404 error during devtools::check()

dls · May 16, 2023, 6:32pm

Hi,

I am still able to install binary packages from P3M using install.packages() but I'm getting this error when running devtools::check(). I've included some of my related settings below the check() results. I get the same error when running devtools::check() in base R and in Rstudio.

Error in output from devtools::check():

✔  checking package namespace information
─  checking package dependencies ...Warning in url(sprintf("%s/%s", cran, path), open = "rb") : (3s)
     cannot open URL 'https://packagemanager.posit.co/cran/__linux__/jammy/latest/web/packages/packages.rds': HTTP status was '404 Not Found'
   Error in url(sprintf("%s/%s", cran, path), open = "rb") : 
     cannot open the connection to 'https://packagemanager.posit.co/cran/__linux__/jammy/latest/web/packages/packages.rds'
   Execution halted

> getOption('HTTPUserAgent')
[1] "R/4.3.0 R (4.3.0 x86_64-pc-linux-gnu x86_64 linux-gnu)"

> getOption('repos')
                                                         CRAN 
"https://packagemanager.posit.co/cran/__linux__/jammy/latest"

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 21.1

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] miniUI_0.1.1.1    compiler_4.3.0    crayon_1.5.2      promises_1.2.0.1  Rcpp_1.0.10       stringr_1.5.0     rcmdcheck_1.4.0  
 [8] callr_3.7.3       later_1.3.1       fastmap_1.1.1     mime_0.12         R6_2.5.1          curl_5.0.0        htmlwidgets_1.6.2
[15] tibble_3.2.1      desc_1.4.2        profvis_0.3.8     rprojroot_2.0.3   shiny_1.7.4       pillar_1.9.0      rlang_1.1.1      
[22] utf8_1.2.3        cachem_1.0.8      stringi_1.7.12    httpuv_1.6.11     fs_1.6.2          pkgload_1.3.2     memoise_2.0.1    
[29] cli_3.6.1         withr_2.5.0       magrittr_2.0.3    ps_1.7.5          digest_0.6.31     processx_3.8.1    rstudioapi_0.14  
[36] xtable_1.8-4      remotes_2.4.2     devtools_2.4.5    lifecycle_1.0.3   prettyunits_1.1.1 vctrs_0.6.2       glue_1.6.2       
[43] xopen_1.0.0       urlchecker_1.0.1  sessioninfo_1.2.2 pkgbuild_1.4.0    fansi_1.0.4       purrr_1.0.1       pkgconfig_2.0.3  
[50] usethis_2.1.6     tools_4.3.0       ellipsis_0.3.2    htmltools_0.5.5

My .Rprofile file:

$ cat .Rprofile
options(repos = c(CRAN =
'https://packagemanager.posit.co/cran/__linux__/jammy/latest'))
options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(),
paste(getRversion(), R.version["platform"], R.version["arch"],
R.version["os"])))

rstub · May 17, 2023, 11:54am

I cannot reproduce this. The quoted URL does indeed produce a 404, but it is not requested in my tests. Does this happen with any R package or only specific ones? Can you provide the output of sessioninfo::session_info() or sessionInfo()?

dls · May 17, 2023, 1:30pm

Same error using a different package, here a git clone of tidyverse/magrittr:

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::check()
══ Documenting ═════════════════════════════════════════════════════════════════════════════════════════════════════════
ℹ Installed roxygen2 version (7.2.3) doesn't match required (7.1.2)
✖ `check()` will not re-document this package
══ Building ════════════════════════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/dave/Desktop/magrittr/DESCRIPTION’ ...
─  preparing ‘magrittr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
✔  creating vignettes (4.4s)
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘magrittr_2.0.3.9000.tar.gz’
   
