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I am using windows and just updated to R 4.0.3 (with RStudio to 1.3.959) and ran the R check for one of my packages which uses Rcpp and RcppArmadillo and I got the following NOTE:
> checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/NIR_Workstation/Documents/GitHub/prospectr.Rcheck/prospectr/libs/i386/prospectr.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/NIR_Workstation/Documents/GitHub/prospectr.Rcheck/prospectr/libs/x64/prospectr.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
This NOTE is not output when I run the checks under R 4.0.2.
I tried to find out what was going in my package on without any success.
I have tried this as well (with R 4.0.3):
Rcpp::Rcpp.package.skeleton("aTest", example_code = TRUE)
rcmdcheck::rcmdcheck(error_on = "warning", check_dir = "check")
and I get the same type of NOTE as the one output for my package. Again for R 4.0.2 this NOTE is not output.
Any idea about this NOTE? or at least any suggestions about things I could try to find out what is going on?
Thanks in advance.
Updated question:
I wanted to conduct additional tests before updating my question.
Here they are:
I made a fresh install of R 4.0.3 in a couple of other windows machines
along with rtools, RStudio and the devtools package which are required to
run the example below (no pre-compiled objects hanging around). I managed to uses reprex() to reproduce the NOTE I got for another template package created with Rcpp.package.skeleton():
mdir <- "./my_dir"
dir.create(mdir)
setwd("./my_dir")
Rcpp::Rcpp.package.skeleton("anotherTest", example_code = TRUE)
#> Creating directories ...
#> Creating DESCRIPTION ...
#> Creating NAMESPACE ...
#> Creating Read-and-delete-me ...
#> Saving functions and data ...
#> Making help files ...
#> Done.
#> Further steps are described in './anotherTest/Read-and-delete-me'.
#>
#> Adding Rcpp settings
#> >> added Imports: Rcpp
#> >> added LinkingTo: Rcpp
#> >> added useDynLib directive to NAMESPACE
#> >> added importFrom(Rcpp, evalCpp) directive to NAMESPACE
#> >> added example src file using Rcpp attributes
#> >> added Rd file for rcpp_hello_world
#> >> compiled Rcpp attributes
devtools::check("./anotherTest")
#> -- Building ----------------------------------------------------- anotherTest --
#> Setting env vars:
#> * CFLAGS : -Wall -pedantic
#> * CXXFLAGS : -Wall -pedantic
#> * CXX11FLAGS: -Wall -pedantic
#> --------------------------------------------------------------------------------
#> checking for file 'C:\Users\raml\AppData\Local\Temp\RtmpqMz20b\reprex4cd8438440a2\my_dir\anotherTest/DESCRIPTION' ... v checking for file 'C:\Users\raml\AppData\Local\Temp\RtmpqMz20b\reprex4cd8438440a2\my_dir\anotherTest/DESCRIPTION' (612ms)
#> - preparing 'anotherTest':
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... v 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
#> - building 'anotherTest_1.0.tar.gz'
#>
#> -- Checking ----------------------------------------------------- anotherTest --
#> 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/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck' (453ms)
#> - using R version 4.0.3 (2020-10-10)
#> - using platform: x86_64-w64-mingw32 (64-bit)
#> - using session charset: ISO8859-1
#> - using options '--no-manual --as-cran'
#> checking for file 'anotherTest/DESCRIPTION' ... checking for file 'anotherTest/DESCRIPTION' ... v checking for file 'anotherTest/DESCRIPTION'
#> - checking extension type ... Package
#> - this is package 'anotherTest' version '1.0'
#> checking package namespace information ... checking package namespace information ... v checking package namespace information
#> checking package dependencies ... checking package dependencies ... v checking package dependencies (1.4s)
#> checking if this is a source package ... v checking if this is a source package
#> v checking if there is a namespace
#> checking for executable files ... checking for executable files ... v checking for executable files (9.7s)
#> checking for hidden files and directories ... v checking for hidden files and directories
#> checking for portable file names ... checking for portable file names ... v checking for portable file names
#> v checking serialization versions
#> checking whether package 'anotherTest' can be installed ... checking whether package 'anotherTest' can be installed ... v checking whether package 'anotherTest' can be installed (29.5s)
#> checking installed package size ... checking installed package size ... v checking installed package size
#> v checking package directory
#> checking for future file timestamps ... checking for future file timestamps ... v checking for future file timestamps
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... v checking DESCRIPTION meta-information (689ms)
#> v checking top-level files
#> v checking for left-over files
#> v checking index information
#> checking package subdirectories ... checking package subdirectories ... v checking package subdirectories
#> checking R files for non-ASCII characters ... checking R files for non-ASCII characters ... v checking R files for non-ASCII characters
#> checking R files for syntax errors ... checking R files for syntax errors ... v checking R files for syntax errors
