Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1956/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.20.0  (landing page)
Brendan Gongol
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: RELEASE_3_20
git_last_commit: edcc107
git_last_commit_date: 2024-10-29 10:41:56 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for signatureSearch on kunpeng2

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.

raw results


Summary

Package: signatureSearch
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-11-20 12:28:58 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:39:55 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 657.1 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/signatureSearch.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.20.0’
* 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 (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  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 ... 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  119.374  1.241 124.127
rand_query_ES   9.084  3.943  13.514
runWF           9.618  1.111  21.618
addGESSannot    2.979  0.395   7.261
get_targets     2.504  0.574   5.454
dtnetplot       2.421  0.527   5.639
* 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-3.20-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.


Installation output

signatureSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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 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) {
      |                         ~~^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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-4.4.1/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)

Tests output

signatureSearch.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
  0.291   0.023   0.214 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot2.9790.3957.261
addMOA0.3160.0040.321
add_pcid0.2420.0040.246
append2H50.0790.0160.095
build_custom_db1.5080.2151.727
cellNtestPlot0.8790.0772.832
cell_info0.030.000.03
cell_info20.0480.0000.048
chembl_moa_list0.0090.0000.009
clue_moa_list0.010.000.01
comp_fea_res0.2300.0080.239
create_empty_h50.0290.0000.029
dim-methods0.0050.0030.009
drug_cell_ranks0.0110.0000.010
drugs-methods0.0020.0000.003
drugs100.0010.0000.002
dtnetplot2.4210.5275.639
enrichGO2000
enrichKEGG2000
enrichMOA0.0490.0080.059
enrichReactome000
fea0.0020.0000.003
feaResult0.0020.0000.003
gctx2h50.4280.0680.502
gess0.0010.0000.001
gessResult0.0030.0000.003
gess_res_vis0.5570.0600.618
getSig1.7130.2554.691
getTreats0.6940.1522.200
get_targets2.5040.5745.454
gmt2h50.1210.0400.210
gseGO20.0030.0000.004
gseKEGG20.0130.0000.013
gseReactome0.010.000.01
head-methods0.0110.0030.014
lincs_expr_inst_info0.0540.0160.070
lincs_pert_info0.3380.0520.391
lincs_pert_info21.7020.0951.802
lincs_sig_info0.0630.0120.075
list2df0.0030.0010.003
list_rev0.0020.0000.002
mabsGO0.0030.0000.003
mabsKEGG0.0150.0000.015
mabsReactome0.0110.0000.011
matrix2h50.0670.0190.087
meanExpr2h50.4100.1400.552
moa_conn0.0350.0160.051
parse_gctx0.2400.0520.293
qSig1.3400.1074.633
rand_query_ES 9.084 3.94313.514
read_gmt0.0000.0040.004
result-methods0.5780.2100.047
runWF 9.618 1.11121.618
set_readable119.374 1.241124.127
show-methods0.0420.0000.042
sim_score_grp0.0120.0000.012
tail-methods0.0080.0000.008
tarReduce000
targetList0.0030.0000.003
vec_char_redu000