VJ Carey
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ldblock |
| Branch: RELEASE_3_10 |
| Last Commit: 1a9e941 |
| Last Changed Date: 2019-10-29 13:09:24 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:24 -0400 (Wed, 15 Apr 2020).
| Package 897/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ldblock 1.16.0 VJ Carey
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ldblock |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ldblock_1.16.0.tar.gz |
| StartedAt: 2020-04-15 04:16:29 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:24:35 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 485.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ldblock.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ldblock.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings ldblock_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/ldblock.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.16.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/hmld.Rd:14: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/ldByGene.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/s3_1kg.Rd:26: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expandSnpSet 22.53 0.67 26.23
ldByGene 7.72 1.58 31.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expandSnpSet 23.89 0.86 24.75
ldByGene 8.44 0.77 9.20
* 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/ldblock.Rcheck/00check.log'
for details.
ldblock.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/ldblock_1.16.0.tar.gz && rm -rf ldblock.buildbin-libdir && mkdir ldblock.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ldblock.buildbin-libdir ldblock_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL ldblock_1.16.0.zip && rm ldblock_1.16.0.tar.gz ldblock_1.16.0.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
18 39.5M 18 7664k 0 0 37.0M 0 0:00:01 --:--:-- 0:00:01 37.6M
100 39.5M 100 39.5M 0 0 80.7M 0 --:--:-- --:--:-- --:--:-- 81.1M
install for i386
* installing *source* package 'ldblock' ...
** using staged installation
** 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-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/hmld.Rd:14: 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-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/ldByGene.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
ldblock-package html
ldmat-ldstruct-method html
ldmat html
ldstruct-class html
s3_1kg html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpg1Vwee/R.INSTALL1a284ed56864/ldblock/man/s3_1kg.Rd:26: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
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_1.16.0.zip
* DONE (ldblock)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'ldblock' successfully unpacked and MD5 sums checked
|
ldblock.Rcheck/tests_i386/ldblock_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 04:24:13 2020
***********************************************
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
13.20 0.90 14.09
|
ldblock.Rcheck/tests_x64/ldblock_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 04:24:27 2020
***********************************************
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
13.28 0.48 13.75
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ldblock.Rcheck/examples_i386/ldblock-Ex.timings
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ldblock.Rcheck/examples_x64/ldblock-Ex.timings
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