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This page was generated on 2022-01-18 11:12:02 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for signatureSearch on merida1


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 1785/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.9.4  (landing page)
Brendan Gongol
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: master
git_last_commit: 7934c5b
git_last_commit_date: 2022-01-06 17:51:07 -0500 (Thu, 06 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'fgsea' which is not available

Summary

Package: signatureSearch
Version: 1.9.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.9.4.tar.gz
StartedAt: 2022-01-18 05:46:05 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 05:56:53 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 648.1 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:signatureSearch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings signatureSearch_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/signatureSearch.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.9.4’
* 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:
  .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 86.7Mb
  sub-directories of 1Mb or more:
    R        82.8Mb
    data      2.0Mb
    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 41 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  54.320  1.017  55.801
runWF         40.226  2.345  50.085
addGESSannot   6.717  0.807   8.085
rand_query_ES  4.947  2.299   7.017
* 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-3.15-bioc/meat/signatureSearch.Rcheck/00check.log’
for details.



Installation output

signatureSearch.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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

signatureSearch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 
  0.330   0.076   0.381 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot6.7170.8078.085
addMOA0.4650.0030.469
add_pcid0.0020.0020.004
append2H50.1120.0080.120
build_custom_db0.4710.0490.521
cellNtestPlot1.0660.0951.474
cell_info0.0340.0030.036
chembl_moa_list0.0050.0030.007
clue_moa_list0.0050.0020.007
comp_fea_res0.2760.0010.278
create_empty_h50.0350.0020.038
dim-methods0.0130.0000.014
drug_cell_ranks0.0150.0010.015
drugs-methods0.0030.0000.003
drugs100.0020.0020.004
dtnetplot2.8230.1453.351
enrichGO2000
enrichKEGG20.0000.0000.001
enrichMOA0.0630.0060.069
enrichReactome0.0000.0010.000
fea0.0020.0020.005
feaResult0.0030.0010.003
gctx2h51.0300.2261.259
gess0.0010.0010.001
gessResult0.0030.0000.003
gess_res_vis0.4530.0030.457
getSig2.0520.1562.828
getTreats0.7110.0581.083
get_targets2.6270.1263.058
gmt2h50.1530.0180.172
gseGO20.0010.0020.003
gseKEGG20.0160.0010.017
gseReactome0.0150.0010.016
head-methods0.0110.0010.011
lincs_expr_inst_info0.0530.0040.057
lincs_pert_info0.1810.0060.187
lincs_pert_info20.4710.0220.493
lincs_sig_info0.0590.0030.062
list2df0.0040.0000.004
list_rev0.0030.0010.004
mabsGO0.0020.0030.004
mabsKEGG0.0160.0010.017
mabsReactome0.0160.0010.016
matrix2h50.0830.0060.088
meanExpr2h51.9740.1962.172
moa_conn0.0420.0030.045
parse_gctx0.1190.0080.127
qSig1.4280.1242.185
rand_query_ES4.9472.2997.017
read_gmt0.0040.0020.005
result-methods0.0520.0080.060
runWF40.226 2.34550.085
set_readable54.320 1.01755.801
show-methods0.0550.0010.056
sim_score_grp0.0210.0010.022
tail-methods0.0100.0000.011
tarReduce0.0000.0000.001
targetList0.0050.0030.007
vec_char_redu0.0010.0000.001