The project is out-of-sync

[JonnaLind]

Hi @langtonhugh,
I'm very new to R (today is the first time I've even opened Rstudio), and I was hoping for an easy access to your IRR-project. But I'm running into problems, and I'm hoping you can help me:

After having installed the packages needed, but not yet installed, I got the following error messages. I'm hoping you could either update your release or give me some advice about how to proceed (please remember I'm a beginner)!

Kind regards, Jonna Lind

Using R 4.4.0 (lockfile was generated with R 4.3.2)

• Project 'C:/Users/JLind/StichtingArq/KC Oorlog Algemeen - Documenten/Bibliotheek/Beheer/Systemen/ASReview/IRR/asreview_irr-v.1.0-alpha' loaded. [renv 1.0.5]

• The project is out-of-sync -- use renv::status() for details.

  renv::status() The following package(s) are in an inconsistent state:

  package installed recorded used askpass y y n
  callr y y n
  httr y y n
  openssl y y n
  processx y y n
  ps y y n
  rvest y y n
  selectr y y n
  sys y y n
  webshot y y n

The following package(s) are out of sync [lockfile != library]:

CRAN -----------------------------------------------------------------------

• bslib [0.7.0 != 0.8.0]
• cachem [1.0.8 != 1.1.0]
• cli [repo: RSPM != CRAN; ver: 3.6.2 != 3.6.3]
• colorspace [repo: RSPM != CRAN; ver: 2.1-0 != 2.1-1]
• cpp11 [repo: RSPM != CRAN; ver: 0.4.7 != 0.5.0]
• crayon [repo: RSPM != CRAN; ver: 1.5.2 != 1.5.3]
• curl [5.2.1 != 5.2.2]
• digest [0.6.35 != 0.6.37]
• evaluate [repo: RSPM != CRAN; ver: 0.23 != 0.24.0]
• farver [repo: RSPM != CRAN; ver: 2.1.1 != 2.1.2]
• fastmap [1.1.1 != 1.2.0]
• fs [repo: RSPM != CRAN; ver: 1.6.3 != 1.6.4]
• ggplot2 [repo: RSPM != CRAN; ver: 3.5.0 != 3.5.1]
• gtable [repo: RSPM != CRAN; ver: 0.3.4 != 0.3.5]
• highr [0.10 != 0.11]
• kableExtra [kupietz/kableExtra@HEAD != 1.4.0]
• knitr [1.46 != 1.48]
• MASS [7.3-60.0.1 != 7.3-61]
• Matrix [1.6-5 != 1.7-0]
• nlme [3.1-164 != 3.1-166]
• openssl [repo: RSPM != CRAN; ver: 2.1.1 != 2.2.1]
• ps [1.7.6 != 1.7.7]
• Rcpp [repo: RSPM != CRAN; ver: 1.0.12 != 1.0.13]
• rlang [repo: RSPM != CRAN; ver: 1.1.3 != 1.1.4]
• rmarkdown [2.26 != 2.28]
• stringi [repo: RSPM != CRAN; ver: 1.8.3 != 1.8.4]
• systemfonts [1.0.6 != 1.1.0]
• tinytex [0.50 != 0.52]
• withr [3.0.0 != 3.0.1]
• xfun [0.43 != 0.47]
• yaml [repo: RSPM != CRAN; ver: 2.3.8 != 2.3.10]

The lockfile was generated with R 4.3.2, but you're using R 4.4.0.

[langtonhugh]

Could you download R 4.3.2, switch to that version with RStudio, and then re-try? You can download old versions from the CRAN website and then you can switch the version you are using from within RStudio (Tools -> Global Options -> General). Let me know if that works!

[JonnaLind]

I’ll ask our ICT-section if they are willing to install old software for me… I’ll keep you posted….

Met vriendelijke groet,

Jonna Lind Sr. Medewerker Kennis- en informatiecentrum ARQ-bibliotheek | Informatie op maat Aanwezig: maandag (Diemen); dinsdag + woensdag (thuis) Soms wijk ik hiervan af.

ARQ Nationaal Psychotrauma Centrum ARQ Kenniscentrum Oorlog, Vervolging en Geweld Nienoord 5 | 1112 XE Diemen T 088 3305 187 M 06-100 73 043 E @.**@.> W arq.orghttp://arq.org/

@.***

Bekijk het ARQ-jaaroverzicht 2023 – ‘50 jaar bevlogenheid’https://arq.org/sites/default/files/2024-07/ARQ_jaaroverzicht_2023.pdf.

