|
beachmat.Rcheck/tests_i386/testthat.Rout.fail
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(beachmat)
> test_check("beachmat")
-- Building ------------------------------------------------------- beachtest --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
v checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg/DESCRIPTION' (829ms)
- preparing 'beachtest': (4.6s)
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 'beachtest_1.0.0.tar.gz'
-- Checking ------------------------------------------------------- beachtest --
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/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpCWQWpG/beachtest.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'beachtest/DESCRIPTION' ... OK
* this is package 'beachtest' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'beachtest' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Registration problems:
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating 'paste0("get_class_", mode)' during check gives error
'cannot coerce type 'closure' to vector of type 'character'':
.Call(paste0("get_class_", mode), test.mat, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating 'paste0("get_row_", mode, "_to_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("get_row_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating 'paste0("get_col_", mode, "_to_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("get_col_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0("set_row_", mode, "_via_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("set_row_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating 'paste0("set_col_", mode, "_via_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("set_col_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'beachtest/libs/i386/beachtest.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'beachtest/libs/x64/beachtest.dll':
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.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [503s]
OK
** running tests for arch 'x64' ...
Running 'testthat.R' [487s]
OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpCWQWpG/beachtest.Rcheck/00check.log'
for details.
-- Building ------------------------------------------------------- morebeach --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\extensions/DESCRIPTION' ...
v checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\extensions/DESCRIPTION' (422ms)
- preparing 'morebeach':
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 'morebeach_1.0.0.tar.gz'
-- Checking ------------------------------------------------------- morebeach --
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/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpCWQWpG/morebeach.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'morebeach/DESCRIPTION' ... OK
* this is package 'morebeach' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'morebeach' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'AaronMatrix'
Undocumented S4 classes:
'AaronMatrix'
Undocumented S4 methods:
generic '[' and siglist 'AaronMatrix,ANY,ANY,ANY'
generic 'as.matrix' and siglist 'AaronMatrix'
generic 'dim' and siglist 'AaronMatrix'
generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'morebeach/libs/i386/morebeach.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'morebeach/libs/x64/morebeach.dll':
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.
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [293s]
OK
** running tests for arch 'x64' ...
Running 'testthat.R' [28s]
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
14. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
15. callr:::run_r(options)
16. base:::with(options, with_envvar(env, do.call(processx::run, ...
17. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
18. base:::eval(substitute(expr), data, enclos = parent.frame())
19. base:::eval(substitute(expr), data, enclos = parent.frame())
20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
21. base:::force(code)
22. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
23. (function (command = NULL, args = character(), error_on_status = TRUE, ...
24. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Execution halted
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpCWQWpG/morebeach.Rcheck/00check.log'
for details.
-- R CMD check results ------------------------------------ morebeach 1.0.0 ----
Duration: 8m 29.5s
> running tests for arch 'x64' ...
See below...
> checking S3 generic/method consistency ... WARNING
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
> checking for missing documentation entries ... WARNING
Undocumented code objects:
'AaronMatrix'
Undocumented S4 classes:
'AaronMatrix'
Undocumented S4 methods:
generic '[' and siglist 'AaronMatrix,ANY,ANY,ANY'
generic 'as.matrix' and siglist 'AaronMatrix'
generic 'dim' and siglist 'AaronMatrix'
generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
> checking compiled code ... NOTE
File 'morebeach/libs/i386/morebeach.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'morebeach/libs/x64/morebeach.dll':
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.
-- Test failures ------------------------------------------- testthat (x64) ----
> library(testthat)
> library(morebeach)
> test_check("morebeach")
Skipping 3 packages not available: beachmat, DelayedArray, BiocGenerics
Running "C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64/Rcmd.exe" INSTALL \
"C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg" \
--install-tests --no-docs --no-multiarch --no-demo
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpsBd2Ho/RLIBS_1c4852923030'
* installing *source* package 'beachtest' ...
** using staged installation
** libs
make: Nothing to be done for 'all'.
make: 'symbols.rds' is up to date.
installing to C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpsBd2Ho/RLIBS_1c4852923030/00LOCK-testpkg/00new/beachtest/libs/x64
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'beachtest' in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpsBd2Ho/RLIBS_1c4852923030/00LOCK-testpkg/00new/beachtest/libs/x64/beachtest.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpsBd2Ho/RLIBS_1c4852923030/beachtest'
* restoring previous 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpsBd2Ho/RLIBS_1c4852923030/beachtest'
Error: System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Stack trace:
1. testthat:::test_check("morebeach")
2. testthat:::test_package_dir(package = package, test_path = test_path, ...
