Why devtools::document fails with unclear C++ error message?
0
I have a vignette that I can build using devtools::build_vignettes() but when I try to build the source package (RStudio/Build/build source package) it fails when executing devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette')) with the following error message:
R(32119,0x7fff7437f000) malloc: *** error for object 0x7fff74dc0c30: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Exited with status 6.
This package uses Rcpp but I am definitely not an expert in Cpp and don't understand at all what is going on. I can use the package locally with no troubles.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.8 knitr_1.20 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[7] pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1 tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1
[13] cli_1.0.1 withr_2.1.2 htmltools_0.3.6 remotes_2.0.2 yaml_2.2.0 assertthat_0.2.0
[19] digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0 clisymbols_1.2.0
[25] base64enc_0.1-3 fs_1.2.6 ps_1.2.1 evaluate_0.12 glue_1.3.0 memoise_1.1.0
[31] rmarkdown_1.10 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
r build
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
|
show 1 more comment
0
I have a vignette that I can build using devtools::build_vignettes() but when I try to build the source package (RStudio/Build/build source package) it fails when executing devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette')) with the following error message:
R(32119,0x7fff7437f000) malloc: *** error for object 0x7fff74dc0c30: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Exited with status 6.
This package uses Rcpp but I am definitely not an expert in Cpp and don't understand at all what is going on. I can use the package locally with no troubles.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.8 knitr_1.20 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[7] pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1 tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1
[13] cli_1.0.1 withr_2.1.2 htmltools_0.3.6 remotes_2.0.2 yaml_2.2.0 assertthat_0.2.0
[19] digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0 clisymbols_1.2.0
[25] base64enc_0.1-3 fs_1.2.6 ps_1.2.1 evaluate_0.12 glue_1.3.0 memoise_1.1.0
[31] rmarkdown_1.10 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
r build
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
2
Minimal, Complete, and Verifiable example? Does the error happen when you calldevtools::document()directly with differentroclets?
– Ralf Stubner
Nov 22 '18 at 18:42
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
Also the commanddevtools::build()works from the RStudio console
– clemlaflemme
Nov 22 '18 at 18:52
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
RemoviingRcpptag ...
– Dirk Eddelbuettel
Nov 22 '18 at 18:56
|
show 1 more comment
0
0
0
I have a vignette that I can build using devtools::build_vignettes() but when I try to build the source package (RStudio/Build/build source package) it fails when executing devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette')) with the following error message:
R(32119,0x7fff7437f000) malloc: *** error for object 0x7fff74dc0c30: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Exited with status 6.
This package uses Rcpp but I am definitely not an expert in Cpp and don't understand at all what is going on. I can use the package locally with no troubles.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.8 knitr_1.20 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[7] pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1 tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1
[13] cli_1.0.1 withr_2.1.2 htmltools_0.3.6 remotes_2.0.2 yaml_2.2.0 assertthat_0.2.0
[19] digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0 clisymbols_1.2.0
[25] base64enc_0.1-3 fs_1.2.6 ps_1.2.1 evaluate_0.12 glue_1.3.0 memoise_1.1.0
[31] rmarkdown_1.10 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
r build
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
I have a vignette that I can build using devtools::build_vignettes() but when I try to build the source package (RStudio/Build/build source package) it fails when executing devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette')) with the following error message:
R(32119,0x7fff7437f000) malloc: *** error for object 0x7fff74dc0c30: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Exited with status 6.
This package uses Rcpp but I am definitely not an expert in Cpp and don't understand at all what is going on. I can use the package locally with no troubles.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 rstudioapi_0.8 knitr_1.20 magrittr_1.5 usethis_1.4.0 devtools_2.0.1
[7] pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1 tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1
[13] cli_1.0.1 withr_2.1.2 htmltools_0.3.6 remotes_2.0.2 yaml_2.2.0 assertthat_0.2.0
[19] digest_0.6.18 rprojroot_1.3-2 crayon_1.3.4 processx_3.2.0 callr_3.0.0 clisymbols_1.2.0
[25] base64enc_0.1-3 fs_1.2.6 ps_1.2.1 evaluate_0.12 glue_1.3.0 memoise_1.1.0
[31] rmarkdown_1.10 compiler_3.5.1 desc_1.2.0 backports_1.1.2 prettyunits_1.0.2
r build
r build
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
edited Nov 22 '18 at 18:57
Dirk Eddelbuettel
278k37514603
278k37514603
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
asked Nov 22 '18 at 18:38
clemlaflemmeclemlaflemme
1,617820
1,617820
2
Minimal, Complete, and Verifiable example? Does the error happen when you calldevtools::document()directly with differentroclets?
– Ralf Stubner
Nov 22 '18 at 18:42
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
Also the commanddevtools::build()works from the RStudio console
– clemlaflemme
Nov 22 '18 at 18:52
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
RemoviingRcpptag ...
– Dirk Eddelbuettel
Nov 22 '18 at 18:56
|
show 1 more comment
2
Minimal, Complete, and Verifiable example? Does the error happen when you calldevtools::document()directly with differentroclets?
– Ralf Stubner
Nov 22 '18 at 18:42
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
Also the commanddevtools::build()works from the RStudio console
– clemlaflemme
Nov 22 '18 at 18:52
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
RemoviingRcpptag ...
– Dirk Eddelbuettel
Nov 22 '18 at 18:56
2
2
Minimal, Complete, and Verifiable example? Does the error happen when you call
devtools::document() directly with different roclets?– Ralf Stubner
Nov 22 '18 at 18:42
Minimal, Complete, and Verifiable example? Does the error happen when you call
devtools::document() directly with different roclets?– Ralf Stubner
Nov 22 '18 at 18:42
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
Also the command
devtools::build() works from the RStudio console– clemlaflemme
Nov 22 '18 at 18:52
Also the command
devtools::build() works from the RStudio console– clemlaflemme
Nov 22 '18 at 18:52
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
Removiing
Rcpp tag ...– Dirk Eddelbuettel
Nov 22 '18 at 18:56
Removiing
Rcpp tag ...– Dirk Eddelbuettel
Nov 22 '18 at 18:56
|
show 1 more comment
0
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2
Minimal, Complete, and Verifiable example? Does the error happen when you call
devtools::document()directly with differentroclets?– Ralf Stubner
Nov 22 '18 at 18:42
The error does not happen when I call the exacte same command from the Rstudio console
– clemlaflemme
Nov 22 '18 at 18:50
Also the command
devtools::build()works from the RStudio console– clemlaflemme
Nov 22 '18 at 18:52
Weird, but impossible to debug without a Minimal, Complete, and Verifiable example. Make a copy of the project and remove stuff from it until you cannot remove anything without also removing this error message.
– Ralf Stubner
Nov 22 '18 at 18:55
Removiing
Rcpptag ...– Dirk Eddelbuettel
Nov 22 '18 at 18:56