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This page was generated on 2022-06-24 11:07:13 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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? 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 1819/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
signatureSearch 1.11.0  (landing page)
Brendan Gongol
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/signatureSearch
git_branch: master
git_last_commit: 5418f6b
git_last_commit_date: 2022-04-26 12:01:12 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: signatureSearch
Version: 1.11.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings signatureSearch_1.11.0.tar.gz
StartedAt: 2022-06-24 05:50:31 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:57:52 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 441.2 seconds
RetCode: 0
Status:   OK  
CheckDir: signatureSearch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:signatureSearch.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings signatureSearch_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/signatureSearch.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'signatureSearch/DESCRIPTION' ... OK
* this is package 'signatureSearch' version '1.11.0'
* 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 88.4Mb
  sub-directories of 1Mb or more:
    R        82.8Mb
    data      2.9Mb
    extdata   1.5Mb
    libs      1.0Mb
* 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 147 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 'F:/biocbuild/bbs-3.16-bioc/R/library/signatureSearch/libs/x64/signatureSearch.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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        26.62   2.82   37.39
set_readable 22.06   1.26   23.47
addGESSannot  4.42   2.00   23.80
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/signatureSearch.Rcheck/00check.log'
for details.



Installation output

signatureSearch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/signatureSearch_1.11.0.tar.gz && rm -rf signatureSearch.buildbin-libdir && mkdir signatureSearch.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=signatureSearch.buildbin-libdir signatureSearch_1.11.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL signatureSearch_1.11.0.zip && rm signatureSearch_1.11.0.tar.gz signatureSearch_1.11.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 80 3822k   80 3087k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 11.7M
100 3822k  100 3822k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 12.5M
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'signatureSearch' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
  444 |         for (int j = 0; j < S.size(); ++j) {
      |                         ~~^~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fgsea_init.c -o fgsea_init.o
g++ -shared -s -static-libgcc -o signatureSearch.dll tmp.def RcppExports.o fastGSEA.o fgsea_init.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/signatureSearch.buildbin-libdir/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
** 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
* MD5 sums
packaged installation of 'signatureSearch' as signatureSearch_1.11.0.zip
* DONE (signatureSearch)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'signatureSearch' successfully unpacked and MD5 sums checked

Tests output

signatureSearch.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
   0.23    0.06    0.23 

Example timings

signatureSearch.Rcheck/signatureSearch-Ex.timings

nameusersystemelapsed
addGESSannot 4.42 2.0023.80
addMOA0.170.030.20
add_pcid0.000.020.02
append2H50.100.030.17
build_custom_db0.340.030.42
cellNtestPlot1.630.061.78
cell_info0.010.000.02
cell_info20.030.020.05
chembl_moa_list0.020.000.01
clue_moa_list000
comp_fea_res0.120.000.13
create_empty_h50.020.010.03
dim-methods0.010.000.01
drug_cell_ranks000
drugs-methods000
drugs100.020.000.02
dtnetplot1.700.252.37
enrichGO2000
enrichKEGG2000
enrichMOA0.050.000.11
enrichReactome000
fea000
feaResult000
gctx2h50.460.140.77
gess000
gessResult000
gess_res_vis0.290.000.28
getSig1.260.251.75
getTreats0.520.050.61
get_targets1.680.312.08
gmt2h50.130.000.41
gseGO20.010.000.01
gseKEGG2000
gseReactome0.020.000.02
head-methods000
lincs_expr_inst_info0.050.000.04
lincs_pert_info0.110.000.11
lincs_pert_info21.290.031.33
lincs_sig_info0.030.000.03
list2df000
list_rev000
mabsGO0.000.010.02
mabsKEGG0.020.000.01
mabsReactome000
matrix2h50.060.020.11
meanExpr2h50.490.170.80
moa_conn0.010.020.03
parse_gctx0.070.010.08
qSig0.890.221.23
rand_query_ES3.500.283.80
read_gmt000
result-methods0.030.000.03
runWF26.62 2.8237.39
set_readable22.06 1.2623.47
show-methods0.040.000.03
sim_score_grp0.030.000.03
tail-methods000
tarReduce000
targetList0.000.020.02
vec_char_redu000