Brendan Gongol
| Snapshot Date: 2026-03-05 13:40 -0500 (Thu, 05 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/signatureSearch |
| git_branch: devel |
| git_last_commit: d4105ac |
| git_last_commit_date: 2026-03-03 19:01:14 -0500 (Tue, 03 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-06 11:35 -0500 (Fri, 06 Mar 2026).
| 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" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4593 |
| 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 2007/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.25.1 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for signatureSearch in R Universe. | ||||||||||||||
|
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. |
| Package: signatureSearch |
| Version: 1.25.1 |
| 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_1.25.1.tar.gz |
| StartedAt: 2026-03-05 22:24:37 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 22:29:04 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 266.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 1 |
##############################################################################
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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_1.25.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 27 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 ... NOTE
Found the following notes/warnings:
SystemRequirements specified C++11: support has been removed
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
Obsolete C++11 standard request will be ignored
* 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 ... 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
EXTID2NAME: no visible global function definition for ‘keytypes’
GESSAttributeCatalog: no visible binding for global variable ‘Rank’
GESSAttributeCatalog: no visible global function definition for
‘setnames’
GESSAttributeCatalog: no visible binding for global variable ‘.SD’
GESSAttributeCatalog: no visible binding for global variable ‘RowSums’
LINCSSigInfoGen: no visible binding for global variable ‘sedb’
getAllSig: no visible global function definition for ‘setnames’
get_GO2TERM_table: no visible global function definition for
‘get_GOTERM’
runWF: no visible global function definition for ‘setnames’
runWF: no visible global function definition for ‘fwrite’
Undefined global functions or variables:
.SD Rank RowSums fwrite get_GOTERM keytypes sedb setnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘$.feaResult’ ‘[.feaResult’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 49.513 8.827 62.406
enrichReactome 25.040 3.866 30.377
rand_query_ES 3.460 2.304 6.092
* 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 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signatureSearch ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastGSEA.cpp -o fastGSEA.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fgsea_init.c -o fgsea_init.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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)
signatureSearch.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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(signatureSearch)
> #
> # test_check("signatureSearch")
>
> proc.time()
user system elapsed
0.097 0.034 0.121
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 0.877 | 0.073 | 1.428 | |
| addMOA | 0.067 | 0.001 | 0.076 | |
| add_pcid | 0.165 | 0.003 | 0.175 | |
| append2H5 | 0.023 | 0.003 | 0.026 | |
| build_custom_db | 0.080 | 0.011 | 0.093 | |
| cellNtestPlot | 0.264 | 0.023 | 0.396 | |
| cell_info | 0.007 | 0.001 | 0.007 | |
| cell_info2 | 0.485 | 0.002 | 0.528 | |
| chembl_moa_list | 0.004 | 0.001 | 0.005 | |
| clue_moa_list | 0.005 | 0.001 | 0.005 | |
| comp_fea_res | 0.148 | 0.002 | 0.158 | |
| create_empty_h5 | 0.005 | 0.001 | 0.006 | |
| dim-methods | 0.002 | 0.000 | 0.003 | |
| drug_cell_ranks | 0.002 | 0.001 | 0.003 | |
| drugs-methods | 0.001 | 0.000 | 0.001 | |
| drugs10 | 0.000 | 0.001 | 0.001 | |
| dtnetplot | 0.620 | 0.063 | 0.861 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichMOA | 0.019 | 0.001 | 0.021 | |
| enrichReactome | 25.040 | 3.866 | 30.377 | |
| fea | 0.001 | 0.001 | 0.003 | |
| feaResult | 0.001 | 0.000 | 0.001 | |
| gctx2h5 | 0.144 | 0.095 | 0.271 | |
| gess | 0.000 | 0.000 | 0.001 | |
| gessResult | 0.001 | 0.000 | 0.001 | |
| gess_res_vis | 0.160 | 0.004 | 0.178 | |
| getSig | 0.445 | 0.073 | 0.959 | |
| getTreats | 0.150 | 0.035 | 0.272 | |
| get_targets | 0.578 | 0.050 | 0.833 | |
| gmt2h5 | 0.030 | 0.013 | 0.058 | |
| gseGO2 | 0.001 | 0.001 | 0.002 | |
| gseReactome | 0.004 | 0.000 | 0.005 | |
| head-methods | 0.002 | 0.001 | 0.002 | |
| lincs_expr_inst_info | 0.021 | 0.001 | 0.024 | |
| lincs_pert_info | 0.129 | 0.005 | 0.147 | |
| lincs_pert_info2 | 0.496 | 0.010 | 0.569 | |
| lincs_sig_info | 0.025 | 0.001 | 0.026 | |
| list2df | 0.000 | 0.000 | 0.001 | |
| list_rev | 0 | 0 | 0 | |
| mabsGO | 0.001 | 0.001 | 0.002 | |
| mabsReactome | 0 | 0 | 0 | |
| matrix2h5 | 0.016 | 0.003 | 0.022 | |
| meanExpr2h5 | 0.123 | 0.082 | 0.229 | |
| moa_conn | 0.012 | 0.002 | 0.014 | |
| parse_gctx | 0.033 | 0.004 | 0.050 | |
| qSig | 0.343 | 0.048 | 0.591 | |
| rand_query_ES | 3.460 | 2.304 | 6.092 | |
| read_gmt | 0.001 | 0.001 | 0.002 | |
| result-methods | 0.010 | 0.006 | 0.022 | |
| runWF | 0.000 | 0.001 | 0.001 | |
| set_readable | 49.513 | 8.827 | 62.406 | |
| show-methods | 0.010 | 0.001 | 0.014 | |
| sim_score_grp | 0.003 | 0.000 | 0.003 | |
| tail-methods | 0.002 | 0.001 | 0.002 | |
| tarReduce | 0.000 | 0.000 | 0.001 | |
| targetList | 0.001 | 0.001 | 0.002 | |
| vec_char_redu | 0.000 | 0.000 | 0.001 | |