Multiple platform build/check report for BioC 3.23 - CHECK results for signatureSearch on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4826
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4561
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4562
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*

CHECK results for signatureSearch on lconway

To the developers/maintainers of the signatureSearch package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signatureSearch.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.

raw results

Summary

Package: signatureSearch

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.25.0.tar.gz

StartedAt: 2025-11-18 05:40:15 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 05:51:56 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 701.9 seconds

RetCode: 0

Status: OK

CheckDir: signatureSearch.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.25.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘signatureSearch’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 85.3Mb
  sub-directories of 1Mb or more:
    R        81.0Mb
    data      2.0Mb
    extdata   1.9Mb
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
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
set_readable  221.505 12.660 235.853
rand_query_ES   8.521  2.764  11.182
runWF           8.244  1.020   9.882
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

Installation output

signatureSearch.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.25.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -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/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fastGSEA.cpp -o fastGSEA.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
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 signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
** 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 (signatureSearch)

Tests output

signatureSearch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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.

> # library(testthat)
> # library(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
  0.195   0.084   0.289

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

name	user	system	elapsed
addGESSannot	2.762	0.258	3.289
addMOA	0.217	0.005	0.223
add_pcid	0.367	0.012	0.380
append2H5	0.067	0.009	0.076
build_custom_db	0.307	0.059	0.369
cellNtestPlot	1.863	0.105	2.064
cell_info	0.024	0.004	0.029
cell_info2	0.034	0.004	0.039
chembl_moa_list	0.010	0.005	0.015
clue_moa_list	0.010	0.003	0.013
comp_fea_res	0.508	0.009	0.520
create_empty_h5	0.018	0.004	0.022
dim-methods	0.009	0.001	0.009
drug_cell_ranks	0.009	0.001	0.010
drugs-methods	0.003	0.000	0.003
drugs10	0.001	0.004	0.004
dtnetplot	1.911	0.238	2.348
enrichGO2	0	0	0
enrichKEGG2	0	0	0
enrichMOA	0.053	0.010	0.064
enrichReactome	0	0	0
fea	0.002	0.005	0.007
feaResult	0.003	0.000	0.003
gctx2h5	0.563	0.212	0.792
gess	0.001	0.001	0.002
gessResult	0.002	0.000	0.002
gess_res_vis	0.563	0.010	0.577
getSig	1.475	0.216	1.912
getTreats	0.624	0.075	0.784
get_targets	2.227	0.192	2.655
gmt2h5	0.097	0.038	0.152
gseGO2	0.002	0.003	0.005
gseKEGG2	0.012	0.001	0.014
gseReactome	0.012	0.001	0.013
head-methods	0.005	0.000	0.005
lincs_expr_inst_info	0.063	0.004	0.067
lincs_pert_info	0.366	0.006	0.375
lincs_pert_info2	1.563	0.017	1.587
lincs_sig_info	0.069	0.004	0.072
list2df	0.002	0.000	0.003
list_rev	0.002	0.000	0.002
mabsGO	0.002	0.004	0.007
mabsKEGG	0.014	0.001	0.015
mabsReactome	0.013	0.001	0.014
matrix2h5	0.050	0.008	0.058
meanExpr2h5	0.605	0.240	0.852
moa_conn	0.031	0.004	0.035
parse_gctx	0.090	0.007	0.098
qSig	1.106	0.168	1.450
rand_query_ES	8.521	2.764	11.182
read_gmt	0.004	0.007	0.010
result-methods	0.038	0.012	0.051
runWF	8.244	1.020	9.882
set_readable	221.505	12.660	235.853
show-methods	0.033	0.001	0.034
sim_score_grp	0.012	0.001	0.013
tail-methods	0.007	0.001	0.007
tarReduce	0.001	0.001	0.001
targetList	0.004	0.003	0.006
vec_char_redu	0	0	0