GuangchuangYu
commented
3 years ago Rscript -e 'library(methods); devtools::document()'
ℹ Updating shinyTempSignal documentation
ℹ Loading shinyTempSignal
Writing NAMESPACE
Writing NAMESPACE
Warning messages:
1: replacing previous import ‘ape::rotate’ by ‘ggpubr::rotate’ when loading ‘shinyTempSignal’
2: replacing previous import ‘ggpubr::rotate’ by ‘ggtree::rotate’ when loading ‘shinyTempSignal’
3: replacing previous import ‘shiny::runExample’ by ‘shinyjs::runExample’ when loading ‘shinyTempSignal’
cd ..;\
R CMD build shinyTempSignal
* checking for file ‘shinyTempSignal/DESCRIPTION’ ... OK
* preparing ‘shinyTempSignal’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘shinyTempSignal_0.0.0.9000.tar.gz’
cd ..;\
Rscript -e 'rcmdcheck::rcmdcheck("shinyTempSignal_0.0.0.9000.tar.gz")'
── R CMD check ─────────────────────────────────────────────────────────────────
─ using log directory ‘/tmp/RtmpHxYFdx/file17fca8d86e1/shinyTempSignal.Rcheck’
─ using R version 4.1.1 (2021-08-10)
─ using platform: x86_64-pc-linux-gnu (64-bit)
─ using session charset: UTF-8
✔ checking for file ‘shinyTempSignal/DESCRIPTION’ ...
─ this is package ‘shinyTempSignal’ version ‘0.0.0.9000’
─ package encoding: UTF-8
✔ checking package namespace information ...
✔ checking package dependencies (1.2s)
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for executable files ...
✔ checking for hidden files and directories
✔ checking for portable file names
✔ checking for sufficient/correct file permissions
W checking whether package ‘shinyTempSignal’ can be installed (4.3s)
Found the following significant warnings:
Warning: replacing previous import ‘ape::rotate’ by ‘ggpubr::rotate’ when loading ‘shinyTempSignal’
Warning: replacing previous import ‘ggpubr::rotate’ by ‘ggtree::rotate’ when loading ‘shinyTempSignal’
Warning: replacing previous import ‘shiny::runExample’ by ‘shinyjs::runExample’ when loading ‘shinyTempSignal’
See ‘/tmp/RtmpHxYFdx/file17fca8d86e1/shinyTempSignal.Rcheck/00install.out’ for details.
✔ checking installed package size ...
✔ checking package directory
W checking DESCRIPTION meta-information ...
Invalid license file pointers: LICENSE
✔ 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 (1.1s)
✔ checking whether the package can be loaded with stated dependencies (1s)
✔ checking whether the package can be unloaded cleanly (1s)
✔ checking whether the namespace can be loaded with stated dependencies (1s)
✔ checking whether the namespace can be unloaded cleanly (1.1s)
✔ checking loading without being on the library search path (1.1s)
N checking dependencies in R code (1s)
Namespaces in Imports field not imported from:
‘DT’ ‘attempt’ ‘glue’ ‘htmltools’ ‘processx’ ‘thinkr’
All declared Imports should be used.
✔ checking S3 generic/method consistency (1.7s)
✔ checking replacement functions (1s)
✔ checking foreign function calls (1s)
N checking R code for possible problems (2.8s)
app_server: no visible binding for global variable ‘Group’
app_server: no visible global function definition for ‘cor’
app_server: no visible global function definition for ‘lm’
Undefined global functions or variables:
Group cor lm
Consider adding
importFrom("stats", "cor", "lm")
to your NAMESPACE file.
✔ checking Rd files ...
✔ checking Rd metadata ...
✔ checking Rd cross-references ...
✔ checking for missing documentation entries (1s)
✔ checking for code/documentation mismatches (3s)
✔ checking Rd \usage sections (1.7s)
✔ checking Rd contents ...
✔ checking for unstated dependencies in examples ...
─ checking examples ... NONE
✔ checking for unstated dependencies in ‘tests’ ...
─ checking tests ...
✔ Running ‘testthat.R’ (1.2s)
✔ checking PDF version of manual (3.3s)
See
‘/tmp/RtmpHxYFdx/file17fca8d86e1/shinyTempSignal.Rcheck/00check.log’
for details.
── R CMD check results ───────────────────────── shinyTempSignal 0.0.0.9000 ────
Duration: 29.6s
❯ checking whether package ‘shinyTempSignal’ can be installed ... WARNING
See below...
❯ checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
❯ checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘DT’ ‘attempt’ ‘glue’ ‘htmltools’ ‘processx’ ‘thinkr’
All declared Imports should be used.
❯ checking R code for possible problems ... NOTE
app_server: no visible binding for global variable ‘Group’
app_server: no visible global function definition for ‘cor’
app_server: no visible global function definition for ‘lm’
Undefined global functions or variables:
Group cor lm
Consider adding
importFrom("stats", "cor", "lm")
to your NAMESPACE file.
0 errors ✔ | 2 warnings ✖ | 2 notes ✖
cd ..;\
rm -f -r shinyTempSignal.Rcheck/接下来fix R check。要求跑R check不能报任何问题。
余老师您好： 这个R包是用gelom进行打包，fill_desc的信息还没有填，其他的照冬瓜画瓢写下来了（参考了老师的MicrobiomeProfiler），可能会有所纰漏，我用自己的电脑试过了，在github下载自己的包，可以用。