for 'rawrr', details:
  call: buildRawrrExe()
  error: Could not find 'msbuild' or 'xbuild' in the path. Therefore, it is not possible to build the 'rawrr.exe' assembly from source code.
Try to run rawrr::installRawrrExe().
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Thanks!

[cpanse]

Good morning @rokaempf

you found a bug. Can you please try that version?

#R 4.1
install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr_1.1.13.tar.gz', repo=NULL)

If it works (please let us know) I will push it to Bioconductor.

Thank you again for reporting,

Christian