'match' requires vector arguments

[mtinti]

Hi, I just updated PTXQC to version 1.0.10 (R 3.6) and i'm getting an error in the middle of the analysis, here the last few lines of stout:

label: nameMapping (with options) List of 2 $ echo : logi FALSE $ results: chr "asis"

|................................................... | 78% ordinary text without R code

|.......................................................... | 89% label: metrics (with options) List of 2 $ echo : logi FALSE $ results: chr "asis"

Quitting from lines 186-222 (PTXQC_report_template.Rmd) Error in match(as.character(x), limits) : 'match' requires vector arguments

Any help please? Thanks Michele

[cbielow]

Hi,

thanks for reporting this!

I usually run every release candidate against a fairly large suite of txt-folders to make sure the code is fine. However, it seems the tests are not sufficient :/

Could you upload the data somewhere and send me a download link. I will have a look at it ASAP. Thanks!

[mtinti]

Here we are: https://dmail-my.sharepoint.com/:t:/g/personal/mtinti_dundee_ac_uk/EWHQqORUUm1AqrrTByBnNMgBMCERy_RC21aXzpGZvperpA?e=yGAyur This worked in version v1.0.9 but failed in v1.0.10. If it helps, v1.0.10 produced the report_v1.0.10_combined_heatmap.txt

thanks again!

[cbielow]

the link seems to contain only the Phospho (STY)Sites.txt (which PTXQC will ignore). Can you upload the full txt-folder? thanks!

[mtinti]

Sorry, this shuld do... https://dmail-my.sharepoint.com/:f:/g/personal/mtinti_dundee_ac_uk/EliODOhqqzFOgdj3efhFcgQBVmqoE6i096LlpHq0XQCoEg?e=JqXUQe

[cbielow]

Hi,

strangely, I cannot reproduce this here. The report is generated just fine. (see attachment) report_v1.0.10_txt_mtinti.zip

I will try another system and get back to you again, maybe its a platform specific thing.

What operating system are you using?

[mtinti]

Hi, thanks for feedback. This is my session info. I will try in other windows OS as well , however I hope it's caused by some outdated R packages (data.table). Thanks again!

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

Matrix products: default

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

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

other attached packages: [1] PTXQC_1.0.9 data.table_1.12.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 highr_0.8 pillar_1.3.1 compiler_3.6.0

[5] RColorBrewer_1.1-2 plyr_1.8.4 tools_3.6.0 digest_0.6.18

[9] jsonlite_1.6 evaluate_0.13 tibble_2.1.1 gtable_0.3.0

[13] viridisLite_0.3.0 pkgconfig_2.0.2 rlang_0.3.4 rstudioapi_0.10

[17] yaml_2.2.0 xfun_0.6 ggdendro_0.1-20 kableExtra_1.1.0

[21] gridExtra_2.3 UpSetR_1.4.0 httr_1.4.0 stringr_1.4.0

[25] knitr_1.22 xml2_1.2.0 hms_0.4.2 ade4_1.7-13

[29] webshot_0.5.1 grid_3.6.0 glue_1.3.1 R6_2.4.0

[33] rmarkdown_1.12 seqinr_3.4-5 reshape2_1.4.3 ggplot2_3.1.1

[37] readr_1.3.1 magrittr_1.5 scales_1.0.0 htmltools_0.3.6

[41] MASS_7.3-51.4 rvest_0.3.3 colorspace_1.4-1 labeling_0.3

[45] stringi_1.4.3 lazyeval_0.2.2 munsell_0.5.0 crayon_1.3.4

[mtinti]

Hi There, a fresh install using R 4.1 did the trick. Sorry I did't think about it before. Thanks for your time, I'm closing myself the thicket.

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

Matrix products: default

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

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

other attached packages: [1] yaml_2.2.1 PTXQC_1.0.10

loaded via a namespace (and not attached): [1] Rcpp_1.0.6 highr_0.9 pillar_1.6.1 compiler_4.1.0 [5] RColorBrewer_1.1-2 plyr_1.8.6 prettyunits_1.1.1 progress_1.2.2 [9] tools_4.1.0 digest_0.6.27 jsonlite_1.7.2 viridisLite_0.4.0 [13] evaluate_0.14 lifecycle_1.0.0 tibble_3.1.2 gtable_0.3.0 [17] pkgconfig_2.0.3 rlang_0.4.11 rstudioapi_0.13 xfun_0.23 [21] ggdendro_0.1.22 gridExtra_2.3 kableExtra_1.3.4 UpSetR_1.4.0 [25] httr_1.4.2 stringr_1.4.0 knitr_1.33 xml2_1.3.2 [29] hms_1.1.0 systemfonts_1.0.2 vctrs_0.3.8 ade4_1.7-16 [33] webshot_0.5.2 grid_4.1.0 svglite_2.0.0 glue_1.4.2 [37] data.table_1.14.0 R6_2.5.0 fansi_0.5.0 rmarkdown_2.8 [41] farver_2.1.0 seqinr_4.2-8 reshape2_1.4.4 ggplot2_3.3.3 [45] magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.2 htmltools_0.5.1.1 [49] MASS_7.3-54 rvest_1.0.0 colorspace_2.0-1 labeling_0.4.2 [53] utf8_1.2.1 stringi_1.6.1 munsell_0.5.0 crayon_1.4.1

[cbielow]

ah ok, good to hear :)

As another check, you can always visit

http://ptxqc.bsc.fu-berlin.de/

for an online version of PTXQC. Just to see if the problem is limited to your installation, or a bug in PTXQC.

[mtinti]

cool, thanks for the tip!