Multiple platform build/check report for BioC 3.14 - CHECK results for GENESIS on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: GENESIS

Version: 2.24.2

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GENESIS_2.24.2.tar.gz

StartedAt: 2022-04-12 20:11:17 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:26:26 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 909.6 seconds

RetCode: 0

Status: OK

CheckDir: GENESIS.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GENESIS_2.24.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GENESIS.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.24.2'
* 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 ... 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 ... 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-3.14-bioc/R/library/GENESIS/libs/i386/GENESIS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-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
pcrelate     11.65   0.36   12.02
effectAllele  2.37   0.07   11.59
fitNullModel  2.10   0.16   24.22
varCompCI     1.52   0.22   27.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
pcrelate     10.25   0.39   10.63
effectAllele  2.65   0.05   11.86
fitNullModel  1.94   0.14   26.25
varCompCI     1.56   0.17   25.02
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GENESIS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GENESIS_2.24.2.tar.gz && rm -rf GENESIS.buildbin-libdir && mkdir GENESIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GENESIS.buildbin-libdir GENESIS_2.24.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GENESIS_2.24.2.zip && rm GENESIS_2.24.2.tar.gz GENESIS_2.24.2.zip
###
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100 2145k  100 2145k    0     0  1689k      0  0:00:01  0:00:01 --:--:-- 1691k

install for i386

* installing *source* package 'GENESIS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3.14-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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GENESIS.buildbin-libdir/GENESIS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.24.2.zip
* DONE (GENESIS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GENESIS' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 12 | SKIP 0 | PASS 673 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 673 ]
> 
> proc.time()
   user  system elapsed 
 124.04    4.56  246.70


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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(GENESIS)
> 
> test_check("GENESIS")
# of selected variants: 10
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 673 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 673 ]
> 
> proc.time()
   user  system elapsed 
 134.03    3.21  266.59

name	user	system	elapsed
admixMap	1.17	0.04	1.22
assocTestAggregate	3.29	0.27	3.62
assocTestSingle	3.00	0.19	3.22
computeVSIF	0.11	0.00	0.11
effectAllele	2.37	0.07	11.59
fitNullModel	2.10	0.16	24.22
jointScoreTest	0.07	0.00	0.08
kin2gds	0.85	0.03	1.03
kingToMatrix	0.72	0.02	0.73
pcair	0.40	0.00	0.41
pcairPartition	0.03	0.00	0.03
pcrelate	11.65	0.36	12.02
plot.pcair	0.37	0.01	0.39
print.pcair	0.34	0.02	0.36
varCompCI	1.52	0.22	27.04

name	user	system	elapsed
admixMap	1.09	0.08	1.17
assocTestAggregate	3.28	0.14	3.47
assocTestSingle	3.27	0.09	3.45
computeVSIF	0.06	0.00	0.06
effectAllele	2.65	0.05	11.86
fitNullModel	1.94	0.14	26.25
jointScoreTest	0.06	0.00	0.06
kin2gds	0.78	0.02	0.80
kingToMatrix	0.42	0.00	0.42
pcair	0.47	0.01	0.48
pcairPartition	0.05	0.02	0.06
pcrelate	10.25	0.39	10.63
plot.pcair	0.41	0.05	0.45
print.pcair	0.36	0.01	0.37
varCompCI	1.56	0.17	25.02

CHECK results for GENESIS on tokay2

Summary

Command output

Installation output

Tests output

Example timings