══ Checking ════════════════════════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• _R_CHECK_CRAN_INCOMING_USE_ASPELL_           : TRUE
• _R_CHECK_CRAN_INCOMING_REMOTE_               : FALSE
• _R_CHECK_CRAN_INCOMING_                      : FALSE
• _R_CHECK_FORCE_SUGGESTS_                     : FALSE
• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
• NOT_CRAN                                     : true
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpV0XWT5/file4e1c31d7c9f9/magrittr.Rcheck’
─  using R version 4.3.0 (2023-04-21)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  R was compiled by
       gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
       GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
─  running under: Linux Mint 21.1
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’
✔  checking for file ‘magrittr/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘magrittr’ version ‘2.0.3.9000’
─  package encoding: UTF-8
✔  checking package namespace information
─  checking package dependencies ...Warning in url(sprintf("%s/%s", cran, path), open = "rb") : (2.8s)
     cannot open URL 'https://packagemanager.posit.co/cran/__linux__/jammy/latest/web/packages/packages.rds': HTTP status was '404 Not Found'
   Error in url(sprintf("%s/%s", cran, path), open = "rb") : 
     cannot open the connection to 'https://packagemanager.posit.co/cran/__linux__/jammy/latest/web/packages/packages.rds'
   Execution halted
   
── R CMD check results ──────────────────────────────────────────────────────────────────────── magrittr 2.0.3.9000 ────
Duration: 3.8s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Re-including sessionInfo() here:

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 21.1

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
 [1] miniUI_0.1.1.1    compiler_4.3.0    crayon_1.5.2      promises_1.2.0.1  Rcpp_1.0.10       stringr_1.5.0    
 [7] rcmdcheck_1.4.0   callr_3.7.3       later_1.3.1       fastmap_1.1.1     mime_0.12         R6_2.5.1         
[13] curl_5.0.0        htmlwidgets_1.6.2 tibble_3.2.1      desc_1.4.2        profvis_0.3.8     rprojroot_2.0.3  
[19] shiny_1.7.4       pillar_1.9.0      rlang_1.1.1       utf8_1.2.3        cachem_1.0.8      stringi_1.7.12   
[25] httpuv_1.6.11     fs_1.6.2          pkgload_1.3.2     memoise_2.0.1     cli_3.6.1         withr_2.5.0      
[31] magrittr_2.0.3    ps_1.7.5          digest_0.6.31     processx_3.8.1    rstudioapi_0.14   xtable_1.8-4     
[37] remotes_2.4.2     devtools_2.4.5    lifecycle_1.0.3   prettyunits_1.1.1 vctrs_0.6.2       glue_1.6.2       
[43] xopen_1.0.0       urlchecker_1.0.1  sessioninfo_1.2.2 pkgbuild_1.4.0    fansi_1.0.4       purrr_1.0.1      
[49] pkgconfig_2.0.3   usethis_2.1.6     tools_4.3.0       ellipsis_0.3.2    htmltools_0.5.5

Options being used for downloading R packages:

> options('repos')
$repos
                                                         CRAN 
"https://packagemanager.posit.co/cran/__linux__/jammy/latest" 

> options('HTTPUserAgent')
$HTTPUserAgent
[1] "R/4.3.0 R (4.3.0 x86_64-pc-linux-gnu x86_64 linux-gnu)"

Thanks much for any suggestions on debugging this issue. I'm getting the same error when I try checking a different package inside a singularity container based on rocker/geospatial:4.2.3, so I don't think it's specific to R 4.3.0 or to Linux Mint.

dls · May 17, 2023, 6:25pm

Hi,

My reply got spam-filtered by Akismet and may show back up eventually, but briefly yes ,this same error does occur with other packages (tested it also using tidyverse/magrittr). I also get the error when I attempt this inside a rocker/geospatial:4.2.3 container, so I don't think it's Linux Mint or R 4.3.0 specific. See the OP for sessionInfo() output.

