Closed RemyMG closed 8 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! 😉
I just merged the mentioned branch. Could you test and tell me if it addresses your issue?
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
✔ Cached copy of lattice 0.22-5 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of Matrix 1.6-2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of nlme 3.1-163 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of DT 0.30 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of R6 2.5.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of Rcpp 1.0.11 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of V8 4.4.0 (x86_64-w64-mingw32) is the latest build
✔ 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
✔ Cached copy of bigD 0.2.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of bs4Dash 2.3.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of bslib 0.6.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of cachem 1.0.8 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of callr 3.7.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of cli 3.6.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of clue 0.3-65 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of colorspace 2.1-0 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of commonmark 1.9.0 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of crayon 1.5.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of curl 5.1.0 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of desc 1.4.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of digest 0.6.33 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of docopt 0.7.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of ellipsis 0.3.2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of evaluate 0.23 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of fansi 1.0.5 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of farver 2.1.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of fastmap 1.1.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of fontawesome 0.5.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of formatR 1.14 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of fresh 0.2.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of fs 1.6.3 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of futile.logger 1.4.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of generics 0.1.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of glue 1.6.2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of gt 0.10.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of highr 0.10 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of hms 1.1.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of htmltools 0.5.7 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of htmlwidgets 1.6.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of httpuv 1.6.12 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of httr2 1.0.0 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of igraph 1.5.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of jquerylib 0.1.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of jsonlite 1.8.7 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of juicyjuice 0.1.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of knitr 1.45 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of lambda.r 1.2.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of later 1.3.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of lazyeval 0.2.2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of lifecycle 1.0.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of magrittr 2.0.3 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of markdown 1.11 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of memoise 2.0.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of msentropy 0.1.4 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of munsell 0.5.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of openssl 2.1.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of pbapply 1.7-2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of pillar 1.9.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of pingr 2.0.2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of pkgconfig 2.0.3 (i386+x86_64-w64-mingw32) is the latest build
✔ 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
✔ Cached copy of progress 1.2.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of promises 1.2.1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of ps 1.7.5 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of rappdirs 0.3.3 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of reactR 0.5.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of reactable 0.4.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of rentrez 1.2.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of rlang 1.1.2 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of rmarkdown 2.25 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of rotl 3.1.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of rprojroot 2.0.4 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of sass 0.4.7 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of scales 1.2.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of shinyWidgets 0.8.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of shiny 1.8.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of shinyhelper 0.3.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of shinyjs 2.1.0 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of sourcetools 0.1.7-1 (x86_64-w64-mingw32) is the latest build
✔ Cached copy of stringr 1.5.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of sys 3.4.2 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of tinytex 0.49 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of utf8 1.2.4 (x86_64-w64-mingw32) is the latest build
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✔ Cached copy of viridisLite 0.4.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of visNetwork 2.1.2 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of waiter 0.2.5 (i386+x86_64-w64-mingw32) is the latest build
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✔ Installed R6 2.5.1 (513ms)
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✔ 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
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/)
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.
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 😉
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 ?Before
Now