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This page was generated on 2021-06-17 02:38:31 -0400 (Thu, 17 Jun 2021).

CHECK results for signatureSearch on nebbiolo1

To the developers/maintainers of the signatureSearch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signatureSearch.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1761/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.6.1  (landing page)
Yuzhu Duan
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/signatureSearch
Branch: RELEASE_3_13
Last Commit: 58af341
Last Changed Date: 2021-05-20 23:45:29 -0400 (Thu, 20 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: signatureSearch
Version: 1.6.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings signatureSearch_1.6.1.tar.gz
StartedAt: 2021-06-15 13:36:59 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 13:42:47 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 348.1 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings signatureSearch_1.6.1.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/signatureSearch.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.6.1’
* 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 ... 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
runWF        44.349  2.622  56.713
set_readable 34.111  0.834  36.704
dtnetplot     5.634  0.573   6.678
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.



Installation output

signatureSearch.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘signatureSearch’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  444 |         for (int j = 0; j < S.size(); ++j) {
      |                         ~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
  0.181   0.041   0.206 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
add_pcid0.0020.0010.002
append2H50.0540.0080.062
build_custom_db0.2230.0040.227
cellNtestPlot1.5190.1232.009
cell_info0.0770.0000.078
chembl_moa_list0.0050.0000.004
clue_moa_list0.0050.0000.005
comp_fea_res0.1350.0000.135
create_empty_h50.020.000.02
dim-methods0.0090.0000.009
drug_cell_ranks0.0040.0040.007
drugs-methods0.0020.0010.002
drugs100.0000.0020.002
dsea_GSEA0.0000.0020.002
dsea_hyperG0.0000.0010.002
dtnetplot5.6340.5736.678
enrichGO20.0000.0000.001
enrichKEGG20.0000.0000.001
enrichMOA0.0370.0020.041
enrichReactome0.0000.0000.001
feaResult0.0000.0020.002
gctx2h50.3480.0650.416
gessResult0.0020.0000.003
gess_cmap0.0010.0000.000
gess_cor0.0000.0000.001
gess_fisher0.0010.0000.000
gess_gcmap0.0010.0000.001
gess_lincs0.0000.0010.001
gess_res_vis0.2400.0020.242
getSig2.6340.0813.257
get_targets3.1610.0873.654
get_treat_info1.2040.0251.418
gmt2h50.0700.0080.080
gseGO20.0010.0000.001
gseKEGG20.0050.0030.009
gseReactome0.0090.0000.009
head-methods0.0050.0000.006
lincs_expr_inst_info0.0290.0000.029
lincs_pert_info0.0690.0070.077
lincs_sig_info0.0320.0000.032
list2df0.0020.0000.002
mabsGO0.0010.0000.001
mabsKEGG0.010.000.01
mabsReactome0.010.000.01
matrix2h50.0420.0000.042
moa_conn0.0210.0030.025
parse_gctx0.0720.0000.072
qSig2.5770.1163.067
rand_query_ES3.1180.2323.354
read_gmt0.0020.0000.002
result-methods0.0220.0000.022
runWF44.349 2.62256.713
set_readable34.111 0.83436.704
show-methods0.0320.0000.032
sim_score_grp0.0150.0000.015
tail-methods0.0070.0010.007
tarReduce0.0000.0010.001
targetList0.0030.0000.003
tsea_dup_hyperG0.0010.0000.002
tsea_mGSEA0.0020.0000.001
tsea_mabs0.0010.0010.001
vec_char_redu000