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This page was generated on 2021-09-27 15:06:25 -0400 (Mon, 27 Sep 2021).

CHECK results for GENESIS on tokay2

To the developers/maintainers of the GENESIS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GENESIS.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 726/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.22.2  (landing page)
Stephanie M. Gogarten
Snapshot Date: 2021-09-26 04:50:10 -0400 (Sun, 26 Sep 2021)
git_url: https://git.bioconductor.org/packages/GENESIS
git_branch: RELEASE_3_13
git_last_commit: df77222
git_last_commit_date: 2021-06-16 02:13:52 -0400 (Wed, 16 Jun 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    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GENESIS
Version: 2.22.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GENESIS_2.22.2.tar.gz
StartedAt: 2021-09-26 23:12:22 -0400 (Sun, 26 Sep 2021)
EndedAt: 2021-09-26 23:20:49 -0400 (Sun, 26 Sep 2021)
EllapsedTime: 507.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GENESIS_2.22.2.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GENESIS.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GENESIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENESIS' version '2.22.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'GENESIS' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Unexported object imported by a ':::' call: 'survey:::saddle'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pcrelate: no visible binding for global variable 'k'
calcISAFBeta: no visible binding for global variable 'k'
pcrelateSampBlock: no visible binding for global variable 'k'
Undefined global functions or variables:
  k
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GENESIS/libs/i386/GENESIS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/GENESIS/libs/x64/GENESIS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
fitNullModel 15.46   0.42   15.89
varCompCI    12.39   0.44   12.82
pcrelate      9.75   0.51   10.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
fitNullModel 15.04   0.37   15.39
varCompCI    10.82   0.44   11.25
pcrelate     10.22   0.35   10.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/GENESIS.Rcheck/00check.log'
for details.



Installation output

GENESIS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GENESIS_2.22.2.tar.gz && rm -rf GENESIS.buildbin-libdir && mkdir GENESIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GENESIS.buildbin-libdir GENESIS_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GENESIS_2.22.2.zip && rm GENESIS_2.22.2.tar.gz GENESIS_2.22.2.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
  0 2139k    0  2487    0     0  30550      0  0:01:11 --:--:--  0:01:11 30329
100 2139k  100 2139k    0     0  2399k      0 --:--:-- --:--:-- --:--:-- 2398k

install for i386

* installing *source* package 'GENESIS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fht.c -o fht.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GENESIS.dll tmp.def fht.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GENESIS.buildbin-libdir/00LOCK-GENESIS/00new/GENESIS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GENESIS'
    finding HTML links ... done
    GENESIS-package                         html  
    HapMap_ASW_MXL_KINGmat                  html  
    admixMap                                html  
    finding level-2 HTML links ... done

    assocTestAggregate                      html  
    assocTestSingle                         html  
    computeVSIF                             html  
    defunct                                 html  
    effectAllele                            html  
    fitNullModel                            html  
    jointScoreTest                          html  
    kin2gds                                 html  
    kingToMatrix                            html  
    makeSparseMatrix                        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GENESIS.buildbin-libdir/00LOCK-GENESIS/00new/GENESIS/help/makeSparseMatrix+2CMatrix-method.html
    pcair                                   html  
    pcairPartition                          html  
    pcrelate                                html  
    pcrelateToMatrix                        html  
    plot.pcair                              html  
    print.pcair                             html  
    sample_annotation_1KG                   html  
    varCompCI                               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

install for x64

* installing *source* package 'GENESIS' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fht.c -o fht.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GENESIS.dll tmp.def fht.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GENESIS.buildbin-libdir/GENESIS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.22.2.zip
* DONE (GENESIS)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GENESIS' successfully unpacked and MD5 sums checked

Tests output

GENESIS.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(GENESIS)
> 
> test_check("GENESIS")
# of selected variants: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 623 ]
> 
> proc.time()
   user  system elapsed 
  87.21    3.46   90.95 

GENESIS.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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(GENESIS)
> 
> test_check("GENESIS")
# of selected variants: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 623 ]
> 
> proc.time()
   user  system elapsed 
 105.23    2.40  107.81 

Example timings

GENESIS.Rcheck/examples_i386/GENESIS-Ex.timings

nameusersystemelapsed
admixMap0.880.090.98
assocTestAggregate3.010.173.19
assocTestSingle2.700.183.00
computeVSIF0.080.000.08
effectAllele1.550.121.67
fitNullModel15.46 0.4215.89
jointScoreTest0.040.030.06
kin2gds0.800.081.04
kingToMatrix0.690.080.82
pcair0.540.050.60
pcairPartition0.070.030.10
pcrelate 9.75 0.5110.26
plot.pcair0.460.050.52
print.pcair0.360.050.41
varCompCI12.39 0.4412.82

GENESIS.Rcheck/examples_x64/GENESIS-Ex.timings

nameusersystemelapsed
admixMap0.870.060.94
assocTestAggregate3.440.083.52
assocTestSingle2.380.082.45
computeVSIF0.060.000.07
effectAllele1.090.061.15
fitNullModel15.04 0.3715.39
jointScoreTest0.060.000.07
kin2gds0.470.070.53
kingToMatrix0.430.010.45
pcair0.320.030.34
pcairPartition0.030.000.04
pcrelate10.22 0.3510.56
plot.pcair0.290.040.34
print.pcair0.390.030.42
varCompCI10.82 0.4411.25