Multiple platform build/check report for BioC 3.13 - CHECK results for signatureSearch on machv2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings signatureSearch_1.6.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/signatureSearch.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.6.3’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  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 98.8Mb
  sub-directories of 1Mb or more:
    R        96.1Mb
    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 19 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 34.879  2.046  37.202
runWF        30.909  1.349  38.914
dtnetplot     5.267  0.599   6.209
* 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-3.13-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
  0.289   0.071   0.335

Example timings

name	user	system	elapsed
add_pcid	0.003	0.002	0.004
append2H5	0.069	0.007	0.076
build_custom_db	0.429	0.063	0.494
cellNtestPlot	0.304	0.035	0.340
cell_info	0.144	0.021	0.165
chembl_moa_list	0.005	0.005	0.011
clue_moa_list	0.003	0.002	0.005
comp_fea_res	0.180	0.017	0.197
create_empty_h5	0.033	0.006	0.039
dim-methods	0.048	0.002	0.050
drug_cell_ranks	0.014	0.001	0.014
drugs-methods	0.003	0.000	0.003
drugs10	0.002	0.003	0.004
dsea_GSEA	0.002	0.003	0.005
dsea_hyperG	0.002	0.002	0.004
dtnetplot	5.267	0.599	6.209
enrichGO2	0.000	0.000	0.001
enrichKEGG2	0	0	0
enrichMOA	0.053	0.005	0.057
enrichReactome	0.000	0.000	0.001
feaResult	0.002	0.001	0.002
gctx2h5	0.830	0.268	1.101
gessResult	0.004	0.001	0.004
gess_cmap	0.001	0.001	0.002
gess_cor	0.001	0.000	0.001
gess_fisher	0.000	0.000	0.001
gess_gcmap	0.001	0.001	0.001
gess_lincs	0.000	0.000	0.001
gess_res_vis	0.341	0.006	0.347
getSig	0.588	0.044	0.632
get_targets	3.796	0.066	4.109
get_treat_info	0.041	0.003	0.045
gmt2h5	0.145	0.026	0.174
gseGO2	0.001	0.002	0.004
gseKEGG2	0.016	0.001	0.017
gseReactome	0.011	0.001	0.011
head-methods	0.007	0.000	0.008
lincs_expr_inst_info	0.044	0.003	0.047
lincs_pert_info	0.115	0.006	0.121
lincs_sig_info	0.052	0.005	0.056
list2df	0.003	0.001	0.003
mabsGO	0.001	0.002	0.003
mabsKEGG	0.012	0.001	0.013
mabsReactome	0.014	0.001	0.016
matrix2h5	0.082	0.007	0.088
moa_conn	0.028	0.002	0.030
parse_gctx	0.127	0.013	0.139
qSig	0.487	0.052	0.539
rand_query_ES	3.885	0.550	4.440
read_gmt	0.003	0.001	0.003
result-methods	0.030	0.001	0.030
runWF	30.909	1.349	38.914
set_readable	34.879	2.046	37.202
show-methods	0.040	0.001	0.041
sim_score_grp	0.019	0.000	0.019
tail-methods	0.011	0.001	0.012
tarReduce	0.001	0.000	0.001
targetList	0.003	0.003	0.007
tsea_dup_hyperG	0.002	0.002	0.005
tsea_mGSEA	0.001	0.002	0.003
tsea_mabs	0.002	0.003	0.005
vec_char_redu	0.000	0.000	0.001

CHECK results for signatureSearch on machv2

Summary

Command output

Installation output

Tests output

Example timings