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taxonomicallyinformedannotation / tima-r

https://taxonomicallyinformedannotation.github.io/tima-r/
https://taxonomicallyinformedannotation.github.io/tima-r
GNU General Public License v3.0
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GNPS job ID is missing from prepare_params.yml #110

Closed RemyMG closed 6 months ago

RemyMG commented 7 months ago

Hi Adriano,

Since the latest (2.9.1) version of timaR, the GNPS job ID si not specified anymore in the prepare_params.yml file. It does not propagate through other yml files. In which file should we specify the ID ?

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Adafede commented 7 months ago

Hi @RemyMG,

Indeed, I removed it from the default as GNPS private jobs policy is somehow problematic to maintain something on the long stay. I also do not like the current state of things regarding reproducible accessibility of GNPS libraries. Hopefully they will come up with a better solution that will allow using it again this way. In the meantime, I am working on exposing all parameters directly in an advanced parameters file. (See #107, #109). If everything goes well I should be able to merge today still.

Good to have feedback from people using the tool! 😉

Adafede commented 7 months ago

I just merged the mentioned branch. Could you test and tell me if it addresses your issue?

RemyMG commented 7 months ago

Hi @Adafede,

I'm not able to install the latest version of tima, the following packages can't be downloaded: MsBackendMsp 1.4.0, BiocGenerics 0.46.0, BiocParallel 1.34.2, MsBackendMgf 1.8.0, ProtGenerics 1.32.0, IRanges 2.34.1, MsCoreUtils 1.12.0 and S4Vectors. and I'm running R 4.3.2

(base) PS C:\Users\marcellr\GitHub\tima-r> Rscript inst/scripts/install.R
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.3/pkgbuild_1.4.2.zip'
Content type 'application/zip' length 192430 bytes (187 KB)
==================================================
downloaded 187 KB

package 'pkgbuild' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\marcellr\AppData\Local\Temp\RtmpqEUble\downloaded_packages
Loading required package: pkgbuild
No need to install Rtools - You've got the relevant version of Rtools installed

Current version is the latest, no need to update.
✔ Loading metadata database ... done
✔ Created lockfile pkg.lock [5.1s]
ℹ Installing lockfile pkg.lock

→ Will install 122 packages.
→ Will download 106 CRAN packages (123.77 MB).
→ Will download 16 packages with unknown size.
+ anytime         0.3.9   [dl] (741.87 kB)
+ ape             5.7-1   [dl] (3.41 MB)
+ askpass         1.2.0   [dl] (74.90 kB)
+ base64url       1.4     [dl] (33.09 kB)
+ bigD            0.2.0   [dl] (1.16 MB)
+ BiocGenerics    0.46.0  [dl]
+ BiocParallel    1.34.2  [dl]
+ bs4Dash         2.3.0   [dl] (1.43 MB)
+ bslib           0.6.0   [dl] (6.48 MB)
+ cachem          1.0.8   [dl] (72.56 kB)
+ callr           3.7.3   [dl] (439.93 kB)
+ cli             3.6.1   [dl] (1.34 MB)
+ clue            0.3-65  [dl] (996.19 kB)
+ colorspace      2.1-0   [dl] (2.63 MB)
+ commonmark      1.9.0   [dl] (142.59 kB)
+ crayon          1.5.2   [dl] (162.39 kB)
+ crosstalk       1.2.1   [dl] (410.41 kB)
+ curl            5.1.0   [dl] (3.22 MB)
+ desc            1.4.2   [dl] (326.60 kB)
+ digest          0.6.33  [dl] (206.14 kB)
+ docopt          0.7.1   [dl] (261.80 kB)
+ DT              0.30    [dl] (1.81 MB)
+ ellipsis        0.3.2   [dl] (40.50 kB)
+ evaluate        0.23    [dl] (84.18 kB)
+ fansi           1.0.5   [dl] (314.28 kB)
+ farver          2.1.1   [dl] (1.51 MB)
+ fastmap         1.1.1   [dl] (132.93 kB)
+ fontawesome     0.5.2   [dl] (1.36 MB)
+ formatR         1.14    [dl] (155.35 kB)
+ fresh           0.2.0   [dl] (1.67 MB)
+ fs              1.6.3   [dl] (393.96 kB)
+ fst             0.9.8   [dl] (455.16 kB)
+ fstcore         0.9.14  [dl] (838.01 kB)
+ futile.logger   1.4.3   [dl] (100.91 kB)
+ generics        0.1.3   [dl] (80.15 kB)
+ glue            1.6.2   [dl] (162.66 kB)
+ gt              0.10.0  [dl] (4.66 MB)
+ highr           0.10    [dl] (46.56 kB)
+ hms             1.1.3   [dl] (104.31 kB)
+ htmltools       0.5.7   [dl] (357.90 kB)
+ htmlwidgets     1.6.3   [dl] (811.99 kB)
+ httpuv          1.6.12  [dl] (1.01 MB)
+ httr            1.4.7   [dl] (485.97 kB)
+ httr2           1.0.0   [dl] (544.43 kB)
+ igraph          1.5.1   [dl] (6.75 MB)
+ IRanges         2.34.1  [dl]
+ jquerylib       0.1.4   [dl] (526.01 kB)
+ jsonlite        1.8.7   [dl] (1.11 MB)
+ juicyjuice      0.1.0   [dl] (1.13 MB)
+ knitr           1.45    [dl] (1.52 MB)
+ lambda.r        1.2.4   [dl] (112.21 kB)
+ later           1.3.1   [dl] (465.05 kB)
+ lazyeval        0.2.2   [dl] (160.76 kB)
+ lifecycle       1.0.4   [dl] (139.73 kB)
+ magrittr        2.0.3   [dl] (226.82 kB)
+ markdown        1.11    [dl] (213.40 kB)
+ memoise         2.0.1   [dl] (49.93 kB)
+ MsBackendMgf    1.8.0   [dl]
+ MsBackendMsp    1.4.0   [dl]
+ MsCoreUtils     1.12.0  [dl]
+ msentropy       0.1.4   [dl] (403.49 kB)
+ munsell         0.5.0   [dl] (244.42 kB)
+ openssl         2.1.1   [dl] (3.19 MB)
+ pbapply         1.7-2   [dl] (100.85 kB)
+ pillar          1.9.0   [dl] (659.23 kB)
+ pingr           2.0.2   [dl] (59.68 kB)
+ pkgconfig       2.0.3   [dl] (22.43 kB)
+ prettyunits     1.2.0   [dl] (157.80 kB)
+ processx        3.8.2   [dl] (686.38 kB)
+ progress        1.2.2   [dl] (86.03 kB)
+ promises        1.2.1   [dl] (2.02 MB)
+ ProtGenerics    1.32.0  [dl]
+ ps              1.7.5   [dl] (553.01 kB)
+ R6              2.5.1   [dl] (84.32 kB)
+ rappdirs        0.3.3   [dl] (51.41 kB)
+ Rcpp            1.0.11  [dl] (2.88 MB)
+ reactable       0.4.4   [dl] (1.05 MB)
+ reactR          0.5.0   [dl] (629.17 kB)
+ rentrez         1.2.3   [dl] (145.76 kB)
+ rlang           1.1.2   [dl] (1.57 MB)
+ rmarkdown       2.25    [dl] (2.68 MB)
+ rncl            0.8.7   [dl] (950.89 kB)
+ rotl            3.1.0   [dl] (564.29 kB)
+ rprojroot       2.0.4   [dl] (113.77 kB)
+ rstudioapi      0.15.0  [dl] (319.21 kB)
+ S4Vectors       0.38.1  [dl]
+ sass            0.4.7   [dl] (2.61 MB)
+ scales          1.2.1   [dl] (614.21 kB)
+ shiny           1.8.0   [dl] (4.52 MB)
+ shinybusy       0.3.2   [dl] (605.61 kB)
+ shinyhelper     0.3.2   [dl] (96.80 kB)
+ shinyjs         2.1.0   [dl] (1.11 MB)
+ shinyvalidate   0.1.3   [dl] (188.04 kB)
+ shinyWidgets    0.8.0   [dl] (1.46 MB)
+ sourcetools     0.1.7-1 [dl] (383.99 kB)
+ Spectra         1.10.3  [bld][dl]
+ stringi         1.8.2   [dl] (15.00 MB)
+ stringr         1.5.1   [dl] (318.95 kB)
+ sys             3.4.2   [dl] (47.08 kB)
+ targets         1.3.2   [dl] (2.51 MB)
+ tibble          3.2.1   [dl] (690.89 kB)
+ tidyfst         1.7.7   [dl] (550.13 kB)
+ tidyselect      1.2.0   [dl] (224.12 kB)
+ tidytable       0.10.2  [dl] (611.74 kB)
+ tinytex         0.49    [dl] (139.91 kB)
+ utf8            1.2.4   [dl] (149.83 kB)
+ V8              4.4.0   [dl] (8.93 MB)
+ vctrs           0.6.4   [dl] (1.33 MB)
+ viridisLite     0.4.2   [dl] (1.30 MB)
+ visNetwork      2.1.2   [dl] (4.70 MB)
+ waiter          0.2.5   [dl] (463.73 kB)
+ withr           2.5.2   [dl] (231.84 kB)
+ xfun            0.41    [dl] (436.38 kB)
+ xml2            1.3.5   [dl] (1.56 MB)
+ xtable          1.8-4   [dl] (706.29 kB)

