##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SPOTlight_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘1.13.1’
* package encoding: UTF-8
* 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 whether package ‘SPOTlight’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
  /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 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 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 ... OK
* checking R code for possible problems ... NOTE
.extract_coord: no visible global function definition for ‘is’
.extract_counts: no visible global function definition for ‘is’
.extract_image: no visible global function definition for ‘is’
.pred_hp: no visible global function definition for ‘as’
.set_groups_if_null: no visible global function definition for ‘is’
plotImage: no visible global function definition for ‘is’
plotSpatialScatterpie: no visible global function definition for ‘is’
plotSpatialScatterpie: no visible global function definition for ‘as’
plotTopicProfiles: no visible global function definition for ‘is’
runDeconvolution: no visible global function definition for ‘is’
runDeconvolution: no visible global function definition for ‘as’
trainNMF: no visible global function definition for ‘is’
trainNMF: no visible global function definition for ‘as’
Undefined global functions or variables:
  as is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) dot-filter.Rd:11-56: Lost braces
    11 |     weight_id = "weight") {
       |                           ^
checkRd: (-1) dot-filter.Rd:13-15: Lost braces
    13 |     if (is.null(n_top)) {
       |                         ^
checkRd: (-1) dot-filter.Rd:29-33: Lost braces
    29 |     mgs <- lapply(mgs, function(df) {
       |                                     ^
checkRd: (-1) dot-filter.Rd:36-40: Lost braces
    36 |     mgs <- lapply(ks, function(k) {
       |                                   ^
checkRd: (-1) dot-filter.Rd:44-50: Lost braces
    44 |     W <- vapply(ks, function(k) {
       |                                 ^
* checking Rd metadata ... 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 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
SPOTlight         6.824  0.302   7.160
plotTopicProfiles 5.753  0.071   6.160
data              4.399  0.060   5.124
* 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:
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 291 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plotInteractions.R:93:5'): plotInteractions(), which = 'network', tunning ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `p[[1]][[10]][[2]][[9]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─testthat::expect_equal(p[[1]][[10]][[2]][[9]], "maroon") at test-plotInteractions.R:93:5
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 291 ]
  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, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SPOTlight.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SPOTlight
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SPOTlight’ ...
** this is package ‘SPOTlight’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -g -O2  -Wall -Werror=format-security  -c nmf.cpp -o nmf.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25,
                 from nmf.cpp:17:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
nmf.cpp: In function ‘void scale(Eigen::MatrixXd&, Eigen::VectorXd&)’:
nmf.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   95 |     for (size_t i = 0; i < w.rows(); ++i)
      |                        ~~^~~~~~~~~~
nmf.cpp:96:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   96 |         for (size_t j = 0; j < w.cols(); ++j)
      |                            ~~^~~~~~~~~~
nmf.cpp: In function ‘void nnls(Eigen::MatrixXd&, Eigen::VectorXd&, Eigen::MatrixXd&, size_t)’:
nmf.cpp:130:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  130 |         for (size_t i = 0; i < h.rows(); ++i) {
      |                            ~~^~~~~~~~~~
nmf.cpp: In function ‘void c_predict(spmat, const Eigen::MatrixXd&, Eigen::MatrixXd&, double, double, int)’:
nmf.cpp:154:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  154 |     for (size_t i = 0; i < h.cols(); ++i) {
      |                        ~~^~~~~~~~~~
nmf.cpp: In function ‘Eigen::MatrixXd predict_nmf(Rcpp::S4&, Eigen::MatrixXd&, double, double, int)’:
nmf.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |     if (w.rows() == A.rows() && w.cols() != A.rows())
      |         ~~~~~~~~~^~~~~~~~~~~
nmf.cpp:168:42: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |     if (w.rows() == A.rows() && w.cols() != A.rows())
      |                                 ~~~~~~~~~^~~~~~~~~~~
nmf.cpp: In function ‘Rcpp::List run_nmf(const Rcpp::S4&, const Rcpp::S4&, double, uint16_t, bool, double, double, uint16_t, Eigen::MatrixXd)’:
nmf.cpp:188:18: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     if (w.rows() == A.rows())
      |         ~~~~~~~~~^~~~~~~~~~~
nmf.cpp:190:23: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  190 |     else if (w.cols() != A.rows())
      |              ~~~~~~~~~^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o SPOTlight.so RcppExports.o nmf.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-SPOTlight/00new/SPOTlight/libs
** R
** 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 (SPOTlight)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> set.seed(321)
> library(testthat)
> library(SPOTlight)
> # plotImage() ----
> test_check("SPOTlight")

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 3.70e-01
   2 | 3.51e-03
   3 | 6.06e-05
   4 | 2.98e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 1.32e-02
   2 | 2.76e-04
   3 | 1.01e-05
   4 | 1.52e-06

iter |      tol 
---------------
   1 | 3.70e-01
   2 | 3.51e-03
   3 | 6.06e-05
   4 | 2.98e-06
[ FAIL 1 | WARN 3 | SKIP 0 | PASS 291 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotInteractions.R:93:5'): plotInteractions(), which = 'network', tunning ──
<subscriptOutOfBoundsError/error/condition>
Error in `p[[1]][[10]][[2]][[9]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─testthat::expect_equal(p[[1]][[10]][[2]][[9]], "maroon") at test-plotInteractions.R:93:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 291 ]
Error: Test failures
Execution halted