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This page was generated on 2025-08-04 12:06 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1972/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.23.0  (landing page)
Brendan Gongol
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: devel
git_last_commit: 467598b
git_last_commit_date: 2025-04-15 11:52:37 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for signatureSearch on nebbiolo2

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: 1.23.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings signatureSearch_1.23.0.tar.gz
StartedAt: 2025-08-04 02:51:58 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 03:13:44 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 1306.2 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings signatureSearch_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.23.0’
* 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: ‘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
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 87.0Mb
  sub-directories of 1Mb or more:
    R        81.1Mb
    data      2.0Mb
    extdata   1.9Mb
    libs      1.8Mb
* 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 ... 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 ... 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
set_readable  151.624  1.637 153.477
rand_query_ES   6.933  2.294   9.601
runWF           7.619  0.892   9.406
addGESSannot    3.853  1.025   5.113
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.


Installation output

signatureSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.23.0’
** using staged installation
** libs
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’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> # library(testthat)
> # library(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
  0.144   0.045   0.176 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot3.8531.0255.113
addMOA0.1880.0130.200
add_pcid0.2090.0110.220
append2H50.0640.0080.073
build_custom_db0.2260.0380.264
cellNtestPlot0.7340.1231.039
cell_info0.0180.0090.027
cell_info20.0320.0080.040
chembl_moa_list0.0090.0030.011
clue_moa_list0.0090.0010.010
comp_fea_res0.1530.0340.187
create_empty_h50.0200.0030.023
dim-methods0.0070.0010.008
drug_cell_ranks0.0080.0020.010
drugs-methods0.0020.0000.003
drugs100.0010.0000.002
dtnetplot2.1570.3772.840
enrichGO2000
enrichKEGG2000
enrichMOA0.0420.0050.047
enrichReactome000
fea0.0020.0000.002
feaResult0.0020.0000.002
gctx2h50.4390.0810.522
gess0.0010.0000.001
gessResult0.0020.0000.003
gess_res_vis0.3930.1130.506
getSig1.4320.1701.902
getTreats0.5210.0820.753
get_targets2.0040.1412.355
gmt2h50.0740.0140.088
gseGO20.0010.0010.002
gseKEGG20.010.000.01
gseReactome0.010.000.01
head-methods0.0060.0010.006
lincs_expr_inst_info0.0520.0020.054
lincs_pert_info0.2530.0050.258
lincs_pert_info21.0290.0161.045
lincs_sig_info0.0600.0010.061
list2df0.0020.0000.002
list_rev0.0010.0000.001
mabsGO0.0020.0000.002
mabsKEGG0.0110.0010.012
mabsReactome0.0120.0000.012
matrix2h50.0470.0070.054
meanExpr2h50.5260.0580.584
moa_conn0.0260.0020.027
parse_gctx0.0690.0010.070
qSig1.1220.0651.486
rand_query_ES6.9332.2949.601
read_gmt0.0020.0010.003
result-methods0.3750.2960.034
runWF7.6190.8929.406
set_readable151.624 1.637153.477
show-methods0.0320.0000.032
sim_score_grp0.0090.0000.009
tail-methods0.0040.0020.006
tarReduce000
targetList0.0020.0010.003
vec_char_redu0.0010.0000.001