3. testthat:::test_dir(path = test_path, reporter = reporter, env = env, ...
4. testthat:::source_test_setup(path, env)
5. testthat:::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
6. base:::lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
7. testthat:::FUN(X[[i]], ...)
8. base:::eval(exprs, env)
9. base:::eval(exprs, env)
10. devtools::install(testpkg, quick = TRUE)
C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpCWQWpG/morebeach.Rcheck/tests_x64/testthat/setup-all.R:2:1
11. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
12. withr::with_path(rtools_path(), code)
13. base:::force(code)
14. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
15. callr:::run_r(options)
16. base:::with(options, with_envvar(env, do.call(processx::run, ...
17. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
18. base:::eval(substitute(expr), data, enclos = parent.frame())
19. base:::eval(substitute(expr), data, enclos = parent.frame())
20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
21. base:::force(code)
22. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
23. (function (command = NULL, args = character(), error_on_status = TRUE, ...
24. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Execution halted
1 error x | 2 warnings x | 1 note x
-- 1. Failure: extension test package CHECKs correctly (@test-check.R#6) ------
`devtools::check(...)` threw an error.
Message: R CMD check found ERRORs
Class: rcmdcheck_error/rcmdcheck_warning/rcmdcheck_note/rcmdcheck_failure/error/condition
Backtrace:
1. testthat::expect_error(...)
6. devtools::check(...)
7. devtools::check_built(...)
10. rcmdcheck::rcmdcheck(...)
11. rcmdcheck:::handle_error_on(res, error_on)
== testthat results ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Failure: extension test package CHECKs correctly (@test-check.R#6)
Error: testthat unit tests failed
Execution halted
|
beachmat.Rcheck/tests_x64/testthat.Rout.fail
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(beachmat)
> test_check("beachmat")
-- Building ------------------------------------------------------- beachtest --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
v checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg/DESCRIPTION' (422ms)
- preparing 'beachtest': (360ms)
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 'beachtest_1.0.0.tar.gz'
-- Checking ------------------------------------------------------- beachtest --
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/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpM1iiPS/beachtest.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'beachtest/DESCRIPTION' ... OK
* this is package 'beachtest' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'beachtest' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Registration problems:
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating 'paste0("get_class_", mode)' during check gives error
'cannot coerce type 'closure' to vector of type 'character'':
.Call(paste0("get_class_", mode), test.mat, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o - 1L, b, PACKAGE = "beachtest")
Evaluating 'paste0("get_row_", mode, "_to_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("get_row_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating 'paste0("get_col_", mode, "_to_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("get_col_", mode, "_to_", alt.mode), test.mat, ordering,
PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, ro, co, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, subr)
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, b, PACKAGE = "beachtest")
Evaluating 'paste0("set_row_", mode, "_via_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("set_row_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating 'paste0("set_col_", mode, "_via_", alt.mode)' during check gives error
'object 'alt.mode' not found':
.Call(paste0("set_col_", mode, "_via_", alt.mode), test.mat,
ordering, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, rbounds, PACKAGE = "beachtest")
Evaluating 'paste0(FUN, "_", mode)' during check gives error
'object 'FUN' not found':
.Call(paste0(FUN, "_", mode), test.mat, o, cbounds, PACKAGE = "beachtest")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'beachtest/libs/i386/beachtest.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'beachtest/libs/x64/beachtest.dll':
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.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [466s]
OK
** running tests for arch 'x64' ...
Running 'testthat.R' [541s]
OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpM1iiPS/beachtest.Rcheck/00check.log'
for details.
-- Building ------------------------------------------------------- morebeach --
Setting env vars:
* CFLAGS : -Wall -pedantic
* CXXFLAGS : -Wall -pedantic
* CXX11FLAGS: -Wall -pedantic
--------------------------------------------------------------------------------
checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\extensions/DESCRIPTION' ...
v checking for file 'C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\extensions/DESCRIPTION' (407ms)
- preparing 'morebeach':
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 'morebeach_1.0.0.tar.gz'
-- Checking ------------------------------------------------------- morebeach --
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/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpM1iiPS/morebeach.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'morebeach/DESCRIPTION' ... OK
* this is package 'morebeach' version '1.0.0'
* 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 serialization versions ... OK
* checking whether package 'morebeach' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'AaronMatrix'
Undocumented S4 classes:
'AaronMatrix'
Undocumented S4 methods:
generic '[' and siglist 'AaronMatrix,ANY,ANY,ANY'
generic 'as.matrix' and siglist 'AaronMatrix'
generic 'dim' and siglist 'AaronMatrix'
generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'morebeach/libs/i386/morebeach.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'morebeach/libs/x64/morebeach.dll':
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.