! R6, callr, cli, crayon, glue, lifecycle, magrittr, prettyunits, processx, ps, rlang, stringi, and stringr are loaded
in the current R session, you probably need to restart R after the installation.

ℹ Getting 106 pkgs (123.77 MB) and 9 pkgs with unknown sizes
✔ Cached copy of cluster 2.1.4 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of codetools 0.2-19 (*) is the latest build
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✔ Cached copy of Rcpp 1.0.11 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of anytime 0.3.9 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of ape 5.7-1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of askpass 1.2.0 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of base64url 1.4 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of generics 0.1.3 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of magrittr 2.0.3 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of memoise 2.0.1 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of prettyunits 1.2.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of processx 3.8.2 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of scales 1.2.1 (i386+x86_64-w64-mingw32) is the latest build
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✔ Installed glue 1.6.2  (2.4s)
✔ Installed gt 0.10.0  (2.4s)
✔ Installed highr 0.10  (2.4s)
✔ Installed hms 1.1.3  (2.4s)
✔ Installed htmltools 0.5.7  (2.4s)
✔ Installed htmlwidgets 1.6.3  (2.5s)
✔ Installed httpuv 1.6.12  (5.3s)
✔ Installed httr2 1.0.0  (5.3s)
✔ Installed httr 1.4.7  (5.3s)
✔ Installed jquerylib 0.1.4  (5.2s)
✔ Installed igraph 1.5.1  (5.5s)
✔ Installed jsonlite 1.8.7  (5.4s)
✔ Installed juicyjuice 0.1.0  (5.3s)
✔ Installed lambda.r 1.2.4  (5s)
✔ Installed knitr 1.45  (5.3s)
✔ Installed later 1.3.1  (5.1s)
✔ Installed lazyeval 0.2.2  (5.1s)
✔ Installed lifecycle 1.0.4  (5.1s)
✔ Installed magrittr 2.0.3  (5.1s)
✔ Installed markdown 1.11  (5.1s)
✔ Installed memoise 2.0.1  (5s)
✔ Installed msentropy 0.1.4  (5s)
✔ Installed munsell 0.5.0  (2.2s)
✔ Installed pbapply 1.7-2  (2s)
✔ Installed openssl 2.1.1  (2.3s)
✔ Installed pillar 1.9.0  (2.2s)
✔ Installed pingr 2.0.2  (2.2s)
✔ Installed pkgconfig 2.0.3  (2.1s)
✔ Installed prettyunits 1.2.0  (2.1s)
✔ Installed processx 3.8.2  (2.3s)
✔ Installed progress 1.2.2  (2.2s)
✔ Installed promises 1.2.1  (2.3s)
✔ Installed ps 1.7.5  (3.1s)
✔ Installed rappdirs 0.3.3  (3.1s)
✔ Installed reactR 0.5.0  (3.1s)
✔ Installed reactable 0.4.4  (3.1s)
✔ Installed rentrez 1.2.3  (3.1s)
✔ Installed rlang 1.1.2  (3.1s)
✔ Installed rncl 0.8.7  (3s)
✔ Installed rotl 3.1.0  (2.9s)
✔ Installed rmarkdown 2.25  (3.5s)
✔ Installed rprojroot 2.0.4  (3.1s)
✔ Installed rstudioapi 0.15.0  (3.1s)
✔ Installed scales 1.2.1  (3s)
✔ Installed sass 0.4.7  (3.3s)
✔ Installed shinybusy 0.3.2  (2.7s)
✔ Installed shiny 1.8.0  (3.1s)
✔ Installed shinyWidgets 0.8.0  (3.6s)
✔ Installed shinyhelper 0.3.2  (2.4s)
✔ Installed shinyjs 2.1.0  (2.5s)
✔ Installed shinyvalidate 0.1.3  (2.4s)
✔ Installed sourcetools 0.1.7-1  (2.5s)
✔ Installed stringr 1.5.1  (2.4s)
✔ Installed sys 3.4.2  (2.4s)
✔ Installed stringi 1.8.2  (2.9s)
✔ Installed targets 1.3.2  (2.7s)
✔ Installed tibble 3.2.1  (2.5s)
✔ Installed tidyfst 1.7.7  (2.6s)
✔ Installed tidyselect 1.2.0  (2.6s)
Error:
! error in pak subprocess
Caused by error in `file(con, "rb")`:
! cannot open the connection
---
Backtrace:
1. pak::lockfile_install()
2. pak:::remote(function(...) { …
3. err$throw(res$error)
---
Subprocess backtrace:
 1. base::withCallingHandlers(cli_message = function(msg) { …
 2. get("lockfile_install_internal", asNamespace("pak"))(...)
 3. plan$install()
 4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
 5. base::withCallingHandlers({ …
 6. pkgdepends:::start_task(state, task)
 7. pkgdepends:::start_task_install(state, task)
 8. pkgdepends:::make_install_process(filename, lib = lib, metadata = metadata)
 9. pkgdepends:::detect_package_archive_type(filename)
10. base::readBin(file, what = "raw", n = 6)
11. base::file(con, "rb")
12. base::.handleSimpleError(function (e) …
13. global h(simpleError(msg, call))
Execution halted
Adafede commented 7 months ago

Hi @RemyMG, sadly I was not able to reproduce your problem.

The install runs fine on "classical" machines so probably has to do with your local permissions on your computer. I did multiple attempts (see above) but I think you have to fix this on your side (see https://www.programmingr.com/r-error-messages/guide-to-fixing-the-r-package-installation-error-library-is-not-writable/)

RemyMG commented 7 months ago

Hi @Adafede !

I run tima well until this section: https://taxonomicallyinformedannotation.github.io/tima-r/articles/III-formatting.html#isdb I have a new issue with source(file = "inst/scripts/annotate_spectra.R") giving me this issue:

> source(file = "inst/scripts/annotate_spectra.R")
2023-12-04 10:29:30.42434 This script performs spectral similarity calculation to annotate against a spectral library. 

2023-12-04 10:29:30.424817 Authors:  AR 

2023-12-04 10:29:30.425159 Contributors: ... 
✖ no targets found [1.2 seconds]
2023-12-04 10:29:32.87311 Script finished in 2.448819 secs

In the annotate_spectra.yml file, the file data/interim/annotations/20221229_IIMN_AF_sub500_spectral_matches.tsv.gz is missing from the directory, while pos/neg files in data/interim/libraries/spectra/is/lotus_neg.rds are also missing since the is directory is missing and finaly the pos/neg files data/interim/libraries/spectra/exp/massbank_neg.rds are named internal_neg.rds instead. data/source/20221229_IIMN_AF_sub500.mgf file is OK. image

Adafede commented 7 months ago

Oh... are you still following all the intermediary steps?

Why don't you just do the following if I may ask?

Rscript inst/scripts/tima_full.R

Is the documentation misleading?

Well at least it allowed to spot some leftovers I just fixed (see https://github.com/taxonomicallyinformedannotation/tima-r/commit/f7ca3d89762238120da46bd0435a9e4683ae0b96)

Do not hesitate to tell me if something is still not working @RemyMG, thank you for your feedbacks 😉