Closed barracuda156 closed 1 year ago
barracuda156
commented
1 year ago Similar error with bayesplot:
* checking tests ...
Running ‘testthat.R’/opt/local/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 556 Bus error ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.BATCH has the following there:
${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} >${out} 2>&1
jgabry
commented
1 year ago Thank you for reporting this.
Similar error with
bayesplot
Is there any way to figure out which particular tests are triggering this?
barracuda156
commented
1 year ago @jgabry Thank you for responding! Turned out, my fix to malloc problem https://github.com/macports/macports-ports/pull/17742 fixed this as well. Closing the issue, since now all tests pass.
---> Testing R-shinystan
* using log directory ‘/opt/local/var/macports/build/_opt_PPCRosettaPorts_R_R-shinystan/R-shinystan/work/shinystan-2.6.0/shinystan.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: powerpc-apple-darwin10.8.0 (32-bit)
* using session charset: UTF-8
* checking for file ‘shinystan/DESCRIPTION’ ... OK
* this is package ‘shinystan’ version ‘2.6.0’
* 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 ‘shinystan’ 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 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 ... WARNING
Missing link or links in documentation object 'as.shinystan.Rd':
‘[rstanarm]{pp_check}’ ‘[rstanarm]{rstanarm}’
Missing link or links in documentation object 'shinystan-package.Rd':
‘[rstanarm]{rstanarm}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘deploy_shinystan.Rmd’, ‘shinystan-package.Rmd’
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
‘deploy_shinystan.Rmd’
‘shinystan-package.Rmd’
* checking running R code from vignettes ...
‘deploy_shinystan.Rmd’ using ‘UTF-8’... OK
‘shinystan-package.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONEOk great, thanks for following up!
On Tue, Feb 21, 2023 at 7:18 AM Sergey Fedorov @.***> wrote:
@jgabry https://github.com/jgabry Thank you for responding! Turned out, my fix to malloc problem macports/macports-ports#17742 https://github.com/macports/macports-ports/pull/17742 fixed this as well. Closing the issue, since now all tests pass.
---> Testing R-shinystan
- using log directory ‘/opt/local/var/macports/build/_opt_PPCRosettaPorts_R_R-shinystan/R-shinystan/work/shinystan-2.6.0/shinystan.
Rcheck’
using R version 4.2.2 (2022-10-31)
using platform: powerpc-apple-darwin10.8.0 (32-bit)
using session charset: UTF-8
checking for file ‘shinystan/DESCRIPTION’ ... OK
this is package ‘shinystan’ version ‘2.6.0’
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 ‘shinystan’ 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 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 ... WARNING
Missing link or links in documentation object 'as.shinystan.Rd':
‘[rstanarm]{pp_check}’ ‘[rstanarm]{rstanarm}’
Missing link or links in documentation object 'shinystan-package.Rd':
‘[rstanarm]{rstanarm}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
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 contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘deploy_shinystan.Rmd’, ‘shinystan-package.Rmd’
checking examples ... OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ...
Running ‘testthat.R’
OK
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
‘deploy_shinystan.Rmd’
‘shinystan-package.Rmd’
checking running R code from vignettes ...
‘deploy_shinystan.Rmd’ using ‘UTF-8’... OK
‘shinystan-package.Rmd’ using ‘UTF-8’... OK
NONE
checking re-building of vignette outputs ... OK
checking PDF version of manual ... OK
DONE
— Reply to this email directly, view it on GitHub https://github.com/stan-dev/shinystan/issues/202#issuecomment-1438571974, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB3PQQZBKCKCXCZCSKL5S5LWYTFENANCNFSM6AAAAAAVAQGHPU . You are receiving this because you were mentioned.Message ID: @.***>
This is on 10.6.8 Rosetta:
P. S. Annoting
mallocerrors are a known problem, caused by duplicatelibstdc++.