Brendan Gongol
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/signatureSearch |
| git_branch: devel |
| git_last_commit: 3ffd95e |
| git_last_commit_date: 2023-10-24 11:18:10 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:20 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1947/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.17.0 (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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.17.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings signatureSearch_1.17.0.tar.gz |
| StartedAt: 2024-03-28 09:40:25 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 09:51:30 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 665.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings signatureSearch_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘signatureSearch’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 88.2Mb
sub-directories of 1Mb or more:
R 82.0Mb
data 2.0Mb
extdata 1.9Mb
libs 2.0Mb
* 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 ... 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 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 119.095 1.731 123.307
runWF 10.981 3.325 23.591
rand_query_ES 8.849 3.562 12.906
addGESSannot 3.353 0.707 8.279
get_targets 2.658 0.331 5.309
dtnetplot 2.496 0.450 5.307
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.
signatureSearch.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL signatureSearch
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const 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 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 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
0.195 0.029 0.211
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 3.353 | 0.707 | 8.279 | |
| addMOA | 1.445 | 0.196 | 1.644 | |
| add_pcid | 0.294 | 0.004 | 0.299 | |
| append2H5 | 0.097 | 0.014 | 0.112 | |
| build_custom_db | 0.360 | 0.016 | 0.377 | |
| cellNtestPlot | 0.856 | 0.152 | 2.808 | |
| cell_info | 0.029 | 0.004 | 0.033 | |
| cell_info2 | 0.045 | 0.004 | 0.049 | |
| chembl_moa_list | 0.010 | 0.000 | 0.011 | |
| clue_moa_list | 0.01 | 0.00 | 0.01 | |
| comp_fea_res | 0.226 | 0.020 | 0.246 | |
| create_empty_h5 | 0.027 | 0.004 | 0.031 | |
| dim-methods | 0.007 | 0.004 | 0.011 | |
| drug_cell_ranks | 0.013 | 0.000 | 0.013 | |
| drugs-methods | 0.000 | 0.002 | 0.003 | |
| drugs10 | 0.002 | 0.001 | 0.001 | |
| dtnetplot | 2.496 | 0.450 | 5.307 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0 | 0 | 0 | |
| enrichMOA | 0.054 | 0.012 | 0.066 | |
| enrichReactome | 0.001 | 0.000 | 0.000 | |
| fea | 0.003 | 0.000 | 0.002 | |
| feaResult | 0.000 | 0.004 | 0.004 | |
| gctx2h5 | 0.423 | 0.136 | 0.564 | |
| gess | 0.000 | 0.002 | 0.002 | |
| gessResult | 0.002 | 0.002 | 0.003 | |
| gess_res_vis | 0.591 | 0.124 | 0.717 | |
| getSig | 1.785 | 0.462 | 4.881 | |
| getTreats | 0.878 | 0.123 | 2.317 | |
| get_targets | 2.658 | 0.331 | 5.309 | |
| gmt2h5 | 0.124 | 0.021 | 0.145 | |
| gseGO2 | 0.003 | 0.000 | 0.003 | |
| gseKEGG2 | 0.016 | 0.004 | 0.020 | |
| gseReactome | 0.012 | 0.000 | 0.011 | |
| head-methods | 0.004 | 0.004 | 0.009 | |
| lincs_expr_inst_info | 0.058 | 0.008 | 0.066 | |
| lincs_pert_info | 0.335 | 0.012 | 0.347 | |
| lincs_pert_info2 | 1.518 | 0.068 | 1.589 | |
| lincs_sig_info | 0.076 | 0.000 | 0.077 | |
| list2df | 0.003 | 0.000 | 0.003 | |
| list_rev | 0.002 | 0.000 | 0.003 | |
| mabsGO | 0.002 | 0.000 | 0.003 | |
| mabsKEGG | 0.012 | 0.000 | 0.013 | |
| mabsReactome | 0.012 | 0.000 | 0.012 | |
| matrix2h5 | 0.082 | 0.000 | 0.083 | |
| meanExpr2h5 | 0.497 | 0.060 | 0.559 | |
| moa_conn | 0.029 | 0.014 | 0.044 | |
| parse_gctx | 1.330 | 0.264 | 1.597 | |
| qSig | 1.336 | 0.179 | 4.911 | |
| rand_query_ES | 8.849 | 3.562 | 12.906 | |
| read_gmt | 0.004 | 0.001 | 0.003 | |
| result-methods | 0.025 | 0.019 | 0.045 | |
| runWF | 10.981 | 3.325 | 23.591 | |
| set_readable | 119.095 | 1.731 | 123.307 | |
| show-methods | 0.049 | 0.000 | 0.050 | |
| sim_score_grp | 0.014 | 0.000 | 0.015 | |
| tail-methods | 0.005 | 0.004 | 0.009 | |
| tarReduce | 0 | 0 | 0 | |
| targetList | 0.004 | 0.000 | 0.004 | |
| vec_char_redu | 0 | 0 | 0 | |