VJ Carey
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/gwascat |
| Branch: RELEASE_3_6 |
| Last Commit: d106e22 |
| Last Changed Date: 2017-10-30 12:39:38 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:34 -0400 (Thu, 12 Apr 2018).
| Package 634/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gwascat 2.10.0 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: gwascat |
| Version: 2.10.0 |
| Command: rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.10.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.10.0.tar.gz |
| StartedAt: 2018-04-12 00:38:33 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:49:14 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 640.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gwascat.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_2.10.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gwascat.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 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.10.0'
* 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 'gwascat' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKQqc8j/R.INSTALL2d60450b4746/gwascat/man/gwascat-package.Rd:76: missing file link 'nodeData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKQqc8j/R.INSTALL2d60450b4746/gwascat/man/ldtagr.Rd:19: missing file link 'genotypeToSnpMatrix'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gwascat.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 39.1Mb
sub-directories of 1Mb or more:
data 30.9Mb
doc 1.0Mb
obo 3.0Mb
olddata 2.2Mb
tab 1.1Mb
* 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
buildq: no visible global function definition for 'read.delim'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'data'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible global function definition for
'read.delim'
makeCurrentGwascat: no visible global function definition for 'data'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
'sessionInfo'
makeCurrentGwascat.legacy: no visible global function definition for
'read.delim'
makeCurrentGwascat.legacy: no visible global function definition for
'data'
makeCurrentGwascat.legacy: no visible binding for global variable
'si.hs.38'
snpGenos: no visible global function definition for 'getSNPlocs'
tfilt: no visible binding for global variable 'phr'
tpad: no visible binding for global variable 'phr'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
PVALUE_MLOG data getSNPlocs gwrngs gwrngs19 phr read.delim
sessionInfo si.hs.37 si.hs.38 snpsBySeqname
Consider adding
importFrom("utils", "data", "read.delim", "sessionInfo")
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 ... NOTE
Note: found 6 marked Latin-1 strings
Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... 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
riskyAlleleCount 11.44 0.08 11.52
gwcex2gviz 7.40 0.37 7.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 9.08 0.10 9.17
gwcex2gviz 7.43 0.23 7.65
* 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 ... NOTE
'::' or ':::' import not declared from: 'BiocStyle'
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/gwascat.Rcheck/00check.log'
for details.
gwascat.Rcheck/00install.out
install for i386
* installing *source* package 'gwascat' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'gwascat'
finding HTML links ... done
bindcadd_snv html
gwascat-package html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKQqc8j/R.INSTALL2d60450b4746/gwascat/man/gwascat-package.Rd:76: missing file link 'nodeData'
gwastagger html
gwaswloc-class html
finding level-2 HTML links ... done
gwcex2gviz html
gwdf_2012_02_02 html
ldtagr html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKQqc8j/R.INSTALL2d60450b4746/gwascat/man/ldtagr.Rd:19: missing file link 'genotypeToSnpMatrix'
locon6 html
makeCurrentGwascat html
obo2graphNEL html
riskyAlleleCount html
topTraits html
traitsManh html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'gwascat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.10.0.zip
* DONE (gwascat)
In R CMD INSTALL
In R CMD INSTALL
|
gwascat.Rcheck/tests_i386/test-all.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("gwascat")
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
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:48:52 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gwascat 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
13.48 0.65 14.26
|
gwascat.Rcheck/tests_x64/test-all.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("gwascat")
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
gwascat loaded. Use data(ebicat38) for hg38 coordinates;
data(ebicat37) for hg19 coordinates.
RUNIT TEST PROTOCOL -- Thu Apr 12 00:49:09 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
gwascat 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
16.14 0.43 16.65
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gwascat.Rcheck/examples_i386/gwascat-Ex.timings
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gwascat.Rcheck/examples_x64/gwascat-Ex.timings
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