VJ Carey
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gwascat |
| Branch: RELEASE_3_9 |
| Last Commit: 805b304 |
| Last Changed Date: 2019-10-14 14:51:42 -0400 (Mon, 14 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:00:56 -0400 (Wed, 16 Oct 2019).
| Package 736/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gwascat 2.16.1 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: gwascat |
| Version: 2.16.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwascat_2.16.1.tar.gz |
| StartedAt: 2019-10-16 02:16:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:22:02 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 351.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gwascat.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gwascat_2.16.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.16.1’
* 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 3.1Mb
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 ... WARNING
Missing link or links in documentation object 'ldtagr.Rd':
‘genotypeToSnpMatrix’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
riskyAlleleCount 14.429 0.075 15.042
gwcex2gviz 12.736 0.220 12.961
* 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/gwascat.Rcheck/00check.log’
for details.
gwascat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gwascat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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 -- Wed Oct 16 02:21:58 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
15.130 0.498 16.479
gwascat.Rcheck/gwascat-Ex.timings
| name | user | system | elapsed | |
| bindcadd_snv | 0.000 | 0.000 | 0.001 | |
| gwascat-package | 0.974 | 0.016 | 0.989 | |
| gwastagger | 1.809 | 0.044 | 1.852 | |
| gwaswloc-class | 0.002 | 0.000 | 0.002 | |
| gwcex2gviz | 12.736 | 0.220 | 12.961 | |
| gwdf_2012_02_02 | 0 | 0 | 0 | |
| ldtagr | 3.636 | 0.196 | 3.851 | |
| locon6 | 0.039 | 0.000 | 0.038 | |
| makeCurrentGwascat | 0.000 | 0.000 | 0.001 | |
| obo2graphNEL | 0.295 | 0.008 | 0.304 | |
| riskyAlleleCount | 14.429 | 0.075 | 15.042 | |
| topTraits | 1.014 | 0.032 | 1.067 | |
| traitsManh | 0 | 0 | 0 | |