qile0317 / apackoftheclones Goto Github PK

See the pkgdown website articles - the legend is generated with the labels but the places where the fill is supposed to be is empty. This is not an issue locally. I did develop 1.1.0 in version 4.3.1 when 4.3.3 was already availiable on a ubuntu release stuck on the R version which might be a reason but probably not.

Hello, I really want to try your package. I have tried many ways, but I can't successfully install this package. May I ask what is the problem?
It will prompt me when I install it :
── R CMD build ────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpR7QS92/remotes661fc7a0fded1/Qile0317-APackOfTheClones-8548f41/DESCRIPTION’ (3.2s)
─ preparing ‘APackOfTheClones’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘APackOfTheClones_1.1.0.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

• installing source package ‘APackOfTheClones’ ...
  ** using staged installation
  ** libs
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c APOTCPlotHelpers.cpp -o APOTCPlotHelpers.o
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c AdjustAPOTCHelpers.cpp -o AdjustAPOTCHelpers.o
  In file included from AdjustAPOTCHelpers.cpp:4:
  ClusterList.h: In member function ‘std::vector<std::__cxx11::basic_string > ClusterList::getClonotypeVector()’:
  ClusterList.h:199:20: warning: structured bindings only available with ‘-std=c++17’ or ‘-std=gnu++17’
  199 | for (auto& [clonotype, index]: clonotypeIndex) {
  | ^
  g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CloneLinkHelpers.cpp -o CloneLinkHelpers.o
  In file included from CloneLinkHelpers.cpp:7:
  ClusterList.h: In member function ‘std::vector<std::__cxx11::basic_string > ClusterList::getClonotypeVector()’:
  ClusterList.h:199:20: warning: structured bindings only available with ‘-std=c++17’ or ‘-std=gnu++17’
  199 | for (auto& [clonotype, index]: clonotypeIndex) {
  | ^
  CloneLinkHelpers.cpp: In member function ‘std::vector LineLinkDataFrameFactory::createCppClusterListVector(Rcpp::List)’:
  CloneLinkHelpers.cpp:105:69: error: call of overloaded ‘ClusterList(Rcpp::Vector<19>::Proxy)’ is ambiguous
  105 | outputClusterListVector[i] = ClusterList(clusterLists[i]);
  | ^
  In file included from CloneLinkHelpers.cpp:7:
  ClusterList.h:28:5: note: candidate: ‘ClusterList::ClusterList(Rcpp::List)’
  28 | ClusterList(const Rcpp::List rClusterList) {
  | ^~~~~~~~~~~
  ClusterList.h:11:7: note: candidate: ‘ClusterList::ClusterList(const ClusterList&)’
  11 | class ClusterList {
  | ^~~~~~~~~~~
  ClusterList.h:11:7: note: candidate: ‘ClusterList::ClusterList(ClusterList&&)’
  make: *** [/usr/lib/R/etc/Makeconf:178: CloneLinkHelpers.o] Error 1
  ERROR: compilation failed for package ‘APackOfTheClones’
• removing ‘/usr/local/lib/R/site-library/APackOfTheClones’
  Warning: installation of package ‘/tmp/RtmpR7QS92/file661fc1fa20b38/APackOfTheClones_1.1.0.tar.gz’ had non-zero exit status

NOTES:

• checking package subdirectories ... NOTE
  Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
  APackOfTheClones
• checking examples ... [12s] NOTE
  Examples with CPU (user + system) or elapsed time > 5s
  user system elapsed
  clonal_expansion_plot 7.12 0.62 7.97
• checking for non-standard things in the check directory ... NOTE
  Found the following files/directories:
  ''NULL''
• checking for detritus in the temp directory ... NOTE
  Found the following files/directories:
  'lastMiKTeXException'

When I set the idents of a Seurat object to the annotated cell types, but the visualization results in vizAPOTC still show colors based on clusters, even though I modified idents, it does not take effect.

First release:

• usethis::use_cran_comments()
• Update (aspirational) install instructions in README
• Proofread Title: and Description:
• Check that all exported functions have @return and @examples
• Check that Authors@R: includes a copyright holder (role 'cph')
• Check licensing of included files
• Review https://github.com/DavisVaughan/extrachecks

Prepare for release:

• git pull
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• rhub::check_for_cran()
• rhub::check(platform = 'ubuntu-rchk')
• rhub::check_with_sanitizers()
• git push

Submit to CRAN:

• usethis::use_version('patch')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• git push
• usethis::use_github_release()
• usethis::use_dev_version()
• git push

Prepare for release:

• git pull
• Check current CRAN check results
• Polish NEWS
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• #3
• rhub::check_for_cran()
• rhub::check(platform = 'ubuntu-rchk')
• rhub::check_with_sanitizers()
• revdepcheck::revdep_check(num_workers = 4)
• Update cran-comments.md
• git push

Submit to CRAN:

• usethis::use_version('patch')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• git push
• usethis::use_github_release()
• usethis::use_dev_version()
• git push

Prepare for release:

• git pull
• Check current CRAN check results
• Check if any deprecation processes should be advanced, as described in Gradual deprecation
• Polish NEWS
• usethis::use_github_links()
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• revdepcheck::revdep_check(num_workers = 4)
• Update cran-comments.md
• git push
• Draft blog post

Submit to CRAN:

• usethis::use_version('minor')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• Add preemptive link to blog post in pkgdown news menu
• usethis::use_github_release()
• usethis::use_dev_version(push = TRUE)
• Finish blog post
• Tweet

Prepare for release:

• git pull
• Check current CRAN check results
• Check if any deprecation processes should be advanced, as described in Gradual deprecation
• Polish NEWS
• usethis::use_github_links()
• urlchecker::url_check()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• revdepcheck::revdep_check(num_workers = 4)
• Update cran-comments.md
• git push
• Draft blog post

Submit to CRAN:

• usethis::use_version('minor')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• Add preemptive link to blog post in pkgdown news menu
• usethis::use_github_release()
• usethis::use_dev_version(push = TRUE)
• Finish blog post
• Tweet