VJ Carey
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ldblock |
| Branch: RELEASE_3_6 |
| Last Commit: 3e56153 |
| Last Changed Date: 2018-04-03 11:29:08 -0400 (Tue, 03 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:46 -0400 (Thu, 12 Apr 2018).
| Package 740/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ldblock 1.8.1 VJ Carey
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ldblock |
| Version: 1.8.1 |
| Command: rm -rf ldblock.buildbin-libdir ldblock.Rcheck && mkdir ldblock.buildbin-libdir ldblock.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ldblock.buildbin-libdir ldblock_1.8.1.tar.gz >ldblock.Rcheck\00install.out 2>&1 && cp ldblock.Rcheck\00install.out ldblock-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ldblock.buildbin-libdir --install="check:ldblock-install.out" --force-multiarch --no-vignettes --timings ldblock_1.8.1.tar.gz |
| StartedAt: 2018-04-12 00:59:55 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:07:29 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 453.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ldblock.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### rm -rf ldblock.buildbin-libdir ldblock.Rcheck && mkdir ldblock.buildbin-libdir ldblock.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ldblock.buildbin-libdir ldblock_1.8.1.tar.gz >ldblock.Rcheck\00install.out 2>&1 && cp ldblock.Rcheck\00install.out ldblock-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ldblock.buildbin-libdir --install="check:ldblock-install.out" --force-multiarch --no-vignettes --timings ldblock_1.8.1.tar.gz
###
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##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ldblock.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.1'
* 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-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/hmld.Rd:19: missing file link 'read.delim'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/ldByGene.Rd:33: missing file link 'readVcf'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/s3_1kg.Rd:51: missing file link 'TabixFile'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ldblock.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 40.3Mb
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 ... 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
downloadPopByChr: no visible global function definition for
'download.file'
hmld: no visible global function definition for 'read.delim'
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 download.file read.delim seqinfo seqinfo<-
Consider adding
importFrom("utils", "download.file", "read.delim")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... 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 37.26 0.78 38.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expandSnpSet 40.91 1.07 41.97
* 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 ... NOTE
'::' or ':::' import not declared from: 'BiocStyle'
'library' or 'require' call not declared from: 'gwascat'
* 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-3.6-bioc/meat/ldblock.Rcheck/00check.log'
for details.
ldblock.Rcheck/00install.out
install for i386
* installing *source* package 'ldblock' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/hmld.Rd:19: missing file link 'read.delim'
ldByGene html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/ldByGene.Rd:33: missing file link 'readVcf'
ldblock-package html
ldstruct-class html
s3_1kg html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWygGKd/R.INSTALL2cf8438e7860/ldblock/man/s3_1kg.Rd:51: missing file link 'TabixFile'
** 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_1.8.1.zip
* DONE (ldblock)
In R CMD INSTALL
In R CMD INSTALL
|
ldblock.Rcheck/tests_i386/ldblock_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
RUNIT TEST PROTOCOL -- Thu Apr 12 01:07:11 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
8.85 0.34 9.28
|
ldblock.Rcheck/tests_x64/ldblock_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
RUNIT TEST PROTOCOL -- Thu Apr 12 01:07:24 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
12.10 0.42 12.62
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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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