Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for ldblock on tokay2

This page was generated on 2018-10-17 08:41:01 -0400 (Wed, 17 Oct 2018).

Package 781/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ldblock 1.10.0
VJ Carey
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ldblock
Branch: RELEASE_3_7
Last Commit: a143371
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ldblock
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ldblock_1.10.0.tar.gz
StartedAt: 2018-10-17 02:56:46 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:04:32 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 465.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ldblock.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ldblock_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.10.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/hmld.Rd:19: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/ldByGene.Rd:33: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/s3_1kg.Rd:50: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 40.2Mb
  sub-directories of 1Mb or more:
    hapmap  39.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics'
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'Homo.sapiens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
stack1kg: no visible global function definition for 'Seqinfo'
stack1kg: no visible global function definition for 'seqinfo<-'
stack1kg: no visible global function definition for 'seqinfo'
Undefined global functions or variables:
  Seqinfo seqinfo seqinfo<-
* checking Rd files ... NOTE
prepare_Rd: downloadPopByChr.Rd:49-51: Dropping empty section \seealso
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
expandSnpSet 26.43   0.96   29.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
expandSnpSet 27.52   1.22   28.74
* 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: 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ldblock.Rcheck/00check.log'
for details.



Installation output

ldblock.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ldblock_1.10.0.tar.gz && rm -rf ldblock.buildbin-libdir && mkdir ldblock.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ldblock.buildbin-libdir ldblock_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ldblock_1.10.0.zip && rm ldblock_1.10.0.tar.gz ldblock_1.10.0.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
 34 39.5M   34 13.5M    0     0  80.0M      0 --:--:-- --:--:-- --:--:-- 82.9M
100 39.5M  100 39.5M    0     0  98.8M      0 --:--:-- --:--:-- --:--:--  100M

install for i386

* installing *source* package 'ldblock' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ldblock'
    finding HTML links ... done
    downloadPopByChr                        html  
    expandSnpSet                            html  
    hmld                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/hmld.Rd:19: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
    ldByGene                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/ldByGene.Rd:33: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    ldblock-package                         html  
    ldstruct-class                          html  
    s3_1kg                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpq806c5/R.INSTALL155836564b43/ldblock/man/s3_1kg.Rd:50: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ldblock' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ldblock' as ldblock_1.10.0.zip
* DONE (ldblock)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ldblock' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

ldblock.Rcheck/tests_i386/ldblock_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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')

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows





RUNIT TEST PROTOCOL -- Wed Oct 17 03:04:12 2018 
*********************************************** 
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 
  11.39    0.96   12.45 

ldblock.Rcheck/tests_x64/ldblock_unit_tests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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')

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows





RUNIT TEST PROTOCOL -- Wed Oct 17 03:04:26 2018 
*********************************************** 
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 
  12.60    0.50   13.29 

Example timings

ldblock.Rcheck/examples_i386/ldblock-Ex.timings

nameusersystemelapsed
downloadPopByChr000
expandSnpSet26.43 0.9629.04
hmld000
ldByGene3.100.513.72
ldblock-package000
ldstruct-class000
s3_1kg000

ldblock.Rcheck/examples_x64/ldblock-Ex.timings

nameusersystemelapsed
downloadPopByChr000
expandSnpSet27.52 1.2228.74
hmld000
ldByGene2.330.592.93
ldblock-package000
ldstruct-class000
s3_1kg000