Multiple platform build/check report for BioC 3.11 - CHECK report for signatureSearch on machv2

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### Running command:
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###   /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_1.2.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/signatureSearch.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.2.5’
* 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 ... OK
* 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 ... 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
runWF         53.509  1.771  61.510
dtnetplot      6.870  0.693   8.226
rand_query_ES  4.846  0.533   5.383
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL signatureSearch
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 
  0.301   0.071   0.348

Example timings

name	user	system	elapsed
append2H5	0.084	0.009	0.093
build_custom_db	0.408	0.045	0.454
cell_info	0.114	0.008	0.122
chembl_moa_list	0.004	0.003	0.006
clue_moa_list	0.003	0.002	0.005
comp_fea_res	0.223	0.006	0.229
create_empty_h5	0.025	0.003	0.028
dim-methods	0.016	0.001	0.017
drug_cell_ranks	0.014	0.001	0.014
drugs-methods	0.004	0.000	0.005
drugs10	0.002	0.003	0.005
dsea_GSEA	0.003	0.002	0.006
dsea_hyperG	0.002	0.002	0.004
dtnetplot	6.870	0.693	8.226
enrichGO2	0.000	0.001	0.001
enrichKEGG2	0.001	0.001	0.000
enrichMOA	0.093	0.006	0.100
feaResult	0.004	0.000	0.004
gctx2h5	1.092	0.340	1.436
gessResult	0.003	0.000	0.004
gess_cmap	0.001	0.001	0.002
gess_cor	0.001	0.001	0.002
gess_fisher	0.001	0.001	0.002
gess_gcmap	0.001	0.001	0.002
gess_lincs	0.002	0.001	0.002
gess_res_vis	0.409	0.004	0.413
getSig	3.061	0.128	3.272
get_targets	3.559	0.070	3.779
gmt2h5	0.217	0.025	0.243
gseGO2	0.002	0.003	0.005
gseKEGG2	0.017	0.000	0.018
head-methods	0.009	0.001	0.009
lincs_expr_inst_info	0.057	0.004	0.061
lincs_sig_info	0.061	0.003	0.065
mabsGO	0.002	0.003	0.004
mabsKEGG	0.014	0.001	0.015
matrix2h5	0.065	0.006	0.071
moa_conn	0.048	0.002	0.052
parse_gctx	0.115	0.009	0.124
qSig	2.790	0.125	2.975
rand_query_ES	4.846	0.533	5.383
read_gmt	0.000	0.000	0.001
result-methods	0.046	0.001	0.047
runWF	53.509	1.771	61.510
show-methods	0.052	0.002	0.053
sim_score_grp	0.200	0.005	0.206
tail-methods	0.011	0.001	0.011
tarReduce	0.000	0.001	0.001
targetList	0.003	0.003	0.006
tsea_dup_hyperG	0.002	0.003	0.005
tsea_mGSEA	0.002	0.003	0.005
tsea_mabs	0.002	0.002	0.005
vec_char_redu	0.001	0.000	0.001

CHECK report for signatureSearch on machv2

Summary

Command output

Installation output

Tests output

Example timings