Package: signatureSearch

Version: 1.0.4

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_1.0.4.tar.gz

StartedAt: 2020-04-15 05:42:26 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:47:40 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 314.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: signatureSearch.Rcheck

Warnings: 1

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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_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/signatureSearch.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.0.4’
* 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 ... WARNING
Undocumented code objects:
  ‘runWF’ ‘tarReduce’ ‘vec_char_redu’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
           user system elapsed
dtnetplot 5.933  0.334    6.74
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.

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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/3.6/Resources/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastGSEA.cpp -o fastGSEA.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fgsea_init.c -o fgsea_init.o
clang++ -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/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.281   0.076   0.333 

name	user	system	elapsed
append2H5	0.102	0.009	0.117
build_custom_db	0.305	0.029	0.336
cell_info	0.042	0.003	0.044
chembl_moa_list	0.004	0.002	0.006
clue_moa_list	0.005	0.002	0.007
comp_fea_res	0.615	0.018	0.637
create_empty_h5	0.017	0.001	0.019
dim-methods	0.014	0.000	0.016
drug_cell_ranks	0.013	0.001	0.014
drugs-methods	0.002	0.000	0.003
drugs10	0.002	0.001	0.002
dsea_GSEA	0.002	0.001	0.004
dsea_hyperG	0.002	0.002	0.004
dtnetplot	5.933	0.334	6.740
enrichGO2	0.000	0.000	0.001
enrichKEGG2	0.001	0.001	0.000
enrichMOA	0.045	0.004	0.049
feaResult	0.004	0.000	0.003
gctx2h5	1.007	0.212	1.227
gessResult	0.003	0.000	0.003
gess_cmap	0.001	0.000	0.001
gess_cor	0.001	0.000	0.001
gess_fisher	0.001	0.000	0.002
gess_gcmap	0.002	0.000	0.002
gess_lincs	0.001	0.000	0.001
gess_res_vis	0.425	0.003	0.434
getSig	2.368	0.183	2.614
get_targets	3.042	0.067	3.244
gseGO2	0.001	0.001	0.002
gseKEGG2	0.011	0.001	0.011
head-methods	0.010	0.001	0.011
mabsGO	0.002	0.002	0.004
mabsKEGG	0.011	0.001	0.011
matrix2h5	0.044	0.004	0.048
moa_conn	0.038	0.002	0.040
parse_gctx	0.130	0.013	0.144
qSig	2.339	0.113	2.537
rand_query_ES	3.595	0.317	3.959
result-methods	0.040	0.001	0.040
show-methods	0.048	0.001	0.050
sim_score_grp	0.008	0.000	0.009
tail-methods	0.006	0.001	0.007
targetList	0.003	0.001	0.004
tsea_dup_hyperG	0.001	0.002	0.003
tsea_mGSEA	0.002	0.002	0.004
tsea_mabs	0.001	0.001	0.003