Closed ramiromagno closed 1 year ago
jennybc
commented
1 year ago What happens with plain old R CMD check in the terminal?
I guess you've already done some additional configuration though:
I am on Archlinux and when I got this error I had aspell installed. I had however to install the word list for the language "en_US", i.e. aspell-en, to have devtools::check() run without that error.
But I doubt this is (was) a devtools issue.
ramiromagno
commented
1 year ago Hi Jenny!
For this test I have uninstalled aspell-en again.
R CMD checkSo, running R CMD build . && R CMD check $(ls -t . | head -n1):
$ R CMD build . && R CMD check $(ls -t . | head -n1)
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘hgnc’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘hgnc_0.1.3.tar.gz’
* using log directory ‘/home/rmagno/sci/code/R/pkg/hgnc/hgnc.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘hgnc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hgnc’ version ‘0.1.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hgnc’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: OKdevtools::check()Running devtools::check(remote = TRUE, manual = TRUE) right after:
> devtools::check(remote = TRUE, manual = TRUE)
══ Documenting ═════════════════════════════════════════════════════════════════════════════════════════════════════════
ℹ Updating hgnc documentation
ℹ Loading hgnc
══ 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/rmagno/sci/code/R/pkg/hgnc/DESCRIPTION’ ...
─ preparing ‘hgnc’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘hgnc_0.1.3.tar.gz’
══ Checking ════════════════════════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• _R_CHECK_CRAN_INCOMING_USE_ASPELL_ : TRUE
• _R_CHECK_CRAN_INCOMING_REMOTE_ : TRUE
• _R_CHECK_CRAN_INCOMING_ : TRUE
• _R_CHECK_FORCE_SUGGESTS_ : FALSE
• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
• NOT_CRAN : true
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────
─ using log directory ‘/tmp/RtmpbTss3r/file2d554245eaa3b3/hgnc.Rcheck’
─ using R version 4.2.3 (2023-03-15)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
─ using option ‘--as-cran’
✔ checking for file ‘hgnc/DESCRIPTION’
─ checking extension type ... Package
─ this is package ‘hgnc’ version ‘0.1.3’
─ package encoding: UTF-8
─ checking CRAN incoming feasibility ...Error in aspell(files, filter = list("dcf", ignore = ignore), control = control, :
Running aspell failed with diagnostics:
Error: The file "/usr/lib/aspell-0.60/en_US" can not be opened for reading.
Execution halted
── R CMD check results ───────────────────────────────────────────────────────────────────────────────── hgnc 0.1.3 ────
Duration: 266ms
0 errors ✔ | 0 warnings ✔ | 0 notes ✔I still don't think these are comparable, in that the problem crops up in "checking CRAN incoming feasibility" which doesn't appear in the R CMD check result, presumably due to different options and env vars.
In any case, I am going to let this go, as I don't think there's evidence of a problem in devtools.
I just opened this issue to point out that it might be better to not just check that aspell is installed but also that the required word list is also available when running
devtools::check().I am on Archlinux and when I got this error I had aspell installed. I had however to install the word list for the language "en_US", i.e. aspell-en, to have
devtools::check()run without that error.Cheers!
gives: