CRAN submission

[alexzhu1998]

Need #4 to continue.

[alexzhu1998]

R CMD check --as-cran RaspberryPiR

[alexzhu1998]

• using log directory ‘/home/pi/Honours/RaspberryPiR.Rcheck’
• using R version 4.0.3 (2020-10-10)
• using platform: armv7l-unknown-linux-gnueabihf (32-bit)
• using session charset: UTF-8
• using option ‘--as-cran’
• checking for file ‘RaspberryPiR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RaspberryPiR’ version ‘1.0’
• checking CRAN incoming feasibility ... NOTE Maintainer: ‘Alex Zhu alexjhzhu@gmail.com’

New submission

The Title field should be in title case. Current version is: ‘R package for collecting and analysing streaming data on Raspberry Pi’ In title case that is: ‘R Package for Collecting and Analysing Streaming Data on Raspberry Pi’

The Date field is over a month old.

The build time stamp is missing.

• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... WARNING Subdirectory ‘RaspberryPiR/src’ contains apparent object files/libraries RaspberryPiR.so RcppExports.o shmem_user.o testingSensor.o wiringPiLib.o Object files/libraries should not be included in a source package.

In addition to the above warning(s), found the following notes:

Found the following apparent object files/libraries: src/utils/DHT11.o src/utils/MQ2.o src/utils/PhotoRes.o src/utils/RPiCam.o src/utils/sensors_control.o src/utils/shared_memory.o Object files/libraries should not be included in a source package.

• checking if there is a namespace ... OK
• checking for executable files ... WARNING Found the following executable file: src/RaspberryPiR.so Source packages should not contain undeclared executable files. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
• checking for hidden files and directories ... NOTE Found the following hidden files and directories: .gitignore .git These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about .git

• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘RaspberryPiR’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking DESCRIPTION meta-information ... NOTE Checking should be performed on sources prepared by ‘R CMD build’.
• checking top-level files ... NOTE Files ‘README.md’ or ‘NEWS.md’ cannot be checked without ‘pandoc’ being installed. Non-standard files/directories found at top level: ‘compile’ ‘License.md’ ‘pictures’ ‘RaspberryPiR.Rproj’ ‘Read-and-delete-me’ ‘README.Rmd’
• checking for left-over files ... OK
• checking index information ... WARNING Empty or missing file ‘demo/00Index’. See sections ‘The INDEX file’ and ‘Package subdirectories’ in the ‘Writing R Extensions’ manual.
• checking package subdirectories ... WARNING Found the following directory with the name of a version control directory: ./.git These should not be in a package tarball.
• 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 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 ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... WARNING Undocumented code objects: ‘DHT11_freeMemory’ ‘DHT11_readMemory’ ‘DHT11_writeMemory’ ‘listActive’ ‘LL_digitalRead’ ‘LL_digitalWrite’ ‘LL_micros’ ‘LL_millis’ ‘LL_pinMode’ ‘LL_pullUpDnControl’ ‘LL_wiringPiSetup’ ‘PhotoRes_freeMemory’ ‘PhotoRes_readMemory’ ‘PhotoRes_writeMemory’ ‘simpleCapture’ ‘testing_freeMemory’ ‘testing_readMemory’ ‘testing_writeMemory’ ‘testingDHT’ ‘testingMQ2’ ‘testingPhotoRes’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... NOTE Found the following Makefile(s) without a final LF: src/Makevars Some ‘make’ programs ignore lines not ending in LF.
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIBOPENMP*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... WARNING File ‘RaspberryPiR/libs/RaspberryPiR.so’: Found ‘exit’, possibly from ‘exit’ (C) Object: ‘utils/shared_memory.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

• checking examples ... OK
• checking PDF version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE Status: 7 WARNINGs, 5 NOTEs

[alexzhu1998]

To generate documentations: roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))

[alexzhu1998]

checking R code for possible problems ... NOTE DHT11_freeMemory: no visible binding for global variable ‘_RaspberryPiR_DHT11_freeMemory’ DHT11_readMemory: no visible binding for global variable ‘_RaspberryPiR_DHT11_readMemory’ DHT11_writeMemory: no visible binding for global variable ‘_RaspberryPiR_DHT11_writeMemory’ LL_digitalRead: no visible binding for global variable ‘_RaspberryPiR_LL_digitalRead’ LL_digitalWrite: no visible binding for global variable ‘_RaspberryPiR_LL_digitalWrite’ LL_micros: no visible binding for global variable ‘_RaspberryPiR_LL_micros’ LL_millis: no visible binding for global variable ‘_RaspberryPiR_LL_millis’ LL_pinMode: no visible binding for global variable ‘_RaspberryPiR_LL_pinMode’ LL_pullUpDnControl: no visible binding for global variable ‘_RaspberryPiR_LL_pullUpDnControl’ LL_wiringPiSetup: no visible binding for global variable ‘_RaspberryPiR_LL_wiringPiSetup’ PhotoRes_freeMemory: no visible binding for global variable ‘_RaspberryPiR_PhotoRes_freeMemory’ PhotoRes_readMemory: no visible binding for global variable ‘_RaspberryPiR_PhotoRes_readMemory’ PhotoRes_writeMemory: no visible binding for global variable ‘_RaspberryPiR_PhotoRes_writeMemory’ simpleCapture: no visible binding for global variable ‘_RaspberryPiR_simpleCapture’ testing_freeMemory: no visible binding for global variable ‘_RaspberryPiR_testing_freeMemory’ testing_readMemory: no visible binding for global variable ‘_RaspberryPiR_testing_readMemory’ testing_writeMemory: no visible binding for global variable ‘_RaspberryPiR_testing_writeMemory’ testingDHT: no visible binding for global variable ‘_RaspberryPiR_testingDHT’ testingMQ2: no visible binding for global variable ‘_RaspberryPiR_testingMQ2’ testingPhotoRes: no visible binding for global variable ‘_RaspberryPiR_testingPhotoRes’ Undefined global functions or variables: _RaspberryPiR_DHT11_freeMemory _RaspberryPiR_DHT11_readMemory _RaspberryPiR_DHT11_writeMemory _RaspberryPiR_LL_digitalRead _RaspberryPiR_LL_digitalWrite _RaspberryPiR_LL_micros _RaspberryPiR_LL_millis _RaspberryPiR_LL_pinMode _RaspberryPiR_LL_pullUpDnControl _RaspberryPiR_LL_wiringPiSetup _RaspberryPiR_PhotoRes_freeMemory _RaspberryPiR_PhotoRes_readMemory _RaspberryPiR_PhotoRes_writeMemory _RaspberryPiR_simpleCapture _RaspberryPiR_testing_freeMemory _RaspberryPiR_testing_readMemory _RaspberryPiR_testing_writeMemory _RaspberryPiR_testingDHT _RaspberryPiR_testingMQ2 _RaspberryPiR_testingPhotoRes

Fixed with a pre-defined global variables function

[alexzhu1998]

devtools::check("RaspberryPiR")

[alexzhu1998]

❯ checking compiled code ... NOTE File ‘RaspberryPiR/libs/RaspberryPiR.so’: Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

[alexzhu1998]

Added the following file src/init.cpp to fix the above NOTE.

// Generated by the rstantools package

include <R.h>

include

include <R_ext/Rdynload.h>

include <R_ext/Visibility.h>

include

void attribute_visible R_init_RaspberryPiR(DllInfo *dll) { // next line is necessary to avoid a NOTE from R CMD check R_registerRoutines(dll, NULL, NULL, NULL, NULL); R_useDynamicSymbols(dll, TRUE); // necessary for .onLoad() to work }