romainfrancois
commented
1 year ago Had to use this to make gcc 4.8 quiet about digest
cc @DavisVaughan you might have a better way.
Closed romainfrancois closed 1 year ago
romainfrancois
commented
1 year ago Had to use this to make gcc 4.8 quiet about digest
cc @DavisVaughan you might have a better way.
romainfrancois
commented
1 year ago revdep_check() gives:
## revdepcheck results
We checked 63 reverse dependencies (56 from CRAN + 7 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 1 new problems
* We failed to check 7 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* triangulr
checking C++ specification ... NOTE
### Failed to check
* epiworldR (NA)
* hilbert (NA)
* igraph (NA)
* RcppAlgos (NA)
* spatialsample (NA)
* svglite (NA)
* vdiffr (NA)I've sent a PR for the unique problem (related to https://www.tidyverse.org/blog/2023/03/cran-checks-compiled-code/#note-regarding-systemrequirements-c11):
(trying cloud_check() now because some of the "failed to check" are because fortran ...)
romainfrancois
commented
1 year ago cloud_check() gives :
> revdepcheck::cloud_summary()
ℹ Syncing results to revdep/cloud.noindex/f7cbb016-c063-4d43-91da-87b8911bdf0d
ℹ Comparing results
✔ ambient 1.0.2 ── E: 0 | W: 0 | N: 0
✔ archive 1.1.5 ── E: 0 | W: 0 | N: 0
✔ area 0.1.0 ── E: 0 | W: 0 | N: 0
✔ arrow 12.0.1 ── E: 0 | W: 0 | N: 2
✔ asciicast 2.3.0 ── E: 0 | W: 0 | N: 0
✔ bignum 0.3.2 ── E: 0 | W: 0 | N: 1
E BiocParallel NA ── E: 1/1 | W: 1/1 | N: 1/1
✔ clock 0.7.0 ── E: 0 | W: 0 | N: 1
✔ CMF 1.0.3 ── E: 0 | W: 0 | N: 0
E CytoML NA ── E: 1/1 | W: 1/1 | N: 1/1
✔ deformula 0.1.2 ── E: 0 | W: 0 | N: 0
✔ epiworldR 0.0.2 ── E: 0 | W: 0 | N: 1
E flowCore NA ── E: 1/1 | W: 1/1 | N: 1/1
E flowWorkspace NA ── E: 1/1 | W: 1/1 | N: 1/1
✔ gtfstools 1.2.0 ── E: 0 | W: 0 | N: 0
✔ haven 2.5.2 ── E: 0 | W: 0 | N: 3
✔ hilbert 0.2.1 ── E: 0 | W: 0 | N: 0
✔ httpgd 1.3.1 ── E: 0 | W: 0 | N: 1
✔ igraph 1.5.0 ── E: 0 | W: 0 | N: 1
✔ jinjar 0.3.0 ── E: 0 | W: 0 | N: 1
✔ literanger 0.0.1 ── E: 0 | W: 0 | N: 1
✔ lobstr 1.1.2 ── E: 0 | W: 0 | N: 0
✔ meltr 1.0.1 ── E: 0 | W: 0 | N: 1
✔ mice 3.16.0 ── E: 0 | W: 0 | N: 0
✔ mnmer 0.99.1 ── E: 0 | W: 0 | N: 0
✔ myTAI 0.9.3 ── E: 0 | W: 0 | N: 1
E NanoMethViz NA ── E: 1/1 | W: 1/1 | N: 1/1
E ncdfFlow NA ── E: 1/1 | W: 1/1 | N: 1/1
E openCyto NA ── E: 1/1 | W: 1/1 | N: 1/1
✔ particles 0.2.3 ── E: 0 | W: 0 | N: 0
✔ pkgbuild 1.4.2 ── E: 0 | W: 0 | N: 0
✔ pkgstats 0.1.1 ── E: 0 | W: 0 | N: 0
✔ rankUncertainty 1.0.2.0 ── E: 0 | W: 0 | N: 0
✔ RcppAlgos 2.7.2 ── E: 0 | W: 0 | N: 1
✔ readNSx 0.0.2 ── E: 0 | W: 0 | N: 0
✔ readr 2.1.4 ── E: 0 | W: 0 | N: 1
✔ readxl 1.4.2 ── E: 0 | W: 0 | N: 1
✔ rjsoncons 1.0.0 ── E: 0 | W: 0 | N: 1
✔ roxygen2 7.2.3 ── E: 0 | W: 0 | N: 0
✔ RSQLite 2.3.1 ── E: 0 | W: 0 | N: 1
✔ shinytest2 0.2.1 ── E: 0 | W: 0 | N: 0
✔ sift 0.1.0 ── E: 0 | W: 0 | N: 1
✔ SpatialKDE 0.8.2 ── E: 0 | W: 0 | N: 0
✔ supercells 0.9.1 ── E: 0 | W: 0 | N: 0
✔ svglite 2.1.1 ── E: 0 | W: 0 | N: 0
✔ systemfonts 1.0.4 ── E: 0 | W: 0 | N: 1
✔ tardis 0.1.4 ── E: 0 | W: 0 | N: 1
✔ textrecipes 1.0.3 ── E: 0 | W: 0 | N: 1
✔ textshaping 0.3.6 ── E: 0 | W: 0 | N: 0
✔ tidygraph 1.2.3 ── E: 0 | W: 0 | N: 0
✔ tidyr 1.3.0 ── E: 0 | W: 0 | N: 1
✔ timechange 0.2.0 ── E: 0 | W: 0 | N: 1
✔ tipitaka 0.1.2 ── E: 0 | W: 0 | N: 3
✔ transformr 0.1.4 ── E: 0 | W: 0 | N: 0
✔ triangulr 1.2.1 ── E: 0 | W: 0 | N: 0
✔ tweenr 2.0.2 ── E: 0 | W: 0 | N: 1
✔ twosamples 2.0.1 ── E: 0 | W: 0 | N: 0
✔ tzdb 0.4.0 ── E: 0 | W: 0 | N: 1
✔ vdiffr 1.0.5 ── E: 0 | W: 0 | N: 0
✔ vroom 1.6.3 ── E: 0 | W: 0 | N: 2
✔ websocket 1.4.1 ── E: 0 | W: 0 | N: 2 These are all bioc packages:
E BiocParallel NA ── E: 1/1 | W: 1/1 | N: 1/1 Have not been able to check BiocParallel, because various latex problems.
