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CHECK report for signatureSearch on malbec1

This page was generated on 2021-05-06 12:29:08 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the signatureSearch package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1706/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.4.6  (landing page)
Yuzhu Duan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/signatureSearch
Branch: RELEASE_3_12
Last Commit: 0befcb1
Last Changed Date: 2021-04-23 09:29:56 -0400 (Fri, 23 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: signatureSearch
Version: 1.4.6
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings signatureSearch_1.4.6.tar.gz
StartedAt: 2021-05-06 06:03:22 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:10:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 425.7 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings signatureSearch_1.4.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/signatureSearch.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearch/DESCRIPTION’ ... OK
* this is package ‘signatureSearch’ version ‘1.4.6’
* 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        64.016  1.164  74.436
set_readable 36.660  0.500  37.709
dtnetplot     6.904  0.172   7.624
get_targets   5.072  0.060   5.559
getSig        4.900  0.040   5.612
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.



Installation output

signatureSearch.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)’:
fastGSEA.cpp:444:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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

signatureSearch.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.236   0.044   0.280 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
add_pcid0.0040.0000.003
append2H50.1040.0000.103
build_custom_db0.4000.0040.402
cellNtestPlot2.9000.1243.439
cell_info0.0760.0160.091
chembl_moa_list0.0000.0040.004
clue_moa_list0.0000.0000.004
comp_fea_res0.1360.0080.145
create_empty_h50.0240.0000.021
dim-methods0.0080.0000.009
drug_cell_ranks0.0080.0000.009
drugs-methods0.0000.0000.002
drugs100.0000.0040.001
dsea_GSEA0.0000.0000.002
dsea_hyperG0.0000.0000.002
dtnetplot6.9040.1727.624
enrichGO2000
enrichKEGG2000
enrichMOA0.0640.0000.094
enrichReactome000
feaResult0.0040.0000.003
gctx2h50.6240.0920.762
gessResult0.0000.0040.003
gess_cmap0.0000.0000.001
gess_cor0.0040.0000.000
gess_fisher000
gess_gcmap0.0000.0000.001
gess_lincs0.0040.0000.000
gess_res_vis0.2400.0080.248
getSig4.9000.0405.612
get_targets5.0720.0605.559
get_treat_info1.8760.0282.172
gmt2h50.1440.0920.244
gseGO20.0000.0000.002
gseKEGG20.0160.0040.018
gseReactome0.0120.0040.014
head-methods0.0120.0000.011
lincs_expr_inst_info0.0560.0000.057
lincs_pert_info0.0920.0080.103
lincs_sig_info0.0600.0000.062
mabsGO0.0040.0000.002
mabsKEGG0.0120.0000.013
mabsReactome0.0120.0000.014
matrix2h50.0760.0120.088
moa_conn0.0480.0000.049
parse_gctx0.1280.0000.127
qSig4.2080.1284.872
rand_query_ES4.0200.1284.208
read_gmt000
result-methods0.0240.0000.027
runWF64.016 1.16474.436
set_readable36.660 0.50037.709
show-methods0.0240.0040.029
sim_score_grp0.0160.0000.016
tail-methods0.0080.0000.007
tarReduce000
targetList0.0040.0000.003
tsea_dup_hyperG0.0000.0000.002
tsea_mGSEA0.0000.0000.001
tsea_mabs0.0000.0000.001
vec_char_redu0.0000.0000.001