Build/check report for BioC 3.23 - CHECK results for signatureSearch on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4857
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 nebbiolo1

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: 1.25.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings signatureSearch_1.25.1.tar.gz

StartedAt: 2026-02-06 03:59:19 -0500 (Fri, 06 Feb 2026)

EndedAt: 2026-02-06 04:39:20 -0500 (Fri, 06 Feb 2026)

EllapsedTime: 2400.8 seconds

RetCode: None

Status: TIMEOUT

CheckDir: signatureSearch.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings signatureSearch_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.25.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
  Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
  Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
Found the following additional notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/home/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* checking installed package size ... INFO
  installed size is 85.5Mb
  sub-directories of 1Mb or more:
    R        80.9Mb
    data      2.0Mb
    extdata   1.4Mb
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘determine_refdb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GESSAttributeCatalog: no visible binding for global variable ‘Rank’
GESSAttributeCatalog: no visible global function definition for
  ‘median’
GESSAttributeCatalog: no visible binding for global variable ‘RowSums’
LINCSSigInfoGen: no visible binding for global variable ‘sedb’
connectivity_score_raw: no visible global function definition for
  ‘na.omit’
fgsea2 : <anonymous>: no visible global function definition for
  ‘na.omit’
gess_res_vis: no visible global function definition for ‘na.omit’
getAllSig : <anonymous>: no visible binding for global variable
  ‘pert_iname’
getAllSig: no visible binding for global variable ‘ENTREZID’
getAllSig: no visible binding for global variable ‘SYMBOL’
get_GO2TERM_table: no visible global function definition for
  ‘get_GOTERM’
tsea_dup_hyperG: no visible global function definition for ‘na.omit’
tsea_mGSEA: no visible global function definition for ‘na.omit’
tsea_mabs: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  ENTREZID Rank RowSums SYMBOL get_GOTERM median na.omit pert_iname
  sedb
Consider adding
  importFrom("stats", "median", "na.omit")
to your NAMESPACE file.
* 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 ... WARNING
  Warning: found non-ASCII string
  'medullary cystic<c2><a0>kidney<c2><a0>disease (MCKD) type 1' in object 'cell_info2'
* 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 ...

Installation output

signatureSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.25.1’
** using staged installation
** libs
specified C++11
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)’:
fastGSEA.cpp:444:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  444 |         for (int j = 0; j < S.size(); ++j) {
      |                         ~~^~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** testing if installed package keeps a record of temporary installation path
* DONE (signatureSearch)

Tests output

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

name	user	system	elapsed
addGESSannot	2.566	0.184	3.057
addMOA	0.310	0.003	0.313
add_pcid	0.202	0.001	0.203
append2H5	0.057	0.001	0.057
build_custom_db	0.234	0.003	0.236
cellNtestPlot	1.722	0.130	2.004
cell_info	0.016	0.001	0.018
cell_info2	0.004	0.000	0.004
chembl_moa_list	0.007	0.001	0.008
clue_moa_list	0.008	0.002	0.009
comp_fea_res	0.413	0.003	0.415
create_empty_h5	0.018	0.001	0.018
dim-methods	0.007	0.000	0.007
drug_cell_ranks	0.008	0.001	0.009
drugs-methods	0.002	0.000	0.002
drugs10	0.002	0.000	0.002
dtnetplot	1.721	0.231	2.161
enrichGO2	0	0	0
enrichMOA	0.042	0.000	0.043
enrichReactome	104.431	0.808	105.251
fea	0.001	0.001	0.002
feaResult	0.002	0.000	0.002
gctx2h5	0.362	0.021	0.384
gess	0.001	0.000	0.001
gessResult	0.002	0.000	0.002
gess_res_vis	0.466	0.003	0.470
getSig	1.410	0.159	1.878
getTreats	0.455	0.060	0.663
get_targets	1.691	0.123	2.022
gmt2h5	0.070	0.005	0.076
gseGO2	0.002	0.000	0.002
gseReactome	0	0	0
head-methods	0.004	0.001	0.006
lincs_expr_inst_info	0.051	0.001	0.052
lincs_pert_info	0.240	0.001	0.241
lincs_pert_info2	0.875	0.006	0.881
lincs_sig_info	0.059	0.001	0.060
list2df	0.002	0.000	0.002
list_rev	0.001	0.000	0.001
mabsGO	0.001	0.001	0.002
mabsReactome	0.001	0.000	0.000
matrix2h5	0.043	0.000	0.043
meanExpr2h5	0.315	0.051	0.367
moa_conn	0.025	0.002	0.027
parse_gctx	0.067	0.000	0.067
qSig	1.042	0.140	1.535
rand_query_ES	7.761	3.340	11.433
read_gmt	0.001	0.002	0.003
result-methods	0.390	0.229	0.034