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This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1924/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.19.0  (landing page)
Brendan Gongol
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: devel
git_last_commit: d3e13a4
git_last_commit_date: 2024-04-30 11:19:09 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for signatureSearch on nebbiolo2

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.

raw results


Summary

Package: signatureSearch
Version: 1.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings signatureSearch_1.19.0.tar.gz
StartedAt: 2024-07-24 04:02:11 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 04:17:30 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 919.6 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings signatureSearch_1.19.0.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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.19.0’
* 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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 87.1Mb
  sub-directories of 1Mb or more:
    R        81.1Mb
    data      2.0Mb
    extdata   1.9Mb
    libs      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 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  77.202  1.304  78.759
rand_query_ES  7.690  2.368  10.369
runWF          7.478  0.776   9.139
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.20-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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: x86_64-pc-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 
  0.157   0.029   0.175 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot3.8060.2054.268
addMOA0.1710.0000.171
add_pcid0.2350.0040.239
append2H50.0690.0040.073
build_custom_db0.2430.0120.255
cellNtestPlot0.7640.0591.029
cell_info0.0210.0000.022
cell_info20.0360.0000.036
chembl_moa_list0.0040.0030.008
clue_moa_list0.0080.0000.008
comp_fea_res0.1540.0230.177
create_empty_h50.0210.0010.020
dim-methods0.0080.0000.007
drug_cell_ranks0.0100.0000.009
drugs-methods0.0020.0000.002
drugs100.0000.0010.001
dtnetplot1.9490.1752.382
enrichGO2000
enrichKEGG20.0010.0000.000
enrichMOA0.0440.0000.044
enrichReactome000
fea0.0000.0020.002
feaResult0.0000.0020.002
gctx2h50.4020.0720.475
gess0.0010.0000.001
gessResult0.0020.0000.002
gess_res_vis0.3590.0000.359
getSig1.4350.0881.777
getTreats0.6450.0470.774
get_targets1.9610.1052.317
gmt2h50.0870.0050.092
gseGO20.0030.0000.002
gseKEGG20.0130.0000.013
gseReactome0.010.000.01
head-methods0.0060.0000.006
lincs_expr_inst_info0.0530.0000.053
lincs_pert_info0.2840.0000.284
lincs_pert_info21.1170.0121.129
lincs_sig_info0.060.000.06
list2df0.0020.0000.002
list_rev0.0020.0000.001
mabsGO0.0020.0000.002
mabsKEGG0.0130.0000.013
mabsReactome0.0110.0000.011
matrix2h50.0390.0120.051
meanExpr2h50.3990.0360.435
moa_conn0.0270.0000.028
parse_gctx0.1970.0200.217
qSig1.1380.0441.440
rand_query_ES 7.690 2.36810.369
read_gmt0.0030.0000.003
result-methods0.0310.0040.035
runWF7.4780.7769.139
set_readable77.202 1.30478.759
show-methods0.0290.0040.033
sim_score_grp0.0510.0000.052
tail-methods0.0060.0000.006
tarReduce0.0010.0000.000
targetList0.0030.0000.003
vec_char_redu000