Marc Elosua-Bayes
| Snapshot Date: 2025-08-07 13:40 -0400 (Thu, 07 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SPOTlight |
| git_branch: RELEASE_3_21 |
| git_last_commit: 55527f6 |
| git_last_commit_date: 2025-05-26 14:07:38 -0400 (Mon, 26 May 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-11 11:45 -0400 (Mon, 11 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2091/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPOTlight 1.12.1 (landing page) Marc Elosua-Bayes
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the SPOTlight package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPOTlight.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SPOTlight |
| Version: 1.12.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPOTlight_1.12.1.tar.gz |
| StartedAt: 2025-08-08 10:47:55 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 10:56:24 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 508.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SPOTlight.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPOTlight_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SPOTlight.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPOTlight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPOTlight’ version ‘1.12.1’
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ‘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 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 ... OK
* 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 11.202 0.518 11.913
plotTopicProfiles 8.502 0.084 8.722
runDeconvolution 6.997 0.041 7.201
data 6.961 0.049 7.041
trainNMF 6.935 0.044 7.042
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/SPOTlight.Rcheck/00check.log’
for details.
SPOTlight.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPOTlight
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SPOTlight’ ...
** this is package ‘SPOTlight’ version ‘1.12.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c nmf.cpp -o nmf.o
nmf.cpp:61:13: warning: private field 'col_' is not used [-Wunused-private-field]
int col_, index, max_index;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o SPOTlight.so RcppExports.o nmf.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
SPOTlight.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.
> 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 0 | WARN 0 | SKIP 0 | PASS 294 ]
>
> proc.time()
user system elapsed
105.470 4.816 113.569
SPOTlight.Rcheck/SPOTlight-Ex.timings
| name | user | system | elapsed | |
| SPOTlight | 11.202 | 0.518 | 11.913 | |
| data | 6.961 | 0.049 | 7.041 | |
| plotCorrelationMatrix | 2.054 | 0.036 | 2.110 | |
| plotImage | 3.397 | 0.178 | 3.606 | |
| plotInteractions | 1.179 | 0.014 | 1.198 | |
| plotSpatialScatterpie | 1.692 | 0.076 | 1.801 | |
| plotTopicProfiles | 8.502 | 0.084 | 8.722 | |
| runDeconvolution | 6.997 | 0.041 | 7.201 | |
| trainNMF | 6.935 | 0.044 | 7.042 | |