| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:28 -0400 (Thu, 09 May 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" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.18.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings signatureSearch_1.18.0.tar.gz |
| StartedAt: 2024-05-09 11:58:09 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 12:09:08 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 659.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: signatureSearch.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings signatureSearch_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/signatureSearch.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.18.0’
* 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 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 119.499 1.318 123.298
rand_query_ES 8.568 2.890 11.865
runWF 10.177 1.242 20.419
addGESSannot 3.226 0.112 7.159
get_targets 3.106 0.072 5.450
dtnetplot 2.659 0.172 5.099
* 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:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL signatureSearch
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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
0.184 0.042 0.210
signatureSearch.Rcheck/signatureSearch-Ex.timings
| name | user | system | elapsed | |
| addGESSannot | 3.226 | 0.112 | 7.159 | |
| addMOA | 0.291 | 0.007 | 0.300 | |
| add_pcid | 0.254 | 0.009 | 0.262 | |
| append2H5 | 0.085 | 0.011 | 0.097 | |
| build_custom_db | 1.406 | 0.040 | 1.449 | |
| cellNtestPlot | 0.925 | 0.020 | 2.727 | |
| cell_info | 0.029 | 0.000 | 0.028 | |
| cell_info2 | 0.051 | 0.000 | 0.050 | |
| chembl_moa_list | 0.009 | 0.000 | 0.009 | |
| clue_moa_list | 0.006 | 0.004 | 0.009 | |
| comp_fea_res | 0.226 | 0.012 | 0.239 | |
| create_empty_h5 | 0.020 | 0.008 | 0.028 | |
| dim-methods | 0.009 | 0.000 | 0.008 | |
| drug_cell_ranks | 0.008 | 0.004 | 0.012 | |
| drugs-methods | 0.002 | 0.000 | 0.003 | |
| drugs10 | 0.001 | 0.000 | 0.001 | |
| dtnetplot | 2.659 | 0.172 | 5.099 | |
| enrichGO2 | 0 | 0 | 0 | |
| enrichKEGG2 | 0 | 0 | 0 | |
| enrichMOA | 0.049 | 0.000 | 0.051 | |
| enrichReactome | 0 | 0 | 0 | |
| fea | 0.003 | 0.000 | 0.002 | |
| feaResult | 0.003 | 0.000 | 0.002 | |
| gctx2h5 | 0.426 | 0.064 | 0.497 | |
| gess | 0.001 | 0.000 | 0.001 | |
| gessResult | 0.002 | 0.000 | 0.002 | |
| gess_res_vis | 0.526 | 0.004 | 0.532 | |
| getSig | 1.648 | 0.108 | 4.385 | |
| getTreats | 0.707 | 0.008 | 2.032 | |
| get_targets | 3.106 | 0.072 | 5.450 | |
| gmt2h5 | 0.105 | 0.011 | 0.117 | |
| gseGO2 | 0.000 | 0.002 | 0.002 | |
| gseKEGG2 | 0.011 | 0.001 | 0.011 | |
| gseReactome | 0.011 | 0.000 | 0.010 | |
| head-methods | 0.008 | 0.000 | 0.007 | |
| lincs_expr_inst_info | 0.061 | 0.000 | 0.061 | |
| lincs_pert_info | 0.306 | 0.004 | 0.313 | |
| lincs_pert_info2 | 1.287 | 0.004 | 1.293 | |
| lincs_sig_info | 0.070 | 0.000 | 0.071 | |
| list2df | 0.002 | 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 | 0.012 | |
| matrix2h5 | 0.068 | 0.004 | 0.072 | |
| meanExpr2h5 | 0.531 | 0.036 | 0.569 | |
| moa_conn | 0.037 | 0.000 | 0.037 | |
| parse_gctx | 0.099 | 0.000 | 0.099 | |
| qSig | 1.448 | 0.055 | 4.590 | |
| rand_query_ES | 8.568 | 2.890 | 11.865 | |
| read_gmt | 0.000 | 0.003 | 0.004 | |
| result-methods | 0.508 | 0.247 | 0.044 | |
| runWF | 10.177 | 1.242 | 20.419 | |
| set_readable | 119.499 | 1.318 | 123.298 | |
| show-methods | 0.042 | 0.000 | 0.043 | |
| sim_score_grp | 0.013 | 0.000 | 0.013 | |
| tail-methods | 0.007 | 0.000 | 0.007 | |
| tarReduce | 0 | 0 | 0 | |
| targetList | 0.004 | 0.000 | 0.004 | |
| vec_char_redu | 0.000 | 0.000 | 0.001 | |