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fix: check that we receive a scalar when expecting a scalar in C code #1051

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merged 4 commits into from
Jan 1, 2024
Merged

fix: check that we receive a scalar when expecting a scalar in C code #1051

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32d1d3e
fix: check that we receive a scalar when expecting a scalar in C code
szhorvat Dec 30, 2023
890ba37
revdepcheck results
krlmlr Dec 31, 2023
6a7b8be
refactoring: split check functions
Antonov548 Jan 1, 2024
3b545ad
chore: clarify use of scalar check functions/macros
szhorvat Jan 1, 2024
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14 changes: 13 additions & 1 deletion revdep/README.md
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# Revdeps

## New problems (17)
## Failed to check (5)

|package |version |error |warning |note |
|:---------|:-------|:-----|:-------|:----|
|bsts |0.9.9 |1 | | |
|MODIStsp |? | | | |
|sen2r |? | | | |
|Seurat |? | | | |
|streamDAG |? | | | |

## New problems (19)

|package |version |error |warning |note |
|:-----------------|:-------|:------|:-------|:----|
|[bnstruct](problems.md#bnstruct)|1.0.14 |__+1__ |1 | |
|[countland](problems.md#countland)|0.1.1 |__+1__ | | |
|[DiagrammeR](problems.md#diagrammer)|1.0.10 |__+1__ | |1 |
|[EGAnet](problems.md#eganet)|2.0.3 |__+1__ | |1 |
|[ggnetwork](problems.md#ggnetwork)|0.5.12 |__+1__ | |1 |
|[inferCSN](problems.md#infercsn)|0.99.8 |__+1__ | |1 |
|[intergraph](problems.md#intergraph)|2.0-3 |__+1__ | | |
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17 changes: 14 additions & 3 deletions revdep/cran.md
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## revdepcheck results

We checked 17 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
We checked 1947 reverse dependencies (1945 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 17 new problems
* We failed to check 0 packages
* We saw 19 new problems
* We failed to check 3 packages

Issues with CRAN packages are summarised below.

### New problems
(This reports the first line of each new failure)

* bnstruct
checking tests ... ERROR

* countland
checking tests ... ERROR

* DiagrammeR
checking tests ... ERROR

* EGAnet
checking examples ... ERROR

* ggnetwork
checking tests ... ERROR

Expand Down Expand Up @@ -64,3 +70,8 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking tests ... ERROR

### Failed to check

* bsts (NA)
* Seurat (NA)
* streamDAG (NA)
297 changes: 296 additions & 1 deletion revdep/failures.md
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*Wow, no problems at all. :)*
# bsts

<details>

* Version: 0.9.9
* GitHub: NA
* Source code: https://github.com/cran/bsts
* Date/Publication: 2022-11-07 08:50:11 UTC
* Number of recursive dependencies: 37

Run `revdepcheck::cloud_details(, "bsts")` for more info

</details>

## In both

* checking whether package ‘bsts’ can be installed ... ERROR
```
Installation failed.
See ‘/tmp/workdir/bsts/new/bsts.Rcheck/00install.out’ for details.
```

## Installation

### Devel

```
* installing *source* package ‘bsts’ ...
** package ‘bsts’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
using C++11
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c aggregate_time_series.cc -o aggregate_time_series.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c bsts.cc -o bsts.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c bsts_init.cc -o bsts_init.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c create_dynamic_intercept_state_model.cpp -o create_dynamic_intercept_state_model.o
...
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate expects 5 arguments, 3 provided
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&)’
106 | class ConditionallyIndependentSharedLocalLevelPosteriorSampler
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&)’
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: create_shared_state_model.o] Error 1
ERROR: compilation failed for package ‘bsts’
* removing ‘/tmp/workdir/bsts/new/bsts.Rcheck/bsts’


```
### CRAN

```
* installing *source* package ‘bsts’ ...
** package ‘bsts’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
using C++11
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c aggregate_time_series.cc -o aggregate_time_series.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c bsts.cc -o bsts.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c bsts_init.cc -o bsts_init.o
g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I`/opt/R/4.3.1/lib/R/bin/Rscript -e "cat(system.file(package='Boom'))"`/include -DADD_ -DR_NO_REMAP -DRLANGUAGE -I'/opt/R/4.3.1/lib/R/site-library/Boom/include' -I/usr/local/include -fpic -g -O2 -c create_dynamic_intercept_state_model.cpp -o create_dynamic_intercept_state_model.o
...
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:125:5: note: candidate expects 5 arguments, 3 provided
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(const BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&)’
106 | class ConditionallyIndependentSharedLocalLevelPosteriorSampler
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate: ‘BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler::ConditionallyIndependentSharedLocalLevelPosteriorSampler(BOOM::ConditionallyIndependentSharedLocalLevelPosteriorSampler&&)’
/opt/R/4.3.1/lib/R/site-library/Boom/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp:106:9: note: candidate expects 1 argument, 3 provided
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: create_shared_state_model.o] Error 1
ERROR: compilation failed for package ‘bsts’
* removing ‘/tmp/workdir/bsts/old/bsts.Rcheck/bsts’


```
# MODIStsp

<details>

* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/MODIStsp
* Number of recursive dependencies: 164

Run `revdepcheck::cloud_details(, "MODIStsp")` for more info

</details>

## Error before installation

### Devel

```






```
### CRAN

```






```
# sen2r

<details>

* Version: NA
* GitHub: NA
* Source code: https://github.com/cran/sen2r
* Number of recursive dependencies: 161

Run `revdepcheck::cloud_details(, "sen2r")` for more info

</details>

## Error before installation

### Devel

```






```
### CRAN

```






```
# Seurat

<details>

* Version: 5.0.1
* GitHub: https://github.com/satijalab/seurat
* Source code: https://github.com/cran/Seurat
* Date/Publication: 2023-11-17 23:10:06 UTC
* Number of recursive dependencies: 264

Run `revdepcheck::cloud_details(, "Seurat")` for more info

</details>

## Error before installation

### Devel

```
* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘Seurat/DESCRIPTION’ ... OK
...
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
Running ‘testthat.R’
* DONE
Status: 3 NOTEs





```
### CRAN

```
* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘Seurat/DESCRIPTION’ ... OK
...
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
Running ‘testthat.R’
* DONE
Status: 3 NOTEs





```
# streamDAG

<details>

* Version: 1.5
* GitHub: NA
* Source code: https://github.com/cran/streamDAG
* Date/Publication: 2023-10-06 18:50:02 UTC
* Number of recursive dependencies: 133

Run `revdepcheck::cloud_details(, "streamDAG")` for more info

</details>

## Error before installation

### Devel

```
* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
* this is package ‘streamDAG’ version ‘1.5’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: ‘asbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR





```
### CRAN

```
* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
* this is package ‘streamDAG’ version ‘1.5’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: ‘asbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR





```
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