metrumresearchgroup / mrgsolve

Simulate from ODE-based population PK/PD and QSP models in R
https://mrgsolve.org
GNU General Public License v2.0
131 stars 36 forks source link

Format warnings #1132

Closed kylebaron closed 11 months ago

kylebaron commented 1 year ago

Dear maintainer, Please see the problems shown on https://cran.r-project.org/web/checks/check_results_mrgsolve.html. Please correct before 2023-12-11 to safely retain your package on CRAN. Best, -k

NEWS.md will be fixed under separate PR.

Version: 1.1.1
Check: whether package can be installed
Result: WARN 
  Found the following significant warnings:
    LSODA.cpp:208:32: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
    LSODA.cpp:249:33: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:256:33: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:286:34: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:318:37: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘double’ [-Wformat=]
    LSODA.cpp:318:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
    LSODA.cpp:318:89: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘double’ [-Wformat=]
    LSODA.cpp:469:34: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:674:32: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:687:38: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
    LSODA.cpp:742:64: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mrgsolve.Rcheck/00install.out’ for details.
  * used C++ compiler: ‘g++-13 (Debian 13.2.0-5) 13.2.0’

Reproducible on winbilder

* using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck'
* using R Under development (unstable) (2023-11-26 r85638 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'mrgsolve/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mrgsolve' version '1.2.0.9000'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Kyle T Baron <kyleb@metrumrg.com>'

Version contains large components (1.2.0.9000)

Found the following (possibly) invalid file URIs:
  URI: ../../issues/43
    From: NEWS.md
  URI: ../../issues/31
    From: NEWS.md
  URI: ../../issues/29
    From: NEWS.md
  URI: ../../issues/39
    From: NEWS.md
  URI: ../../issues/34
    From: NEWS.md
  URI: ../../issues/9
    From: NEWS.md
  URI: ../../issues/16
    From: NEWS.md
  URI: ../../issues/19
    From: NEWS.md
  URI: ../../issues/23
    From: NEWS.md
  URI: ../../issues/13
    From: NEWS.md
  URI: ../../issues/15
    From: NEWS.md
  URI: ../../issues/11
    From: NEWS.md
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mrgsolve' can be installed ... WARNING
Found the following significant warnings:
  LSODA.cpp:208:32: warning: format '%i' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  LSODA.cpp:249:33: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:256:33: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:286:34: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:469:34: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:674:32: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:687:38: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  LSODA.cpp:742:64: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [15s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [21s] OK
  Running 'testthat.R' [21s]
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [19s] OK
* DONE
Status: 1 WARNING, 1 NOTE
kylebaron commented 1 year ago

Fixed with C-style casts

* using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck'
* using R Under development (unstable) (2023-11-26 r85638 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'mrgsolve/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mrgsolve' version '1.2.0.9000'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Kyle T Baron <kyleb@metrumrg.com>'

Version contains large components (1.2.0.9000)

Found the following (possibly) invalid file URIs:
  URI: ../../issues/43
    From: NEWS.md
  URI: ../../issues/31
    From: NEWS.md
  URI: ../../issues/29
    From: NEWS.md
  URI: ../../issues/39
    From: NEWS.md
  URI: ../../issues/34
    From: NEWS.md
  URI: ../../issues/9
    From: NEWS.md
  URI: ../../issues/16
    From: NEWS.md
  URI: ../../issues/19
    From: NEWS.md
  URI: ../../issues/23
    From: NEWS.md
  URI: ../../issues/13
    From: NEWS.md
  URI: ../../issues/15
    From: NEWS.md
  URI: ../../issues/11
    From: NEWS.md
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mrgsolve' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [14s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [21s] OK
  Running 'testthat.R' [21s]
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [19s] OK
* DONE
Status: 1 NOTE