Anirban166
commented
4 years ago Resolved by creating a fresh RStudio session, installing Rlang and purrr (packages which showed warnings/errors previously) and thereby running RCMD devtools::check(): (successfully)
Log:
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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> install.packages("rlang")
Installing package into ‘C:/Users/HP/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/rlang_0.4.6.zip'
Content type 'application/zip' length 1130356 bytes (1.1 MB)
downloaded 1.1 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘rlang’
Warning in install.packages :
problem copying C:\Users\HP\Documents\R\win-library\3.6\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\HP\Documents\R\win-library\3.6\rlang\libs\x64\rlang.dll: Permission denied
Warning in install.packages :
restored ‘rlang’
The downloaded binary packages are in
C:\Users\HP\AppData\Local\Temp\RtmpKCiReW\downloaded_packages
> install.packages("purrr")
Installing package into ‘C:/Users/HP/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/purrr_0.3.4.zip'
Content type 'application/zip' length 430172 bytes (420 KB)
downloaded 420 KB
package ‘purrr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\HP\AppData\Local\Temp\RtmpKCiReW\downloaded_packages
> library(devtools)
Loading required package: usethis
Warning messages:
1: package ‘devtools’ was built under R version 3.6.3
2: package ‘usethis’ was built under R version 3.6.3
> load_all()
Loading testComplexity
Attaching package: ‘testthat’
The following object is masked from ‘package:devtools’:
test_file
Warning message:
package ‘testthat’ was built under R version 3.6.3
> check()
Updating testComplexity documentation
Updating roxygen version in F:\testComplexity/DESCRIPTION
Loading testComplexity
Writing NAMESPACE
Writing NAMESPACE
Writing asymptoticMemoryUsage.Rd
Writing plotTimings.Rd
-- Building -------------------------------------------------- testComplexity --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
√ checking for file 'F:\testComplexity/DESCRIPTION' (434ms)
- preparing 'testComplexity': (1.4s)
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts (955ms)
- checking for empty or unneeded directories
- building 'testComplexity_0.0.0.9000.tar.gz'
-- Checking -------------------------------------------------- testComplexity --
Setting env vars:
* _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
* _R_CHECK_CRAN_INCOMING_ : FALSE
* _R_CHECK_FORCE_SUGGESTS_ : FALSE
* NOT_CRAN : true
-- R CMD check -------------------------------------------------------------------------------------------
- using log directory 'C:/Users/HP/AppData/Local/Temp/RtmpKCiReW/testComplexity.Rcheck' (538ms)
- using R version 3.6.1 (2019-07-05)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- using options '--no-manual --as-cran'
√ checking for file 'testComplexity/DESCRIPTION' ...
- this is package 'testComplexity' version '0.0.0.9000'
- package encoding: UTF-8
√ checking package namespace information
√ checking package dependencies (3.1s)
√ checking if this is a source package ...
√ checking if there is a namespace
√ checking for .dll and .exe files
√ checking for hidden files and directories ...
√ checking for portable file names ...
√ checking serialization versions
√ checking whether package 'testComplexity' can be installed (11.5s)
√ checking package directory (524ms)
√ checking for future file timestamps (1.5s)
√ checking DESCRIPTION meta-information (808ms)
N checking top-level files
Non-standard files/directories found at top level:
'Images' '_config.yml'
√ 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 (956ms)
√ checking whether the package can be loaded with stated dependencies (832ms)
√ checking whether the package can be unloaded cleanly (1.1s)
√ checking whether the namespace can be loaded with stated dependencies (974ms)
√ checking whether the namespace can be unloaded cleanly (1s)
√ checking loading without being on the library search path (980ms)
√ checking dependencies in R code (870ms)
√ checking S3 generic/method consistency (1.4s)
√ checking replacement functions (758ms)
√ checking foreign function calls (860ms)
N checking R code for possible problems (6s)
asymptoticTimeComplexityClass: no visible global function definition
for 'glm'
plotTimings: no visible binding for global variable 'Data set sizes'
plotTimings: no visible binding for global variable 'Timings'
Undefined global functions or variables:
Data set sizes Timings glm
Consider adding
importFrom("stats", "glm")
to your NAMESPACE file.
√ checking Rd files (336ms)
√ checking Rd metadata ...
√ checking Rd line widths ...
√ checking Rd cross-references (533ms)
√ checking for missing documentation entries (957ms)
√ checking for code/documentation mismatches (2.4s)
√ checking Rd \usage sections (1.8s)
√ checking Rd contents ...
√ checking for unstated dependencies in examples ...
- checking examples ... NONE
√ checking for unstated dependencies in 'tests' ...
- checking tests ...
√ Running 'testthat.R' (4.8s)
See
'C:/Users/HP/AppData/Local/Temp/RtmpKCiReW/testComplexity.Rcheck/00check.log'
for details.
-- R CMD check results ---------------------------------------------------- testComplexity 0.0.0.9000 ----
Duration: 46.7s
> checking top-level files ... NOTE
Non-standard files/directories found at top level:
'Images' '_config.yml'
> checking R code for possible problems ... NOTE
asymptoticTimeComplexityClass: no visible global function definition
for 'glm'
plotTimings: no visible binding for global variable 'Data set sizes'
plotTimings: no visible binding for global variable 'Timings'
Undefined global functions or variables:
Data set sizes Timings glm
Consider adding
importFrom("stats", "glm")
to your NAMESPACE file.
0 errors √ | 0 warnings √ | 2 notes x
> Kept for future reference.
while pushing
asymptoticMemoryUsagefrom Memtest branch (It does not affect this issue and build will work/deploy successfully on Travis, since this is a local case) I checked locally in my RStudio session for any issues:The last two lines show the error that threw up on the basis of package purrr, which seemed to be a rather common issue (based on package dependencies, and not isolated to that package) which could be resolved by updating/installing the package, so I tried that:
As you can see, neither worked.
So I resorted to remove it manually from the package window. Then, to make sure I install a version equal to or above 0.3.3 (as specified in the namespace compilation error), I went to their CRAN page, copied the latest source download link (0.3.4) and accordingly installed that source version:
Here is the result:
As one can see, there were some warnings midway regarding rlang. This again, leads to: