Multiple platform build/check report for BioC 3.16 - CHECK results for signatureSearch on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4480
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4276
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4304
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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/signatureSearch.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.batchtools.conf.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘signatureSearch’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 87.6Mb
  sub-directories of 1Mb or more:
    R        82.8Mb
    data      2.9Mb
    extdata   1.5Mb
* 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 LazyData ... OK
* 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  24.359  3.917  28.680
runWF         23.878  2.157  46.271
rand_query_ES  6.924  5.758  15.137
addGESSannot   4.071  0.799   6.948
* 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-3.16-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/4.2/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fastGSEA.cpp -o fastGSEA.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/Resources/library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
*** moving datasets to lazyload DB
** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.171   0.064   0.220

Example timings

name	user	system	elapsed
addGESSannot	4.071	0.799	6.948
addMOA	0.146	0.010	0.156
add_pcid	0.001	0.002	0.002
append2H5	0.055	0.011	0.066
build_custom_db	0.228	0.043	0.274
cellNtestPlot	0.627	0.079	0.858
cell_info	0.016	0.001	0.017
cell_info2	0.026	0.002	0.027
chembl_moa_list	0.003	0.002	0.005
clue_moa_list	0.003	0.001	0.004
comp_fea_res	0.142	0.003	0.146
create_empty_h5	0.016	0.002	0.018
dim-methods	0.006	0.000	0.006
drug_cell_ranks	0.007	0.001	0.007
drugs-methods	0.001	0.000	0.002
drugs10	0.001	0.002	0.003
dtnetplot	1.658	0.131	1.979
enrichGO2	0	0	0
enrichKEGG2	0	0	0
enrichMOA	0.031	0.004	0.036
enrichReactome	0	0	0
fea	0.001	0.001	0.003
feaResult	0.001	0.000	0.002
gctx2h5	0.477	0.149	0.631
gess	0.001	0.000	0.001
gessResult	0.002	0.000	0.002
gess_res_vis	0.229	0.004	0.234
getSig	1.148	0.125	1.475
getTreats	0.475	0.043	0.617
get_targets	2.547	0.134	2.869
gmt2h5	0.087	0.023	0.138
gseGO2	0.001	0.002	0.003
gseKEGG2	0.010	0.000	0.012
gseReactome	0.008	0.000	0.009
head-methods	0.005	0.000	0.006
lincs_expr_inst_info	0.030	0.002	0.032
lincs_pert_info	0.197	0.012	0.210
lincs_pert_info2	1.057	0.050	1.111
lincs_sig_info	0.028	0.001	0.030
list2df	0.001	0.000	0.002
list_rev	0.001	0.000	0.001
mabsGO	0.000	0.001	0.002
mabsKEGG	0.008	0.001	0.009
mabsReactome	0.008	0.001	0.009
matrix2h5	0.042	0.005	0.048
meanExpr2h5	0.467	0.166	0.637
moa_conn	0.018	0.002	0.020
parse_gctx	0.077	0.003	0.080
qSig	0.898	0.117	1.223
rand_query_ES	6.924	5.758	15.137
read_gmt	0.003	0.011	0.015
result-methods	1.607	1.376	0.125
runWF	23.878	2.157	46.271
set_readable	24.359	3.917	28.680
show-methods	0.033	0.003	0.036
sim_score_grp	0.009	0.000	0.011
tail-methods	0.006	0.001	0.007
tarReduce	0.000	0.001	0.001
targetList	0.003	0.003	0.006
vec_char_redu	0.000	0.000	0.001

CHECK results for signatureSearch on lconway

Summary

Command output

Installation output

Tests output

Example timings