R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
────────────────────────────────────────────────────────────────────────────────
checking for file ‘/home/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’ ...
✔ checking for file ‘/home/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/testpkg/DESCRIPTION’
─ preparing ‘beachtest’:
checking DESCRIPTION meta-information ...
✔ 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 ‘/tmp/RtmpLx9gvs/beachtest.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘beachtest’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 50.0Mb
sub-directories of 1Mb or more:
libs 49.8Mb
* 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 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/beachtest.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.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [479s/479s]
OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs
See
‘/tmp/RtmpLx9gvs/beachtest.Rcheck/00check.log’
for details.
── Building ─────────────────────────────────────────────────────── morebeach ──
Setting env vars:
● CFLAGS : -Wall -pedantic
● CXXFLAGS : -Wall -pedantic
● CXX11FLAGS: -Wall -pedantic
────────────────────────────────────────────────────────────────────────────────
checking for file ‘/home/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’ ...
✔ checking for file ‘/home/biocbuild/bbs-3.11-bioc-longtests/meat/beachmat.Rcheck/beachmat/extensions/DESCRIPTION’
─ preparing ‘morebeach’:
checking DESCRIPTION meta-information ...
✔ 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 ‘/tmp/RtmpLx9gvs/morebeach.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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/morebeach.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.
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [226s/266s]
OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/tmp/RtmpLx9gvs/morebeach.Rcheck/00check.log’
for details.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
1072.788 25.321 1143.361