| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 2013/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.24.0 (landing page) Brendan Gongol
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: signatureSearch |
| Version: 1.24.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings signatureSearch_1.24.0.tar.gz |
| StartedAt: 2025-11-11 14:52:01 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 15:07:21 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 920.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings signatureSearch_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.24.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
installed size is 88.7Mb
sub-directories of 1Mb or more:
R 82.8Mb
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 254.631 1.335 294.522
rand_query_ES 7.746 2.777 14.044
runWF 8.767 0.937 26.128
addGESSannot 2.947 0.189 8.943
get_targets 2.344 0.110 6.693
dtnetplot 2.284 0.088 7.312
getSig 1.827 0.110 5.869
qSig 1.293 0.076 8.503
cellNtestPlot 1.026 0.062 5.288
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL signatureSearch
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.24.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/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) {
| ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fgsea_init.c -o fgsea_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)
signatureSearch.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.211 0.011 0.322
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 2.947 | 0.189 | 8.943 | |
| addMOA | 0.343 | 0.012 | 0.463 | |
| add_pcid | 0.226 | 0.004 | 0.230 | |
| append2H5 | 1.019 | 0.087 | 1.407 | |
| build_custom_db | 0.342 | 0.016 | 0.359 | |
| cellNtestPlot | 1.026 | 0.062 | 5.288 | |
| cell_info | 0.022 | 0.008 | 0.029 | |
| cell_info2 | 0.044 | 0.004 | 0.048 | |
| chembl_moa_list | 0.008 | 0.000 | 0.009 | |
| clue_moa_list | 0.009 | 0.000 | 0.009 | |
| comp_fea_res | 0.674 | 0.072 | 0.773 | |
| create_empty_h5 | 0.031 | 0.000 | 0.060 | |
| dim-methods | 0.009 | 0.000 | 0.013 | |
| drug_cell_ranks | 0.012 | 0.000 | 0.012 | |
| drugs-methods | 0.003 | 0.000 | 0.003 | |
| drugs10 | 0.002 | 0.000 | 0.001 | |
| dtnetplot | 2.284 | 0.088 | 7.312 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0.000 | 0.000 | 0.001 | |
| enrichMOA | 0.041 | 0.014 | 0.111 | |
| enrichReactome | 0 | 0 | 0 | |
| fea | 0.002 | 0.000 | 0.007 | |
| feaResult | 0.003 | 0.000 | 0.007 | |
| gctx2h5 | 0.493 | 0.088 | 0.867 | |
| gess | 0.001 | 0.000 | 0.001 | |
| gessResult | 0.002 | 0.000 | 0.003 | |
| gess_res_vis | 0.740 | 0.008 | 0.761 | |
| getSig | 1.827 | 0.110 | 5.869 | |
| getTreats | 0.592 | 0.048 | 2.724 | |
| get_targets | 2.344 | 0.110 | 6.693 | |
| gmt2h5 | 0.111 | 0.004 | 0.131 | |
| gseGO2 | 0.002 | 0.000 | 0.002 | |
| gseKEGG2 | 0.01 | 0.00 | 0.01 | |
| gseReactome | 0.01 | 0.00 | 0.01 | |
| head-methods | 0.004 | 0.004 | 0.008 | |
| lincs_expr_inst_info | 0.056 | 0.000 | 0.057 | |
| lincs_pert_info | 0.302 | 0.000 | 0.302 | |
| lincs_pert_info2 | 1.287 | 0.004 | 2.432 | |
| lincs_sig_info | 0.068 | 0.000 | 0.136 | |
| list2df | 0.003 | 0.000 | 0.007 | |
| list_rev | 0.002 | 0.000 | 0.007 | |
| mabsGO | 0.002 | 0.000 | 0.003 | |
| mabsKEGG | 0.007 | 0.008 | 0.027 | |
| mabsReactome | 0.013 | 0.000 | 0.025 | |
| matrix2h5 | 0.077 | 0.000 | 0.153 | |
| meanExpr2h5 | 0.508 | 0.060 | 0.901 | |
| moa_conn | 0.035 | 0.000 | 0.035 | |
| parse_gctx | 0.091 | 0.000 | 0.091 | |
| qSig | 1.293 | 0.076 | 8.503 | |
| rand_query_ES | 7.746 | 2.777 | 14.044 | |
| read_gmt | 0.002 | 0.002 | 0.008 | |
| result-methods | 0.493 | 0.174 | 0.046 | |
| runWF | 8.767 | 0.937 | 26.128 | |
| set_readable | 254.631 | 1.335 | 294.522 | |
| show-methods | 0.043 | 0.004 | 0.083 | |
| sim_score_grp | 0.013 | 0.000 | 0.014 | |
| tail-methods | 0.009 | 0.000 | 0.008 | |
| tarReduce | 0.000 | 0.000 | 0.001 | |
| targetList | 0.004 | 0.000 | 0.004 | |
| vec_char_redu | 0 | 0 | 0 | |