VJ Carey
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gwascat |
| Branch: master |
| Last Commit: 9941882 |
| Last Changed Date: 2019-03-19 13:34:25 -0400 (Tue, 19 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:03:51 -0400 (Tue, 09 Apr 2019).
| Package 725/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gwascat 2.15.1 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: gwascat |
| Version: 2.15.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.15.1.tar.gz |
| StartedAt: 2019-04-09 02:38:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:46:52 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 515.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gwascat.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gwascat_2.15.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.15.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gwascat’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 36.6Mb
sub-directories of 1Mb or more:
data 28.7Mb
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
* 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
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘snpsBySeqname’
lo38to19: no visible binding for global variable ‘si.hs.37’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
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 global function definition for ‘autoplot’
traitsManh: no visible global function definition for ‘aes’
traitsManh: no visible binding for global variable ‘PVALUE_MLOG’
variantProps: no visible binding for global variable ‘gwrngs’
Undefined global functions or variables:
PVALUE_MLOG aes autoplot getSNPlocs gwrngs gwrngs19 phr si.hs.37
si.hs.38 snpsBySeqname
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 19.635 0.248 21.028
gwcex2gviz 18.046 1.038 20.168
ldtagr 5.166 0.198 5.989
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck/00check.log’
for details.
gwascat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gwascat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘gwascat’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (gwascat)
gwascat.Rcheck/tests/test-all.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, 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 -- Tue Apr 9 02:46:43 2019
***********************************************
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
16.441 1.391 17.860
gwascat.Rcheck/gwascat-Ex.timings
| name | user | system | elapsed | |
| bindcadd_snv | 0.000 | 0.001 | 0.001 | |
| gwascat-package | 1.017 | 0.071 | 1.089 | |
| gwastagger | 2.670 | 0.113 | 2.787 | |
| gwaswloc-class | 0.004 | 0.001 | 0.004 | |
| gwcex2gviz | 18.046 | 1.038 | 20.168 | |
| gwdf_2012_02_02 | 0.001 | 0.000 | 0.000 | |
| ldtagr | 5.166 | 0.198 | 5.989 | |
| locon6 | 0.045 | 0.011 | 0.067 | |
| makeCurrentGwascat | 0 | 0 | 0 | |
| obo2graphNEL | 0.343 | 0.011 | 0.378 | |
| riskyAlleleCount | 19.635 | 0.248 | 21.028 | |
| topTraits | 0.770 | 0.066 | 0.835 | |
| traitsManh | 0.000 | 0.001 | 0.001 | |