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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (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 1970/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.18.0  (landing page)
Brendan Gongol
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: RELEASE_3_19
git_last_commit: 8c6cc1e
git_last_commit_date: 2024-04-30 11:19:09 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for signatureSearch on palomino3

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: 1.18.0
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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot 6.44 2.3112.30
addMOA0.350.010.36
add_pcid0.250.020.27
append2H50.080.030.25
build_custom_db0.310.090.53
cellNtestPlot0.900.351.48
cell_info0.040.000.03
cell_info20.040.050.09
chembl_moa_list0.000.060.07
clue_moa_list0.020.030.04
comp_fea_res0.140.000.14
create_empty_h50.030.020.05
dim-methods0.020.000.02
drug_cell_ranks0.010.000.01
drugs-methods000
drugs100.000.020.02
dtnetplot2.410.433.36
enrichGO2000
enrichKEGG2000
enrichMOA0.070.050.13
enrichReactome000
fea0.000.020.01
feaResult000
gctx2h50.570.151.18
gess000
gessResult000
gess_res_vis0.440.010.45
getSig1.740.362.27
getTreats0.790.130.95
get_targets2.470.292.94
gmt2h50.100.050.45
gseGO20.000.020.02
gseKEGG20.010.000.02
gseReactome000
head-methods000
lincs_expr_inst_info0.050.000.05
lincs_pert_info0.330.020.34
lincs_pert_info21.070.061.14
lincs_sig_info0.10.00.1
list2df0.010.000.01
list_rev000
mabsGO0.000.020.02
mabsKEGG0.020.000.01
mabsReactome0.010.000.02
matrix2h50.110.010.20
meanExpr2h50.740.131.24
moa_conn0.060.040.11
parse_gctx0.140.000.14
qSig1.380.251.71
rand_query_ES8.500.479.19
read_gmt000
result-methods0.030.000.03
runWF 8.58 1.3610.19
set_readable86.86 4.0691.00
show-methods0.040.000.04
sim_score_grp0.010.000.01
tail-methods000
tarReduce0.020.000.02
targetList000
vec_char_redu000