I see that the same error is also mentioned on this rocker webpage, see section 4.1:

https://rocker-project.org/images/versioned/r-ver

dls · May 17, 2023, 6:49pm

A little more sleuthing turned up this:

github.com/rocker-org/rocker-versioned2

cannot open URL in check --as-cran

opened 01:20PM - 05 Sep 22 UTC

closed 07:23PM - 05 Sep 22 UTC

raul-ortega

question

### Container image name rocker/tidyverse ### Container image digest ro…cker/tidyverse@sha256:cbf4f03e1dc840b3b7dfcec775b2bfbff4848d77015265ed5adf6ee2ec4eda56 ### What operating system are you seeing the problem on? Linux ### System information Client: Docker Engine - Community Version: 20.10.16 API version: 1.41 Go version: go1.17.10 Git commit: aa7e414 Built: Thu May 12 09:17:23 2022 OS/Arch: linux/amd64 Context: default Experimental: true Server: Docker Engine - Community Engine: Version: 20.10.14 API version: 1.41 (minimum version 1.12) Go version: go1.16.15 Git commit: 87a90dc Built: Thu Mar 24 01:45:53 2022 OS/Arch: linux/amd64 Experimental: false containerd: Version: 1.6.4 GitCommit: 212e8b6fa2f44b9c21b2798135fc6fb7c53efc16 runc: Version: 1.1.1 GitCommit: v1.1.1-0-g52de29d docker-init: Version: 0.19.0 GitCommit: de40ad0 ### Bug description * checking CRAN incoming feasibility ...Warning in url(sprintf("%s/%s", cran, path), open = "rb") : cannot open URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest/src/contrib/Meta/current.rds': HTTP status was '404 Not Found' Error in url(sprintf("%s/%s", cran, path), open = "rb") : cannot open the connection to 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest/src/contrib/Meta/current.rds' Execution halted ### How to reproduce this bug? ```sh # run container docker run -ti rocker/tidyverse /bin/bash ``` Once in the container prompt: ```sh # instal dependencies apt-get update apt-get install -y --no-install-recommends libcurl4-openssl-dev libssh2-1-dev libssl-dev libxml2-dev zlib1g-dev git libv8-dev apt-get install -y --no-install-recommends qpdf pandoc pandoc-citeproc # install R packages R -e 'install.packages(c("covr", "testthat", "spelling"));' R -e 'install.packages(c("circlize", "xml2", "httr", "circlize", "RColorBrewer", "R6"));' # clone repository avidaR git clone https://gitlab.com/fortunalab/avidaR.git # build package R CMD build avidaR/ --no-build-vignettes --no-manual ../avidaR.zip # check as CRAN R CMD check --as-cran --no-manual avidaR_1.1.3.tar.gz ```

I'm not sure if this is best seen as a bug or not, but it appears that binary package installs through P3M are not compatible with a devtools:check() development workflow.

The workaround given in the rocker issue, changing the repo to a traditional source CRAN url, does work in my case, but of course might be nicer if no workaround was needed.

thanks again,

rstub · May 22, 2023, 2:07pm

Thanks for the tests. So far I cannot reproduce this. To narrow the search space: Does this also work with R CMD check, i.e.

R CMD build magrittr
R CMD check magrittr_2.0.3.9000.tar.gz

In the directory where you checked out magrittr.

dls · May 22, 2023, 10:42pm

Yes.

dave@dave-linux-macbook:~/Desktop$ R CMD check magrittr_2.0.3.9000.tar.gz
* using log directory ‘/home/dave/Desktop/magrittr.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Linux Mint 21.1
* using session charset: UTF-8
* checking for file ‘magrittr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘magrittr’ version ‘2.0.3.9000’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK

...

rstub · May 24, 2023, 3:20pm

OK, I think I have found the reason for this. I have installed R using GitHub - r-lib/rig: The R Installation Manager which sets:

> options("repos")
$repos
                                                         RSPM 
"https://packagemanager.posit.co/cran/__linux__/jammy/latest" 
                                                         CRAN 
                                "https://cloud.r-project.org"

Internally, the check functions in R explicitly searches for "CRAN", so https://cloud.r-project.org is used to retrieve the file in question. However, normal calls to install.packages() go through the repository list one by one and use the first one that has the package available, which will be the binary packages from package manager.

I will ask internally if there is a possibility to also provide the web part of CRAN via package manager.