#> - loading checks for arch 'i386'
#> checking whether the package can be loaded ... checking whether the package can be loaded ... ** checking whether the package can be loaded ... OK
#> checking whether the package can be loaded with stated dependencies ... checking whether the package can be loaded with stated dependencies ... ** checking whether the package can be loaded with stated dependencies ... OK
#> checking whether the package can be unloaded cleanly ... checking whether the package can be unloaded cleanly ... ** checking whether the package can be unloaded cleanly ... OK
#> checking whether the namespace can be loaded with stated dependencies ... checking whether the namespace can be loaded with stated dependencies ... ** checking whether the namespace can be loaded with stated dependencies ... OK
#> checking whether the namespace can be unloaded cleanly ... checking whether the namespace can be unloaded cleanly ... ** checking whether the namespace can be unloaded cleanly ... OK
#> checking loading without being on the library search path ... checking loading without being on the library search path ... ** checking loading without being on the library search path ... OK
#> - loading checks for arch 'x64'
#> checking whether the package can be loaded ... checking whether the package can be loaded ... ** checking whether the package can be loaded ... OK
#> checking whether the package can be loaded with stated dependencies ... checking whether the package can be loaded with stated dependencies ... ** checking whether the package can be loaded with stated dependencies ... OK
#> checking whether the package can be unloaded cleanly ... checking whether the package can be unloaded cleanly ... ** checking whether the package can be unloaded cleanly ... OK
#> checking whether the namespace can be loaded with stated dependencies ... checking whether the namespace can be loaded with stated dependencies ... ** checking whether the namespace can be loaded with stated dependencies ... OK
#> checking whether the namespace can be unloaded cleanly ... checking whether the namespace can be unloaded cleanly ... ** checking whether the namespace can be unloaded cleanly ... OK
#> checking loading without being on the library search path ... checking loading without being on the library search path ... ** checking loading without being on the library search path ... OK
#> checking dependencies in R code ... checking dependencies in R code ... v checking dependencies in R code (475ms)
#> checking S3 generic/method consistency ... checking S3 generic/method consistency ... v checking S3 generic/method consistency (959ms)
#> checking replacement functions ... checking replacement functions ... v checking replacement functions (568ms)
#> checking foreign function calls ... checking foreign function calls ... v checking foreign function calls (575ms)
#> checking R code for possible problems ... checking R code for possible problems ... v checking R code for possible problems (4s)
#> checking Rd files ... checking Rd files ... v checking Rd files (375ms)
#> checking Rd metadata ... checking Rd metadata ... v checking Rd metadata
#> checking Rd line widths ... checking Rd line widths ... v checking Rd line widths
#> checking Rd cross-references ... checking Rd cross-references ... v checking Rd cross-references (364ms)
#> checking for missing documentation entries ... checking for missing documentation entries ... v checking for missing documentation entries (562ms)
#> checking for code/documentation mismatches ... checking for code/documentation mismatches ... v checking for code/documentation mismatches (1.8s)
#> checking Rd \usage sections ... checking Rd \usage sections ... v checking Rd \usage sections (1.3s)
#> checking Rd contents ... checking Rd contents ... v checking Rd contents
#> checking for unstated dependencies in examples ... checking for unstated dependencies in examples ... v checking for unstated dependencies in examples
#> checking line endings in C/C++/Fortran sources/headers ... v checking line endings in C/C++/Fortran sources/headers
#> checking pragmas in C/C++ headers and code ... checking pragmas in C/C++ headers and code ... v checking pragmas in C/C++ headers and code
#> v checking compilation flags used
#> checking compiled code ... checking compiled code ... N checking compiled code (27.9s)
#> Note: information on .o files for i386 is not available
#> Note: information on .o files for x64 is not available
#> File 'C:/Users/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck/anotherTest/libs/i386/anotherTest.dll':
#> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
#> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
#> Found 'printf', possibly from 'printf' (C)
#> File 'C:/Users/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck/anotherTest/libs/x64/anotherTest.dll':
#> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
#> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
#> Found 'printf', possibly from 'printf' (C)
#>
#> Compiled code should not call entry points which might terminate R nor
#> write to stdout/stderr instead of to the console, nor use Fortran I/O
#> nor system RNGs. The detected symbols are linked into the code but
#> might come from libraries and not actually be called.
#>
#> See 'Writing portable packages' in the 'Writing R Extensions' manual.
#> checking examples ... - checking examples (360ms)
#> running examples for arch 'i386' ... running examples for arch 'i386' ... ** running examples for arch 'i386' ... OK
#> running examples for arch running examples for arch 'x64' ... running examples for arch 'x64' ... ** running examples for arch 'x64' ... OK
#> v checking for non-standard things in the check directory
#> v checking for detritus in the temp directory
#>
#> See
#> 'C:/Users/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck/00check.log'
#> for details.
#>
#>
#>
#> -- R CMD check results ------------------------------------ anotherTest 1.0 ----
#> Duration: 1m 31.9s
#>
#> > checking compiled code ... NOTE
#> Note: information on .o files for i386 is not available
#> Note: information on .o files for x64 is not available
#> File 'C:/Users/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck/anotherTest/libs/i386/anotherTest.dll':
#> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
#> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
#> Found 'printf', possibly from 'printf' (C)
#> File 'C:/Users/raml/AppData/Local/Temp/RtmpCM99SH/anotherTest.Rcheck/anotherTest/libs/x64/anotherTest.dll':
#> Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
#> Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
#> Found 'printf', possibly from 'printf' (C)
#>
#> Compiled code should not call entry points which might terminate R nor
#> write to stdout/stderr instead of to the console, nor use Fortran I/O
#> nor system RNGs. The detected symbols are linked into the code but
#> might come from libraries and not actually be called.
#>
#> See 'Writing portable packages' in the 'Writing R Extensions' manual.
#>
#> 0 errors v | 0 warnings v | 1 note x
Created on 2020-10-18 by the reprex package (v0.3.0)
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.0.3 (2020-10-10)
#> os Windows 7 x64 SP 1
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate German_Switzerland.1252
#> ctype German_Switzerland.1252
#> tz Europe/Berlin
#> date 2020-10-18
#>
#> - Packages -------------------------------------------------------------------
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
#> backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.3)
#> callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
#> cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.3)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.3)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.3)
#> devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.3)
#> digest 0.6.26 2020-10-17 [1] CRAN (R 4.0.3)
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.3)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.3)
#> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.3)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.3)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.3)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.3)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.3)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.3)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.3)
#> ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.3)
#> rcmdcheck 1.3.3 2019-05-07 [1] CRAN (R 4.0.3)
#> Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.3)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.3)
#> rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.3)
#> rmarkdown 2.4 2020-09-30 [1] CRAN (R 4.0.3)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.3)
#> rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.3)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.3)
#> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.3)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.3)
#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.3)
#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.3)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
#> xfun 0.18 2020-09-29 [1] CRAN (R 4.0.3)
#> xopen 1.0.0 2018-09-17 [1] CRAN (R 4.0.3)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.3)
#>
#> [1] C:/Program Files/R/R-4.0.3/library
In addition to the above tests, I ran the same code with:
R 4.0.3 with rtools35
R 4.0.2 with rtools40
R 4.0.3 in linux (x86_64-pc-linux-gnu (64-bit))
For these three tests the checks passed cleanly.
In summary, the problem only emerges with R 4.0.3 with rtools40. Is it right
to assume the issue comes from rtools40? If so, what are the implications for
CRAN checks/submissions?
Thanks
824
I have had the same questions for the past few months. I noticed the same issue (false positive calls of abort etc) with R-devel for Windows some months ago.
The issue is not specific to Rcpp. I can reproduce the NOTE for packages that contain only Fortran, or only C, or only C++. I run R CMD at the Windows command prompt with Rtools40 and R 4.0.3 in the PATH. The NOTE is currently appearing in the Bioconductor 3.12 checks for hundreds of packages, seemingly for any package that contains any Fortran, C or C++ source code. As you have noted, the NOTE appears only with Windows, R 4.0.3 or higher and Rtools40. The NOTE does not appear for the same packages under Linux or Mac or for older versions of R.
I submitted a package to CRAN two days ago and CRAN did not identify the NOTE as a problem, even though I see the NOTE when I run R CMD check on the same package. So I don't think it will cause you problems with a CRAN submission.
Update 30 March 2022
The issue was still present in R 4.1.3 and Rtools40v2, but is now gone in R 4.2.0alpha for Windows and Rtools42.
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