Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:33 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 ldblock on tokay2


To the developers/maintainers of the ldblock package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ldblock.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 990/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ldblock 1.24.0  (landing page)
VJ Carey
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/ldblock
git_branch: RELEASE_3_14
git_last_commit: e757bbd
git_last_commit_date: 2021-10-26 12:22:15 -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: ldblock
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ldblock_1.24.0.tar.gz
StartedAt: 2022-01-20 22:04:27 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 22:12:25 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 478.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ldblock.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ldblock_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ldblock.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 'ldblock/DESCRIPTION' ... OK
* this is package 'ldblock' version '1.24.0'
* 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 'ldblock' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 40.6Mb
  sub-directories of 1Mb or more:
    hapmap  39.9Mb
* 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
downloadPopByChr: no visible global function definition for
  'download.file'
hmld: no visible global function definition for 'read.delim'
ldmat: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  download.file read.delim
Consider adding
  importFrom("utils", "download.file", "read.delim")
to your NAMESPACE file.
* 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
expandSnpSet 30.15   0.73   32.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
expandSnpSet 24.71   1.06   25.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'ldblock_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'ldblock_unit_tests.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/ldblock.Rcheck/00check.log'
for details.



Installation output

ldblock.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ldblock_1.24.0.tar.gz && rm -rf ldblock.buildbin-libdir && mkdir ldblock.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ldblock.buildbin-libdir ldblock_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ldblock_1.24.0.zip && rm ldblock_1.24.0.tar.gz ldblock_1.24.0.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
  0 39.7M    0  272k    0     0  1043k      0  0:00:38 --:--:--  0:00:38 1045k
  8 39.7M    8 3614k    0     0  2881k      0  0:00:14  0:00:01  0:00:13 2882k
 19 39.7M   19 7928k    0     0  3496k      0  0:00:11  0:00:02  0:00:09 3495k
 32 39.7M   32 12.8M    0     0  4028k      0  0:00:10  0:00:03  0:00:07 4028k
 47 39.7M   47 18.7M    0     0  4503k      0  0:00:09  0:00:04  0:00:05 4503k
 64 39.7M   64 25.6M    0     0  5004k      0  0:00:08  0:00:05  0:00:03 5210k
 84 39.7M   84 33.6M    0     0  5501k      0  0:00:07  0:00:06  0:00:01 6159k
 88 39.7M   88 35.3M    0     0  4972k      0  0:00:08  0:00:07  0:00:01 5641k
 89 39.7M   89 35.4M    0     0  4388k      0  0:00:09  0:00:08  0:00:01 4623k
 89 39.7M   89 35.5M    0     0  3928k      0  0:00:10  0:00:09  0:00:01 3436k
 89 39.7M   89 35.5M    0     0  3547k      0  0:00:11  0:00:10  0:00:01 2021k
 95 39.7M   95 38.1M    0     0  3465k      0  0:00:11  0:00:11 --:--:--  924k
100 39.7M  100 39.7M    0     0  3509k      0  0:00:11  0:00:11 --:--:-- 1049k

install for i386

* installing *source* package 'ldblock' ...
** 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 'ldblock'
    finding HTML links ... done
    EUR_singletons                          html  
    downloadPopByChr                        html  
    expandSnpSet                            html  
    hmld                                    html  
    ldByGene                                html  
    finding level-2 HTML links ... done

    ldblock-package                         html  
    ldmat-ldstruct-method                   html  
    ldmat                                   html  
    ldstruct-class                          html  
    s3_1kg                                  html  
    sampinf_1kg                             html  
    stack1kg                                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 'ldblock' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ldblock' as ldblock_1.24.0.zip
* DONE (ldblock)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ldblock' successfully unpacked and MD5 sums checked

Tests output

ldblock.Rcheck/tests_i386/ldblock_unit_tests.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.

> BiocGenerics:::testPackage('ldblock')


RUNIT TEST PROTOCOL -- Thu Jan 20 22:12:02 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ldblock RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.26    1.00   16.26 

ldblock.Rcheck/tests_x64/ldblock_unit_tests.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.

> BiocGenerics:::testPackage('ldblock')


RUNIT TEST PROTOCOL -- Thu Jan 20 22:12:18 2022 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ldblock RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  15.00    0.71   15.70 

Example timings

ldblock.Rcheck/examples_i386/ldblock-Ex.timings

nameusersystemelapsed
downloadPopByChr000
expandSnpSet30.15 0.7332.44
hmld000
ldByGene000
ldblock-package000
ldmat000
ldstruct-class000
s3_1kg0.010.000.01
stack1kg000

ldblock.Rcheck/examples_x64/ldblock-Ex.timings

nameusersystemelapsed
downloadPopByChr000
expandSnpSet24.71 1.0625.78
hmld000
ldByGene000
ldblock-package000
ldmat000
ldstruct-class000
s3_1kg0.020.000.02
stack1kg000