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [34s]
OK
** running tests for arch 'x64' ...
Running 'testthat.R' [20s]
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
14. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
15. callr:::run_r(options)
16. base:::with(options, with_envvar(env, do.call(processx::run, ...
17. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
18. base:::eval(substitute(expr), data, enclos = parent.frame())
19. base:::eval(substitute(expr), data, enclos = parent.frame())
20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
21. base:::force(code)
22. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
23. (function (command = NULL, args = character(), error_on_status = TRUE, ...
24. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Execution halted
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpM1iiPS/morebeach.Rcheck/00check.log'
for details.
-- R CMD check results ------------------------------------ morebeach 1.0.0 ----
Duration: 4m 6.4s
> running tests for arch 'x64' ...
See below...
> checking S3 generic/method consistency ... WARNING
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
as.matrix:
function(x, ...)
as.matrix.AaronMatrix:
function(x)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
> checking for missing documentation entries ... WARNING
Undocumented code objects:
'AaronMatrix'
Undocumented S4 classes:
'AaronMatrix'
Undocumented S4 methods:
generic '[' and siglist 'AaronMatrix,ANY,ANY,ANY'
generic 'as.matrix' and siglist 'AaronMatrix'
generic 'dim' and siglist 'AaronMatrix'
generic 'type' and siglist 'AaronMatrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
> checking compiled code ... NOTE
File 'morebeach/libs/i386/morebeach.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'morebeach/libs/x64/morebeach.dll':
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.
-- Test failures ------------------------------------------- testthat (x64) ----
> library(testthat)
> library(morebeach)
> test_check("morebeach")
Skipping 3 packages not available: beachmat, DelayedArray, BiocGenerics
Running "C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64/Rcmd.exe" INSTALL \
"C:\Users\biocbuild\bbs-3.11-bioc-longtests\meat\beachmat.Rcheck\beachmat\testpkg" \
--install-tests --no-docs --no-multiarch --no-demo
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/Rtmp8MdOJt/RLIBS_18cc7b8f3069'
* installing *source* package 'beachtest' ...
** using staged installation
** libs
make: Nothing to be done for 'all'.
make: 'symbols.rds' is up to date.
installing to C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/Rtmp8MdOJt/RLIBS_18cc7b8f3069/00LOCK-testpkg/00new/beachtest/libs/x64
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'beachtest' in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/Rtmp8MdOJt/RLIBS_18cc7b8f3069/00LOCK-testpkg/00new/beachtest/libs/x64/beachtest.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/Rtmp8MdOJt/RLIBS_18cc7b8f3069/beachtest'
* restoring previous 'C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/Rtmp8MdOJt/RLIBS_18cc7b8f3069/beachtest'
Error: System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Stack trace:
1. testthat:::test_check("morebeach")
2. testthat:::test_package_dir(package = package, test_path = test_path, ...
3. testthat:::test_dir(path = test_path, reporter = reporter, env = env, ...
4. testthat:::source_test_setup(path, env)
5. testthat:::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
6. base:::lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
7. testthat:::FUN(X[[i]], ...)
8. base:::eval(exprs, env)
9. base:::eval(exprs, env)
10. devtools::install(testpkg, quick = TRUE)
C:/Users/biocbuild/bbs-3.11-bioc-longtests/tmpdir/RtmpM1iiPS/morebeach.Rcheck/tests_x64/testthat/setup-all.R:2:1
11. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
12. withr::with_path(rtools_path(), code)
13. base:::force(code)
14. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
15. callr:::run_r(options)
16. base:::with(options, with_envvar(env, do.call(processx::run, ...
17. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
18. base:::eval(substitute(expr), data, enclos = parent.frame())
19. base:::eval(substitute(expr), data, enclos = parent.frame())
20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
21. base:::force(code)
22. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
23. (function (command = NULL, args = character(), error_on_status = TRUE, ...
24. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Execution halted
1 error x | 2 warnings x | 1 note x
-- 1. Failure: extension test package CHECKs correctly (@test-check.R#6) ------
`devtools::check(...)` threw an error.
Message: R CMD check found ERRORs
Class: rcmdcheck_error/rcmdcheck_warning/rcmdcheck_note/rcmdcheck_failure/error/condition
Backtrace:
1. testthat::expect_error(...)
6. devtools::check(...)
7. devtools::check_built(...)
10. rcmdcheck::rcmdcheck(...)
11. rcmdcheck:::handle_error_on(res, error_on)
== testthat results ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
1. Failure: extension test package CHECKs correctly (@test-check.R#6)
Error: testthat unit tests failed
Execution halted
|