Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-02 12:05 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 1991/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.23.0  (landing page)
Brendan Gongol
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 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 24.04.3 LTS) / x86_64  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 13.7.7 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 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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2025-10-02 00:27:52 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 00:39:25 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 693.5 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ... 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  214.279 14.255 230.432
rand_query_ES   8.673  2.994  11.544
runWF           7.800  0.958   9.416
addGESSannot    5.376  1.215   6.969
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.


Installation output

signatureSearch.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.23.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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/4.5-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/4.5-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/4.5-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/4.5-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 version 4.5.1 Patched (2025-09-10 r88807) -- "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.

> # library(testthat)
> # library(signatureSearch)
> # 
> # test_check("signatureSearch")
> 
> proc.time()
   user  system elapsed 
  0.220   0.083   0.304 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot5.3761.2156.969
addMOA0.1960.0040.201
add_pcid0.3120.0090.323
append2H50.0650.0110.075
build_custom_db0.2950.0400.337
cellNtestPlot0.9130.0771.077
cell_info0.0210.0040.025
cell_info20.0360.0030.039
chembl_moa_list0.0100.0030.013
clue_moa_list0.0110.0040.014
comp_fea_res0.4900.0070.498
create_empty_h50.0190.0020.021
dim-methods0.0060.0000.006
drug_cell_ranks0.0080.0000.008
drugs-methods0.0010.0000.002
drugs100.0010.0020.003
dtnetplot3.4900.2373.904
enrichGO2000
enrichKEGG20.0010.0000.000
enrichMOA0.0470.0060.054
enrichReactome000
fea0.0020.0020.004
feaResult0.0030.0000.003
gctx2h50.5470.1990.755
gess0.0010.0010.002
gessResult0.0030.0000.003
gess_res_vis0.5840.0080.594
getSig1.5170.2041.874
getTreats0.5400.0650.679
get_targets2.2760.1622.581
gmt2h50.0950.0240.136
gseGO20.0020.0030.004
gseKEGG20.0100.0010.011
gseReactome0.0110.0010.012
head-methods0.0080.0010.008
lincs_expr_inst_info0.0590.0030.062
lincs_pert_info0.4200.0100.432
lincs_pert_info21.7740.0171.803
lincs_sig_info0.0720.0030.074
list2df0.0020.0000.003
list_rev0.0020.0010.001
mabsGO0.0030.0020.004
mabsKEGG0.0130.0010.014
mabsReactome0.0120.0010.013
matrix2h50.0510.0070.059
meanExpr2h50.6210.2030.831
moa_conn0.0260.0030.029
parse_gctx0.0810.0080.090
qSig1.1120.1411.402
rand_query_ES 8.673 2.99411.544
read_gmt0.0030.0030.007
result-methods0.0400.0190.060
runWF7.8000.9589.416
set_readable214.279 14.255230.432
show-methods0.0360.0020.038
sim_score_grp0.0110.0000.011
tail-methods0.0070.0000.007
tarReduce0.0010.0000.001
targetList0.0030.0030.005
vec_char_redu0.0000.0010.000