Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-15 12:12 -0400 (Fri, 15 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 1975/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
signatureSearch 1.23.0 (landing page) Brendan Gongol
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2025-08-15 11:07:23 -0000 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 11:22:03 -0000 (Fri, 15 Aug 2025) |
EllapsedTime: 879.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: signatureSearch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * 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 ‘1.23.0’ * 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: ‘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 200.765 0.927 242.992 rand_query_ES 7.707 2.766 12.513 runWF 8.957 0.709 25.392 addGESSannot 3.875 0.239 9.839 get_targets 2.271 0.135 6.200 dtnetplot 2.240 0.079 5.863 getSig 1.721 0.080 6.879 qSig 1.300 0.059 6.282 * 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL signatureSearch ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘signatureSearch’ ... ** this is package ‘signatureSearch’ version ‘1.23.0’ ** 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 0.229 0.007 0.364
signatureSearch.Rcheck/signatureSearch-Ex.timings
name | user | system | elapsed | |
addGESSannot | 3.875 | 0.239 | 9.839 | |
addMOA | 0.282 | 0.000 | 0.282 | |
add_pcid | 0.213 | 0.000 | 0.214 | |
append2H5 | 0.092 | 0.003 | 0.096 | |
build_custom_db | 0.306 | 0.036 | 0.343 | |
cellNtestPlot | 0.897 | 0.073 | 3.392 | |
cell_info | 0.028 | 0.003 | 0.062 | |
cell_info2 | 0.049 | 0.004 | 0.106 | |
chembl_moa_list | 0.009 | 0.000 | 0.009 | |
clue_moa_list | 0.009 | 0.000 | 0.009 | |
comp_fea_res | 0.216 | 0.023 | 0.240 | |
create_empty_h5 | 0.028 | 0.000 | 0.029 | |
dim-methods | 0.005 | 0.004 | 0.009 | |
drug_cell_ranks | 0.008 | 0.003 | 0.012 | |
drugs-methods | 0.000 | 0.003 | 0.003 | |
drugs10 | 0.001 | 0.001 | 0.002 | |
dtnetplot | 2.240 | 0.079 | 5.863 | |
enrichGO2 | 0 | 0 | 0 | |
enrichKEGG2 | 0 | 0 | 0 | |
enrichMOA | 0.049 | 0.000 | 0.101 | |
enrichReactome | 0 | 0 | 0 | |
fea | 0.003 | 0.000 | 0.002 | |
feaResult | 0.003 | 0.000 | 0.008 | |
gctx2h5 | 0.485 | 0.052 | 1.092 | |
gess | 0.001 | 0.000 | 0.001 | |
gessResult | 0.002 | 0.001 | 0.002 | |
gess_res_vis | 0.537 | 0.004 | 0.796 | |
getSig | 1.721 | 0.080 | 6.879 | |
getTreats | 0.745 | 0.029 | 3.063 | |
get_targets | 2.271 | 0.135 | 6.200 | |
gmt2h5 | 0.118 | 0.008 | 0.183 | |
gseGO2 | 0.002 | 0.000 | 0.002 | |
gseKEGG2 | 0.011 | 0.000 | 0.012 | |
gseReactome | 0.010 | 0.000 | 0.011 | |
head-methods | 0.009 | 0.001 | 0.008 | |
lincs_expr_inst_info | 0.057 | 0.000 | 0.058 | |
lincs_pert_info | 0.302 | 0.015 | 0.319 | |
lincs_pert_info2 | 1.366 | 0.012 | 2.263 | |
lincs_sig_info | 0.065 | 0.000 | 0.065 | |
list2df | 0.003 | 0.000 | 0.003 | |
list_rev | 0.002 | 0.000 | 0.001 | |
mabsGO | 0.002 | 0.000 | 0.002 | |
mabsKEGG | 0.012 | 0.000 | 0.012 | |
mabsReactome | 0.012 | 0.000 | 0.011 | |
matrix2h5 | 0.060 | 0.012 | 0.072 | |
meanExpr2h5 | 0.615 | 0.020 | 0.639 | |
moa_conn | 0.042 | 0.000 | 0.041 | |
parse_gctx | 0.088 | 0.004 | 0.092 | |
qSig | 1.300 | 0.059 | 6.282 | |
rand_query_ES | 7.707 | 2.766 | 12.513 | |
read_gmt | 0.004 | 0.000 | 0.003 | |
result-methods | 0.525 | 0.204 | 0.097 | |
runWF | 8.957 | 0.709 | 25.392 | |
set_readable | 200.765 | 0.927 | 242.992 | |
show-methods | 0.046 | 0.004 | 0.050 | |
sim_score_grp | 0.015 | 0.000 | 0.015 | |
tail-methods | 0.01 | 0.00 | 0.01 | |
tarReduce | 0 | 0 | 0 | |
targetList | 0.004 | 0.000 | 0.004 | |
vec_char_redu | 0 | 0 | 0 | |