Mac ARM64 build report for BioC 3.20 - CHECK results for signatureSearch on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4381
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_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/signatureSearch.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 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 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  72.578  6.144  80.042
runWF         10.737  1.078  15.135
rand_query_ES  8.691  2.857  11.571
addGESSannot   5.599  0.864   8.264
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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/4.4-arm64/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fastGSEA.cpp -o fastGSEA.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.218   0.066   0.271

Example timings

name	user	system	elapsed
addGESSannot	5.599	0.864	8.264
addMOA	0.195	0.005	0.201
add_pcid	0.356	0.007	0.363
append2H5	0.069	0.014	0.083
build_custom_db	0.253	0.042	0.296
cellNtestPlot	0.782	0.105	1.374
cell_info	0.021	0.005	0.027
cell_info2	0.039	0.007	0.045
chembl_moa_list	0.012	0.004	0.017
clue_moa_list	0.013	0.004	0.017
comp_fea_res	0.233	0.012	0.246
create_empty_h5	0.016	0.002	0.018
dim-methods	0.007	0.000	0.007
drug_cell_ranks	0.008	0.001	0.008
drugs-methods	0.002	0.000	0.002
drugs10	0.001	0.003	0.005
dtnetplot	2.551	0.171	3.587
enrichGO2	0.001	0.000	0.001
enrichKEGG2	0	0	0
enrichMOA	0.056	0.007	0.065
enrichReactome	0	0	0
fea	0.002	0.004	0.005
feaResult	0.003	0.000	0.003
gctx2h5	0.544	0.154	0.700
gess	0.002	0.001	0.002
gessResult	0.003	0.001	0.002
gess_res_vis	0.370	0.006	0.378
getSig	1.485	0.159	2.601
getTreats	0.791	0.064	1.346
get_targets	2.462	0.155	3.470
gmt2h5	0.088	0.023	0.116
gseGO2	0.002	0.003	0.005
gseKEGG2	0.016	0.001	0.017
gseReactome	0.015	0.001	0.016
head-methods	0.006	0.001	0.007
lincs_expr_inst_info	0.063	0.003	0.067
lincs_pert_info	0.457	0.009	0.466
lincs_pert_info2	1.857	0.014	1.876
lincs_sig_info	0.081	0.004	0.084
list2df	0.002	0.001	0.002
list_rev	0.001	0.000	0.001
mabsGO	0.003	0.002	0.006
mabsKEGG	0.022	0.001	0.022
mabsReactome	0.020	0.001	0.022
matrix2h5	0.049	0.007	0.056
meanExpr2h5	0.718	0.146	0.869
moa_conn	0.042	0.005	0.047
parse_gctx	0.094	0.009	0.105
qSig	1.243	0.129	2.516
rand_query_ES	8.691	2.857	11.571
read_gmt	0.003	0.003	0.005
result-methods	0.030	0.017	0.048
runWF	10.737	1.078	15.135
set_readable	72.578	6.144	80.042
show-methods	0.037	0.002	0.040
sim_score_grp	0.01	0.00	0.01
tail-methods	0.009	0.001	0.010
tarReduce	0.000	0.000	0.001
targetList	0.004	0.003	0.007
vec_char_redu	0	0	0

CHECK results for signatureSearch on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings