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This page was generated on 2022-01-18 11:08:23 -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 riesling1


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: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings signatureSearch_1.9.4.tar.gz
StartedAt: 2022-01-17 20:09:03 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 20:15:44 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 400.5 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:signatureSearch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings signatureSearch_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/signatureSearch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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:
  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 whether package 'signatureSearch' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 88.0Mb
  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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/signatureSearch/libs/x64/signatureSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runWF        24.25   3.63   36.22
set_readable 21.39   2.01   23.85
addGESSannot  4.75   1.10    6.55
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/signatureSearch.Rcheck/00check.log'
for details.



Installation output

signatureSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'signatureSearch' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 long unsigned int'} [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-signatureSearch/00new/signatureSearch/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'signatureSearch'
    finding HTML links ... done
    GCT-object                              html  
    addGESSannot                            html  
    addMOA                                  html  
    add_pcid                                html  
    append2H5                               html  
    build_custom_db                         html  
    calcGseaStatBatchCpp                    html  
    cellNtestPlot                           html  
    cell_info                               html  
    chembl_moa_list                         html  
    clue_moa_list                           html  
    comp_fea_res                            html  
    create_empty_h5                         html  
    dim-methods                             html  
    drug_cell_ranks                         html  
    drugs-methods                           html  
    drugs10                                 html  
    dtnetplot                               html  
    enrichGO2                               html  
    enrichKEGG2                             html  
    enrichMOA                               html  
    enrichReactome                          html  
    fea                                     html  
    feaResult-class                         html  
    feaResult                               html  
    gctx2h5                                 html  
    gess                                    html  
    gessResult-class                        html  
    gessResult                              html  
    gess_res_vis                            html  
    getALLEG                                html  
    getDb                                   html  
    getSig                                  html  
    getTreats                               html  
    get_targets                             html  
    gmt2h5                                  html  
    gseGO2                                  html  
    gseKEGG2                                html  
    gseReactome                             html  
    head-methods                            html  
    lincs_expr_inst_info                    html  
    lincs_pert_info                         html  
    lincs_pert_info2                        html  
    lincs_sig_info                          html  
    list2df                                 html  
    list_rev                                html  
    mabsGO                                  html  
    mabsKEGG                                html  
    mabsReactome                            html  
    matrix2h5                               html  
    meanExpr2h5                             html  
    moa_conn                                html  
    parse_gctx                              html  
    qSig-class                              html  
    qSig                                    html  
    rand_query_ES                           html  
    read_gmt                                html  
    result-methods                          html  
    runWF                                   html  
    set_readable                            html  
    show-methods                            html  
    signatureSearch-package                 html  
    sim_score_grp                           html  
    tail-methods                            html  
    tarReduce                               html  
    targetList                              html  
    vec_char_redu                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (signatureSearch)
Making 'packages.html' ... done

Tests output

signatureSearch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.14    0.06    0.17 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot4.751.106.55
addMOA0.170.000.17
add_pcid000
append2H50.070.000.11
build_custom_db0.250.050.34
cellNtestPlot0.570.140.97
cell_info0.010.020.03
chembl_moa_list000
clue_moa_list0.020.000.02
comp_fea_res0.170.010.18
create_empty_h50.020.000.04
dim-methods000
drug_cell_ranks0.010.000.01
drugs-methods000
drugs100.000.020.02
dtnetplot1.840.192.45
enrichGO2000
enrichKEGG2000
enrichMOA0.030.000.03
enrichReactome000
fea000
feaResult000
gctx2h51.350.091.56
gess000
gessResult000
gess_res_vis0.230.030.26
getSig1.170.241.96
getTreats0.440.030.75
get_targets1.520.112.02
gmt2h50.140.000.72
gseGO20.000.010.01
gseKEGG2000
gseReactome0.020.000.02
head-methods000
lincs_expr_inst_info0.030.000.03
lincs_pert_info0.090.000.09
lincs_pert_info20.190.050.24
lincs_sig_info0.090.010.11
list2df0.020.000.01
list_rev000
mabsGO000
mabsKEGG000
mabsReactome0.010.000.02
matrix2h50.020.000.08
meanExpr2h50.340.110.50
moa_conn0.020.000.01
parse_gctx0.050.020.07
qSig0.790.081.39
rand_query_ES2.720.483.20
read_gmt000
result-methods0.020.000.01
runWF24.25 3.6336.22
set_readable21.39 2.0123.85
show-methods0.010.000.01
sim_score_grp000
tail-methods000
tarReduce0.010.000.01
targetList000
vec_char_redu000