Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:06:30 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 DominoEffect on tokay2


To the developers/maintainers of the DominoEffect package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DominoEffect.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 534/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DominoEffect 1.14.0  (landing page)
Marija Buljan
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/DominoEffect
git_branch: RELEASE_3_14
git_last_commit: edcdc89
git_last_commit_date: 2021-10-26 12:42:03 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: DominoEffect
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DominoEffect.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DominoEffect_1.14.0.tar.gz
StartedAt: 2022-01-18 18:41:51 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 18:49:19 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 448.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DominoEffect.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DominoEffect.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DominoEffect_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DominoEffect.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.14.0'
* 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 ... 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 LazyData ... 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 (user + system) or elapsed time > 5s
                 user system elapsed
DominoEffect     6.19   0.34   11.23
GPo_of_hotspots  5.00   0.14    8.84
map_to_func_elem 4.86   0.05    8.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DominoEffect     5.08   0.16    9.86
GPo_of_hotspots  3.91   0.14    7.89
map_to_func_elem 3.66   0.06    7.47
* 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-3.14-bioc/meat/DominoEffect.Rcheck/00check.log'
for details.



Installation output

DominoEffect.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DominoEffect_1.14.0.tar.gz && rm -rf DominoEffect.buildbin-libdir && mkdir DominoEffect.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DominoEffect.buildbin-libdir DominoEffect_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DominoEffect_1.14.0.zip && rm DominoEffect_1.14.0.tar.gz DominoEffect_1.14.0.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
 21  462k   21   99k    0     0   751k      0 --:--:-- --:--:-- --:--:--  751k
100  462k  100  462k    0     0  1962k      0 --:--:-- --:--:-- --:--:-- 1958k

install for i386

* installing *source* package 'DominoEffect' ...
** using staged installation
** 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 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 'DominoEffect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DominoEffect' as DominoEffect_1.14.0.zip
* DONE (DominoEffect)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DominoEffect' successfully unpacked and MD5 sums checked

Tests output

DominoEffect.Rcheck/tests_i386/test-all.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> 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

================================================================================
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  31.25    1.56   46.85 

DominoEffect.Rcheck/tests_x64/test-all.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> 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

================================================================================
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  28.18    0.73   42.37 

Example timings

DominoEffect.Rcheck/examples_i386/DominoEffect-Ex.timings

nameusersystemelapsed
DominoEffect 6.19 0.3411.23
GPo_of_hotspots5.000.148.84
align_to_unip0.250.030.28
calculate_boundary000
identify_hotspots0.250.050.29
import_txdb000
map_to_func_elem4.860.058.67

DominoEffect.Rcheck/examples_x64/DominoEffect-Ex.timings

nameusersystemelapsed
DominoEffect5.080.169.86
GPo_of_hotspots3.910.147.89
align_to_unip0.220.000.21
calculate_boundary000
identify_hotspots0.180.000.19
import_txdb000
map_to_func_elem3.660.067.47