Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 1970/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
signatureSearch 1.18.0 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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. |
Package: signatureSearch |
Version: 1.18.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings signatureSearch_1.18.0.tar.gz |
StartedAt: 2024-06-27 06:12:03 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 06:21:56 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 592.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: signatureSearch.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings signatureSearch_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/signatureSearch.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'signatureSearch/DESCRIPTION' ... OK * this is package 'signatureSearch' version '1.18.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 whether package 'signatureSearch' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 86.1Mb 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 ... NOTE Note: found 147 marked UTF-8 strings * 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 for x64 is not available File 'F:/biocbuild/bbs-3.19-bioc/R/library/signatureSearch/libs/x64/signatureSearch.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed set_readable 86.86 4.06 91.00 runWF 8.58 1.36 10.19 rand_query_ES 8.50 0.47 9.19 addGESSannot 6.44 2.31 12.30 * 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: 4 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/signatureSearch.Rcheck/00check.log' for details.
signatureSearch.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL signatureSearch ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'signatureSearch' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int'} [-Wsign-compare] 444 | for (int j = 0; j < S.size(); ++j) { | ~~^~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fgsea_init.c -o fgsea_init.o g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-signatureSearch/00new/signatureSearch/libs/x64 ** 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 ** 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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.14 0.10 0.21
signatureSearch.Rcheck/signatureSearch-Ex.timings
name | user | system | elapsed | |
addGESSannot | 6.44 | 2.31 | 12.30 | |
addMOA | 0.35 | 0.01 | 0.36 | |
add_pcid | 0.25 | 0.02 | 0.27 | |
append2H5 | 0.08 | 0.03 | 0.25 | |
build_custom_db | 0.31 | 0.09 | 0.53 | |
cellNtestPlot | 0.90 | 0.35 | 1.48 | |
cell_info | 0.04 | 0.00 | 0.03 | |
cell_info2 | 0.04 | 0.05 | 0.09 | |
chembl_moa_list | 0.00 | 0.06 | 0.07 | |
clue_moa_list | 0.02 | 0.03 | 0.04 | |
comp_fea_res | 0.14 | 0.00 | 0.14 | |
create_empty_h5 | 0.03 | 0.02 | 0.05 | |
dim-methods | 0.02 | 0.00 | 0.02 | |
drug_cell_ranks | 0.01 | 0.00 | 0.01 | |
drugs-methods | 0 | 0 | 0 | |
drugs10 | 0.00 | 0.02 | 0.02 | |
dtnetplot | 2.41 | 0.43 | 3.36 | |
enrichGO2 | 0 | 0 | 0 | |
enrichKEGG2 | 0 | 0 | 0 | |
enrichMOA | 0.07 | 0.05 | 0.13 | |
enrichReactome | 0 | 0 | 0 | |
fea | 0.00 | 0.02 | 0.01 | |
feaResult | 0 | 0 | 0 | |
gctx2h5 | 0.57 | 0.15 | 1.18 | |
gess | 0 | 0 | 0 | |
gessResult | 0 | 0 | 0 | |
gess_res_vis | 0.44 | 0.01 | 0.45 | |
getSig | 1.74 | 0.36 | 2.27 | |
getTreats | 0.79 | 0.13 | 0.95 | |
get_targets | 2.47 | 0.29 | 2.94 | |
gmt2h5 | 0.10 | 0.05 | 0.45 | |
gseGO2 | 0.00 | 0.02 | 0.02 | |
gseKEGG2 | 0.01 | 0.00 | 0.02 | |
gseReactome | 0 | 0 | 0 | |
head-methods | 0 | 0 | 0 | |
lincs_expr_inst_info | 0.05 | 0.00 | 0.05 | |
lincs_pert_info | 0.33 | 0.02 | 0.34 | |
lincs_pert_info2 | 1.07 | 0.06 | 1.14 | |
lincs_sig_info | 0.1 | 0.0 | 0.1 | |
list2df | 0.01 | 0.00 | 0.01 | |
list_rev | 0 | 0 | 0 | |
mabsGO | 0.00 | 0.02 | 0.02 | |
mabsKEGG | 0.02 | 0.00 | 0.01 | |
mabsReactome | 0.01 | 0.00 | 0.02 | |
matrix2h5 | 0.11 | 0.01 | 0.20 | |
meanExpr2h5 | 0.74 | 0.13 | 1.24 | |
moa_conn | 0.06 | 0.04 | 0.11 | |
parse_gctx | 0.14 | 0.00 | 0.14 | |
qSig | 1.38 | 0.25 | 1.71 | |
rand_query_ES | 8.50 | 0.47 | 9.19 | |
read_gmt | 0 | 0 | 0 | |
result-methods | 0.03 | 0.00 | 0.03 | |
runWF | 8.58 | 1.36 | 10.19 | |
set_readable | 86.86 | 4.06 | 91.00 | |
show-methods | 0.04 | 0.00 | 0.04 | |
sim_score_grp | 0.01 | 0.00 | 0.01 | |
tail-methods | 0 | 0 | 0 | |
tarReduce | 0.02 | 0.00 | 0.02 | |
targetList | 0 | 0 | 0 | |
vec_char_redu | 0 | 0 | 0 | |