Multiple platform build/check report for BioC 3.18 - CHECK results for signatureSearch on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/signatureSearch.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.16.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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        82.8Mb
    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 R 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 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  97.613  5.511 104.032
rand_query_ES  8.471  2.876  11.225
runWF          7.752  0.985   9.528
addGESSannot   5.604  1.174   7.138
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL signatureSearch
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fastGSEA.cpp -o fastGSEA.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 
  0.211   0.076   0.274

Example timings

name	user	system	elapsed
addGESSannot	5.604	1.174	7.138
addMOA	0.243	0.005	0.251
add_pcid	0.345	0.011	0.356
append2H5	0.078	0.009	0.087
build_custom_db	0.269	0.050	0.321
cellNtestPlot	0.783	0.087	1.285
cell_info	0.026	0.003	0.030
cell_info2	0.046	0.004	0.050
chembl_moa_list	0.012	0.004	0.016
clue_moa_list	0.011	0.003	0.015
comp_fea_res	0.181	0.003	0.185
create_empty_h5	0.023	0.002	0.026
dim-methods	0.009	0.000	0.010
drug_cell_ranks	0.011	0.000	0.011
drugs-methods	0.003	0.001	0.003
drugs10	0.001	0.003	0.004
dtnetplot	2.327	0.200	2.702
enrichGO2	0.001	0.000	0.000
enrichKEGG2	0	0	0
enrichMOA	0.052	0.007	0.061
enrichReactome	0	0	0
fea	0.002	0.003	0.004
feaResult	0.002	0.000	0.002
gctx2h5	0.548	0.186	0.741
gess	0.002	0.001	0.003
gessResult	0.002	0.001	0.003
gess_res_vis	0.500	0.010	0.513
getSig	1.536	0.188	1.896
getTreats	0.536	0.068	0.687
get_targets	2.307	0.162	2.675
gmt2h5	0.108	0.025	0.148
gseGO2	0.002	0.002	0.004
gseKEGG2	0.013	0.001	0.014
gseReactome	0.013	0.002	0.016
head-methods	0.007	0.001	0.008
lincs_expr_inst_info	0.062	0.003	0.065
lincs_pert_info	0.372	0.008	0.381
lincs_pert_info2	1.511	0.020	1.539
lincs_sig_info	0.049	0.002	0.051
list2df	0.002	0.001	0.002
list_rev	0.002	0.000	0.002
mabsGO	0.003	0.002	0.004
mabsKEGG	0.013	0.001	0.013
mabsReactome	0.015	0.001	0.017
matrix2h5	0.052	0.007	0.060
meanExpr2h5	0.735	0.185	0.926
moa_conn	0.045	0.004	0.049
parse_gctx	0.090	0.008	0.098
qSig	1.235	0.150	1.559
rand_query_ES	8.471	2.876	11.225
read_gmt	0.002	0.002	0.004
result-methods	0.041	0.010	0.052
runWF	7.752	0.985	9.528
set_readable	97.613	5.511	104.032
show-methods	0.038	0.002	0.041
sim_score_grp	0.012	0.001	0.012
tail-methods	0.008	0.001	0.008
tarReduce	0.001	0.000	0.001
targetList	0.004	0.002	0.007
vec_char_redu	0.001	0.000	0.000

CHECK results for signatureSearch on lconway

Summary

Command output

Installation output

Tests output

Example timings