Code in test and vignette are annotated to shorten the compile time.
The test code is for development which can be annotated with no side effect.
And some plot code in vignette are for the same type of plot, which have also been annotated.
In my pc, the devtools::check() time is
Time difference of 14.72798 mins
Details of check log
r$> my_check()
══ Documenting ════════════════════════════════════════════════════════════════════════════
ℹ Updating ChIPseeker documentation
ℹ Loading ChIPseeker
ChIPseeker v1.39.0
If you use ChIPseeker in published research, please cite:
Qianwen Wang, Ming Li, Tianzhi Wu, Li Zhan, Lin Li, Meijun Chen, Wenqin Xie, Zijing Xie, Erqiang Hu, Shuangbin Xu, Guangchuang Yu. Exploring epigenomic datasets by ChIPseeker. Current Protocols 2022, 2(10): e585
══ Building ═══════════════════════════════════════════════════════════════════════════════
Setting env vars:
• CFLAGS : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
── R CMD build ────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/Users/mingli/ChIPseeker/DESCRIPTION’ ...
─ preparing ‘ChIPseeker’:
✔ checking DESCRIPTION meta-information ...
─ installing the package to build vignettes
✔ creating vignettes (5m 34s)
─ 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 ‘ChIPseeker_1.39.0.tar.gz’ (1.8s)
══ Checking ═══════════════════════════════════════════════════════════════════════════════
Setting env vars:
• _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
• _R_CHECK_CRAN_INCOMING_ : FALSE
• _R_CHECK_FORCE_SUGGESTS_ : FALSE
• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
• NOT_CRAN : true
── R CMD check ────────────────────────────────────────────────────────────────────────────
─ using log directory ‘/private/var/folders/87/15j0wd2x1072h_xnx5fgmds40000gn/T/Rtmps1xsQn/file1058d3bb9dc85/ChIPseeker.Rcheck’
─ using R version 4.2.3 (2023-03-15)
─ using platform: x86_64-apple-darwin17.0 (64-bit)
─ using session charset: UTF-8
─ using options ‘--no-manual --as-cran’ (342ms)
✔ checking for file ‘ChIPseeker/DESCRIPTION’
─ checking extension type ... Package
─ this is package ‘ChIPseeker’ version ‘1.39.0’
─ package encoding: UTF-8
✔ checking package namespace information ...
N checking package dependencies (17.8s)
Packages suggested but not available for checking:
'ggimage', 'ggupset', 'ggVennDiagram'
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for executable files (687ms)
✔ checking for hidden files and directories
✔ checking for portable file names ...
✔ checking for sufficient/correct file permissions ...
─ checking whether package ‘ChIPseeker’ can be installed ... [26s/27s] OK (27.1s)
N checking installed package size ...
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 4.5Mb
doc 1.8Mb
✔ checking package directory ...
✔ checking for future file timestamps (740ms)
✔ checking ‘build’ directory ...
✔ checking DESCRIPTION meta-information ...
✔ checking top-level files ...
✔ checking for left-over files
✔ checking index information ...
✔ checking package subdirectories ...
✔ checking R files for non-ASCII characters ...
✔ checking R files for syntax errors ...
✔ checking whether the package can be loaded (7.9s)
✔ checking whether the package can be loaded with stated dependencies (7.5s)
✔ checking whether the package can be unloaded cleanly (7.4s)
✔ checking whether the namespace can be loaded with stated dependencies (7.4s)
✔ checking whether the namespace can be unloaded cleanly (7.7s)
✔ checking dependencies in R code (7.9s)
✔ checking S3 generic/method consistency (9.2s)
✔ checking replacement functions (7.3s)
✔ checking foreign function calls (8s)
─ checking R code for possible problems ... [37s/37s] OK (37.4s)
✔ checking Rd files (351ms)
✔ checking Rd metadata ...
N checking Rd line widths ...
Rd file 'plotAnnoPie-methods.Rd':
\usage lines wider than 90 characters:
plotAnnoPie(x,ndigit=2,cex=0.9,col=NA,legend.position="rightside",pie3D=FALSE,radius=0.8,...)
These lines will be truncated in the PDF manual.
N checking Rd cross-references (9.9s)
Package unavailable to check Rd xrefs: ‘ggVennDiagram’
✔ checking for missing documentation entries (7.7s)
✔ checking for code/documentation mismatches (22.3s)
✔ checking Rd \usage sections (9.3s)
✔ checking Rd contents ...
✔ checking for unstated dependencies in examples ...
✔ checking contents of ‘data’ directory (4s)
✔ checking data for non-ASCII characters (2.1s)
✔ checking data for ASCII and uncompressed saves ...
✔ checking installed files from ‘inst/doc’ ...
✔ checking files in ‘vignettes’ ...
─ checking examples ... [11s/11s] OK (10.9s)
✔ checking for unstated dependencies in ‘tests’ ...
─ checking tests ...
✔ Running ‘testthat.R’ (9.1s)
✔ checking for unstated dependencies in vignettes ...
✔ checking package vignettes in ‘inst/doc’ ...
─ checking re-building of vignette outputs ... [302s/308s] OK (5m 8.3s)
✔ checking for non-standard things in the check directory
✔ checking for detritus in the temp directory
See
‘/private/var/folders/87/15j0wd2x1072h_xnx5fgmds40000gn/T/Rtmps1xsQn/file1058d3bb9dc85/ChIPseeker.Rcheck/00check.log’
for details.
Code in test and vignette are annotated to shorten the compile time. The test code is for development which can be annotated with no side effect. And some plot code in vignette are for the same type of plot, which have also been annotated. In my pc, the devtools::check() time is
Details of check log