##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:destiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings destiny_3.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/destiny.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘3.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .lintr
  .vscode
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rgl’ ‘SingleCellExperiment’
A package should be listed in only one of these fields.
'LinkingTo' for ‘grDevices’ is unused as it has no 'include' directory
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) Gene-Relevance.Rd:94: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DiffusionMap-class.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'ExpressionSet-helpers.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'dm_predict.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'find_sigmas.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'guo.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'projection_dist.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'coercions.Rd':
  ‘fortify.DiffusionMap’ ‘fortify.DPT’

S3 methods shown with full name in Rd file 'plot.DPT.Rd':
  ‘plot.DPT’

S3 methods shown with full name in Rd file 'plot.DiffusionMap.Rd':
  ‘plot.DiffusionMap’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Gene-Relevance-plotting 6.929  0.698   7.828
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  y[1]: "element_blank"
  ── Failure ('test_ggplot.r:39:2'): ggplot plots have the ticks/boxes they should have ──
  class(p3$theme$panel.border)[[1L]] not identical to "element_blank".
  1/1 mismatches
  x[1]: "ggplot2::element_blank"
  y[1]: "element_blank"
  ── Failure ('test_ggplot.r:40:2'): ggplot plots have the ticks/boxes they should have ──
  class(p4$theme$panel.border)[[1L]] not identical to "element_rect".
  1/1 mismatches
  x[1]: "ggplot2::element_rect"
  y[1]: "element_rect"
  
  [ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/destiny.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL destiny
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘destiny’ ...
** this is package ‘destiny’ version ‘3.22.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include   -ggdb -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include   -ggdb -fPIC  -falign-functions=64 -Wall -g -O2   -c censoring.cpp -o censoring.o
In file included from censoring.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from censoring.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from censoring.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from censoring.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
censoring.cpp:57:14: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:68:19: note: uninitialized use occurs here
                        * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                       ^~
censoring.cpp:57:10: note: remove the 'if' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:57:14: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~
censoring.cpp:68:19: note: uninitialized use occurs here
                        * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                       ^~
censoring.cpp:57:14: note: remove the '&&' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~
censoring.cpp:52:12: note: initialize the variable 'm0' to silence this warning
                double m0, m1;
                         ^
                          = 0.0
censoring.cpp:57:14: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:68:47: note: uninitialized use occurs here
                        * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                                                   ^~
censoring.cpp:57:10: note: remove the 'if' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:57:14: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~
censoring.cpp:68:47: note: uninitialized use occurs here
                        * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                                                                   ^~
censoring.cpp:57:14: note: remove the '&&' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~
censoring.cpp:52:16: note: initialize the variable 'm1' to silence this warning
                double m0, m1;
                             ^
                              = 0.0
censoring.cpp:57:14: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:63:20: note: uninitialized use occurs here
                const double v = use_d ? d : c;
                                 ^~~~~
censoring.cpp:57:10: note: remove the 'if' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:57:14: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~
censoring.cpp:63:20: note: uninitialized use occurs here
                const double v = use_d ? d : c;
                                 ^~~~~
censoring.cpp:57:14: note: remove the '&&' if its condition is always true
                } else if (!one_uncertain && one_missing) {
                           ^~~~~~~~~~~~~~~~~
censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning
        bool use_d;
                  ^
                   = false
11 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/grDevices/include' -I/opt/R/arm64/include   -ggdb -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o destiny.so RcppExports.o censoring.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-destiny/00new/destiny/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (destiny)

R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(destiny)
> 
> test_check('destiny')
[ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• Not yet stable (1): 'test_gr.r:23:2'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_ggplot.r:31:2'): ggplot plots have the ticks/boxes they should have ──
class(p1$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:32:2'): ggplot plots have the ticks/boxes they should have ──
class(p2$theme$axis.ticks)[[1L]] not identical to "element_line".
1/1 mismatches
x[1]: "ggplot2::element_line"
y[1]: "element_line"
── Failure ('test_ggplot.r:33:2'): ggplot plots have the ticks/boxes they should have ──
class(p3$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:34:2'): ggplot plots have the ticks/boxes they should have ──
class(p4$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:37:2'): ggplot plots have the ticks/boxes they should have ──
class(p1$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:38:2'): ggplot plots have the ticks/boxes they should have ──
class(p2$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:39:2'): ggplot plots have the ticks/boxes they should have ──
class(p3$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:40:2'): ggplot plots have the ticks/boxes they should have ──
class(p4$theme$panel.border)[[1L]] not identical to "element_rect".
1/1 mismatches
x[1]: "ggplot2::element_rect"
y[1]: "element_rect"

[ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]
Error: Test failures
Execution halted