Van: Sam Langton @.> Verzonden: donderdag 5 september 2024 15:15 Aan: langtonhugh/asreview_irr @.> CC: Jonna Lind @.>; Author @.> Onderwerp: Re: [langtonhugh/asreview_irr] The project is out-of-sync (Issue #24)

Could you download R 4.3.2, switch to that version with RStudio, and then re-try? You can download old versions from the CRAN websitehttps://cran.r-project.org/bin/windows/base/old/ and then you can switch the version you are using from within RStudio (Tools -> Global Options -> General). Let me know if that works!

— Reply to this email directly, view it on GitHubhttps://github.com/langtonhugh/asreview_irr/issues/24#issuecomment-2331654647, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4SKCJXHFS6V45RK4B3DT2DZVBKMFAVCNFSM6AAAAABNUJ4QUKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZRGY2TINRUG4. You are receiving this because you authored the thread.Message ID: @.**@.>>

[langtonhugh]

If you cannot download different versions of R, you can still try and build the report. The warning you are seeing is related to the renv package, which manages libraries, rather than this tool itself. You can build a report without any usage of renv / ignoring different package versions, and while using a different version of R (although it's not ideal!).

[JonnaLind]

Could you give me some hints on how to do this? I’m very new to R…..

Met vriendelijke groet,

Jonna Lind Sr. Medewerker Kennis- en informatiecentrum ARQ-bibliotheek | Informatie op maat Aanwezig: maandag (Diemen); dinsdag + woensdag (thuis) Soms wijk ik hiervan af.

ARQ Nationaal Psychotrauma Centrum ARQ Kenniscentrum Oorlog, Vervolging en Geweld Nienoord 5 | 1112 XE Diemen T 088 3305 187 M 06-100 73 043 E @.**@.> W arq.orghttp://arq.org/

@.***

Bekijk het ARQ-jaaroverzicht 2023 – ‘50 jaar bevlogenheid’https://arq.org/sites/default/files/2024-07/ARQ_jaaroverzicht_2023.pdf.

Van: Sam Langton @.> Verzonden: maandag 9 september 2024 10:37 Aan: langtonhugh/asreview_irr @.> CC: Jonna Lind @.>; Author @.> Onderwerp: Re: [langtonhugh/asreview_irr] The project is out-of-sync (Issue #24)

If you cannot download different versions of R, you can still try and build the report. The warning you are seeing is related to the renvhttps://rstudio.github.io/renv/articles/renv.html package, which manages libraries, rather than this tool itself. You can build a report without any usage of renv, and while using a different version of R (although it's not ideal!).

— Reply to this email directly, view it on GitHubhttps://github.com/langtonhugh/asreview_irr/issues/24#issuecomment-2337484289, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4SKCJTTITN3AYKLLDOZTITZVVM37AVCNFSM6AAAAABNUJ4QUKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZXGQ4DIMRYHE. You are receiving this because you authored the thread.Message ID: @.**@.>>

[langtonhugh]

If you follow the instructions, are you able to produce a report (even if there are warnings)?

[JonnaLind]

I got error messages when opening the project… the parser (or something like that) gave the error messages, that I sent to you…. Should I just ignore them?

Met vriendelijke groet,

Jonna Lind Sr. Medewerker Kennis- en informatiecentrum ARQ-bibliotheek | Informatie op maat Aanwezig: maandag (Diemen); dinsdag + woensdag (thuis) Soms wijk ik hiervan af.

ARQ Nationaal Psychotrauma Centrum ARQ Kenniscentrum Oorlog, Vervolging en Geweld Nienoord 5 | 1112 XE Diemen T 088 3305 187 M 06-100 73 043 E @.**@.> W arq.orghttp://arq.org/

@.***

Bekijk het ARQ-jaaroverzicht 2023 – ‘50 jaar bevlogenheid’https://arq.org/sites/default/files/2024-07/ARQ_jaaroverzicht_2023.pdf.

Van: Sam Langton @.> Verzonden: maandag 9 september 2024 11:37 Aan: langtonhugh/asreview_irr @.> CC: Jonna Lind @.>; Author @.> Onderwerp: Re: [langtonhugh/asreview_irr] The project is out-of-sync (Issue #24)

If you follow the instructionshttps://github.com/langtonhugh/asreview_irr do you get any errors?

