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CHECK report for DominoEffect on tokay1

This page was generated on 2019-04-13 11:28:54 -0400 (Sat, 13 Apr 2019).

Package 428/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DominoEffect 1.2.1
Marija Buljan
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DominoEffect
Branch: RELEASE_3_8
Last Commit: f16db7f
Last Changed Date: 2019-02-22 09:30:08 -0400 (Fri, 22 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DominoEffect
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DominoEffect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DominoEffect_1.2.1.tar.gz
StartedAt: 2019-04-13 01:52:40 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:59:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 431.2 seconds
RetCode: 0
Status:  OK  
CheckDir: DominoEffect.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DominoEffect.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DominoEffect_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DominoEffect.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DominoEffect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DominoEffect' version '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'DominoEffect' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
import_txdb: no visible binding for global variable 'TXTYPE'
Undefined global functions or variables:
  TXTYPE
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
DominoEffect  1.5   0.47   12.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
DominoEffect     2.60   0.14    5.97
map_to_func_elem 2.23   0.02    5.25
GPo_of_hotspots  2.18   0.03    5.24
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/DominoEffect.Rcheck/00check.log'
for details.



Installation output

DominoEffect.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DominoEffect_1.2.1.tar.gz && rm -rf DominoEffect.buildbin-libdir && mkdir DominoEffect.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DominoEffect.buildbin-libdir DominoEffect_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DominoEffect_1.2.1.zip && rm DominoEffect_1.2.1.tar.gz DominoEffect_1.2.1.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  461k  100  461k    0     0  10.8M      0 --:--:-- --:--:-- --:--:-- 12.1M

install for i386

* installing *source* package 'DominoEffect' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DominoEffect'
    finding HTML links ... done
    DominoEffect                            html  
    GPo_of_hotspots                         html  
    align_to_unip                           html  
    calculate_boundary                      html  
    data                                    html  
    identify_hotspots                       html  
    import_txdb                             html  
    map_to_func_elem                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DominoEffect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DominoEffect' as DominoEffect_1.2.1.zip
* DONE (DominoEffect)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DominoEffect' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

DominoEffect.Rcheck/tests_i386/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
> test_check("DominoEffect")
Loading required package: DominoEffect
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
== testthat results  ===========================================================
OK: 15 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  20.10    1.39   36.14 

DominoEffect.Rcheck/tests_x64/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
> test_check("DominoEffect")
Loading required package: DominoEffect
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

================================================================================
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain' length 655 bytes
==================================================
downloaded 655 bytes

================================================================================
== testthat results  ===========================================================
OK: 15 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  23.04    0.50   36.82 

Example timings

DominoEffect.Rcheck/examples_i386/DominoEffect-Ex.timings

nameusersystemelapsed
DominoEffect 1.50 0.4712.55
GPo_of_hotspots1.480.084.67
align_to_unip0.110.020.13
calculate_boundary000
identify_hotspots0.760.030.80
import_txdb000
map_to_func_elem1.700.034.79

DominoEffect.Rcheck/examples_x64/DominoEffect-Ex.timings

nameusersystemelapsed
DominoEffect2.600.145.97
GPo_of_hotspots2.180.035.24
align_to_unip0.230.000.24
calculate_boundary000
identify_hotspots1.740.001.73
import_txdb000
map_to_func_elem2.230.025.25