E CytoML NA ── E: 1/1 | W: 1/1 | N: 1/1Getting this: this is unrelated to this update.
ld: library not found for -lcrypto
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CytoML.so] Error 1
ERROR: compilation failed for package ‘CytoML’E flowCore NA ── E: 1/1 | W: 1/1 | N: 1/1 I'm getting a lot of Rcpp/RcppArmadillo noise, and the dev version of the 📦 does not seem to be using cpp11 anymore: https://github.com/RGLab/flowCore/blob/master/DESCRIPTION
E flowWorkspace NA ── E: 1/1 | W: 1/1 | N: 1/1 This gnerates a few warnings related to external pointers:
-fdiagnostics-color=always -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:4:
In file included from ./flowWorkspace_types.h:5:
In file included from /Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/declarations.hpp:8:
In file included from /Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11.hpp:10:
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete obj;
^
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Users/romainfrancois/.R/library/4.3/cpp11/include' -I'/Users/romainfrancois/.R/library/4.3/BH/include' -I'/Users/romainfrancois/.R/library/4.3/RProtoBufLib/include' -I'/Users/romainfrancois/.R/library/4.3/cytolib/include' -I'/Users/romainfrancois/.R/library/4.3/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -Wall -O3 -Wall -pedantic -fdiagnostics-color=always -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from cytoframeAPI.cpp:1:
In file included from /Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11.hpp:10:
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete obj;
^
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Users/romainfrancois/.R/library/4.3/cpp11/include' -I'/Users/romainfrancois/.R/library/4.3/BH/include' -I'/Users/romainfrancois/.R/library/4.3/RProtoBufLib/include' -I'/Users/romainfrancois/.R/library/4.3/cytolib/include' -I'/Users/romainfrancois/.R/library/4.3/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -Wall -O3 -Wall -pedantic -fdiagnostics-color=always -c cytosetAPI.cpp -o cytosetAPI.o
In file included from cytosetAPI.cpp:2:
In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:10:
In file included from /Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11.hpp:10:
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
delete obj;
^
/Users/romainfrancois/.R/library/4.3/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter<cytolib::CytoFrameView>' requested here
template <typename T, void Deleter(T*) = default_deleter<T>>
^
1 warning generated.but also:
ld: library not found for -lcrypto
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [flowWorkspace.so] Error 1
ERROR: compilation failed for package ‘flowWorkspace’I have not ben able to sort that out yet.
E NanoMethViz NA ── E: 1/1 | W: 1/1 | N: 1/1Locally, this gives:
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plot_region'
‘heatmap_subsample’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking package dependencies ... NOTE
Imports includes 34 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
❯ checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
R 2.1Mb
doc 5.4Mb
0 errors ✔ | 2 warnings ✖ | 2 notes ✖
Error: R CMD check found WARNINGs
Execution halted
Exited with status 1.so I think it's fine.
E ncdfFlow NA ── E: 1/1 | W: 1/1 | N: 1/1dev version not using cpp11, but rather Rcpp / RcppArmadillo / BH ... and also getting the ld: library not found for -lcrypto thing ...
E openCyto NA ── E: 1/1 | W: 1/1 | N: 1/1 this does not use cpp11
Prepare for release:
git pullurlchecker::url_check()devtools::check(remote = TRUE, manual = TRUE)devtools::check_win_devel()rhub::check_for_cran()revdepcheck::cloud_check(): see some details https://github.com/r-lib/cpp11/issues/321#issuecomment-1610908662 but I think it's fine.cran-comments.mdgit pushSubmit to CRAN:
usethis::use_version('patch')devtools::submit_cran()Wait for CRAN...
git pushusethis::use_github_release()usethis::use_dev_version()git push