— Reply to this email directly, view it on GitHubhttps://github.com/langtonhugh/asreview_irr/issues/24#issuecomment-2337622713, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4SKCJQKJP7BO6RJDY2N4XTZVVT5PAVCNFSM6AAAAABNUJ4QUKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZXGYZDENZRGM. You are receiving this because you authored the thread.Message ID: @.**@.>>

[langtonhugh]

You can ignore the warnings but it is not ideal, because your R environment will not match the environment used when we built and tested the tool (i.e., the same R version, the same R package versions).

I would recommend reading more about renv package to understand the warning properly. In short, running renv::restore() and matching the version of R (like this) might fix the problem. If you still have problems, you are welcome to contact me via email, since this is more generic advice about R and renv, rather than specific issues with the report tool.

That said, I will update the README with some more information about renv so that new users can get the tool running more easily. Thanks for raising the issue.

[JonnaLind]

Thanks!

Met vriendelijke groet,

Jonna Lind Sr. Medewerker Kennis- en informatiecentrum ARQ-bibliotheek | Informatie op maat Aanwezig: maandag (Diemen); dinsdag + woensdag (thuis) Soms wijk ik hiervan af.

ARQ Nationaal Psychotrauma Centrum ARQ Kenniscentrum Oorlog, Vervolging en Geweld Nienoord 5 | 1112 XE Diemen T 088 3305 187 M 06-100 73 043 E @.**@.> W arq.orghttp://arq.org/

@.***

Bekijk het ARQ-jaaroverzicht 2023 – ‘50 jaar bevlogenheid’https://arq.org/sites/default/files/2024-07/ARQ_jaaroverzicht_2023.pdf.

Van: Sam Langton @.> Verzonden: maandag 9 september 2024 14:27 Aan: langtonhugh/asreview_irr @.> CC: Jonna Lind @.>; Author @.> Onderwerp: Re: [langtonhugh/asreview_irr] The project is out-of-sync (Issue #24)

You can ignore the warnings but it is not ideal, because your R environment will not match the environment used when we built and tested the tool (i.e., the same R version, the same R package versions).

I would recommend reading more about renv packagehttps://rstudio.github.io/renv/articles/renv.html to understand the warning properly. In short, running renv::restore() and matching the version of R (like thishttps://github.com/langtonhugh/asreview_irr/issues/24#issuecomment-2331654647) might fix the problem. If you still have problems, you are welcome to contact me via email, since this is more generic advice about R and renv, rather than specific issues with the report tool.

That said, I will update the README with some more information about renv so that new users can get the tool running more easily.

— Reply to this email directly, view it on GitHubhttps://github.com/langtonhugh/asreview_irr/issues/24#issuecomment-2337989749, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4SKCJTY7DLLENH2XGBFH4LZVWH23AVCNFSM6AAAAABNUJ4QUKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZXHE4DSNZUHE. You are receiving this because you authored the thread.Message ID: @.**@.>>

[langtonhugh]

That said, apologies, a correction: there are some sync issues on my own machine that I had not noticed. I have now updated the lockfile, so please re-clone/download the repository, execute renv::restore() and see whether that fixes the problem (ideally, please also match the R version with the lockfile).

[JonnaLind]

I set R to 4.3.2, opend the project, ran renv::restore(). But I did get an error message - can you give me any hints on how to deal with this?

Kind regards, Jonna

Error: Error installing package 'MASS':

• installing source package 'MASS' ... package 'MASS' successfully unpacked and MD5 sums checked using staged installation ** libs Error in system(paste(MAKE, p1(paste("-f", shQuote(makefiles))), "compilers"), : 'make' not found
• removing 'C:/Users/JLind/StichtingArq/KC Oorlog Algemeen - Documenten/Bibliotheek/Beheer/Systemen/ASReview/IRR/IRR met R 432/asreview_irr-v.1.0-alpha/renv/staging/1/MASS' install of package 'MASS' failed [error code 1]

[langtonhugh]

Do you have Rtools installed? If not (or if you are not sure), try installing Rtools, restart RStudio, and run renv::restore() again. If you are on R version 4.3.2 you can install Rtools here: https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html.

[JonnaLind]

I installed Rtools from your link, ran renv again, but got a new error message , see the file. foutmelding R 20241010.txt Can you help me again? My Rtools is installed in C:\Users\JLind\OneDrive - StichtingArq\programfiles\rtools43, I don't know if that makes a difference?