Holger Schwender
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/trio |
| Branch: RELEASE_3_10 |
| Last Commit: 8f51c41 |
| Last Changed Date: 2020-04-11 14:10:35 -0400 (Sat, 11 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:07:58 -0400 (Wed, 15 Apr 2020).
| Package 1756/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| trio 3.24.3 Holger Schwender
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: trio |
| Version: 3.24.3 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings trio_3.24.3.tar.gz |
| StartedAt: 2020-04-15 01:49:39 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:52:27 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 168.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trio.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings trio_3.24.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/trio.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.24.3’
* 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 ‘trio’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.C("clogreg", ..., PACKAGE = "LogicReg")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
print.trioFS 8.880 0.080 9.015
trioFS 8.568 0.036 8.621
trio.permTest 7.464 0.100 7.576
colGxGPerms 6.856 0.020 6.897
plot.trioLR 5.604 0.044 5.701
* 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 NOTE
See
‘/home/biocbuild/bbs-3.10-bioc/meat/trio.Rcheck/00check.log’
for details.
trio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL trio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘trio’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘trio.Rnw’ ** 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 (trio)
trio.Rcheck/trio-Ex.timings
| name | user | system | elapsed | |
| allelicTDT | 0.024 | 0.000 | 0.025 | |
| colEMlrt | 0.148 | 0.000 | 0.151 | |
| colGxE | 0.012 | 0.000 | 0.013 | |
| colGxGPerms | 6.856 | 0.020 | 6.897 | |
| colPOlrt | 0.024 | 0.000 | 0.023 | |
| colTDTmaxTest | 0.068 | 0.000 | 0.070 | |
| colTDTsam | 0.048 | 0.000 | 0.049 | |
| findLDblocks | 0.032 | 0.000 | 0.031 | |
| getLD | 0.024 | 0.000 | 0.023 | |
| getMatPseudo | 0.02 | 0.00 | 0.02 | |
| lrControl | 0.000 | 0.000 | 0.001 | |
| ped2geno | 0.000 | 0.000 | 0.001 | |
| plot.LDblocks | 0.072 | 0.000 | 0.074 | |
| plot.getLD | 0.036 | 0.000 | 0.033 | |
| plot.trioLR | 5.604 | 0.044 | 5.701 | |
| poly4root | 0.000 | 0.000 | 0.001 | |
| print.colGxE | 0.048 | 0.000 | 0.047 | |
| print.trioFS | 8.880 | 0.080 | 9.015 | |
| print.trioLR | 2.512 | 0.000 | 2.519 | |
| probTDT | 0.040 | 0.000 | 0.039 | |
| read.pedfile | 0.000 | 0.000 | 0.001 | |
| removeSNPs | 0.008 | 0.000 | 0.006 | |
| scoreTDT | 0.012 | 0.000 | 0.010 | |
| tdt | 0.032 | 0.000 | 0.032 | |
| tdtGxG | 1.872 | 0.000 | 1.874 | |
| trio.check | 1.040 | 0.004 | 1.044 | |
| trio.data | 0.008 | 0.000 | 0.008 | |
| trio.permTest | 7.464 | 0.100 | 7.576 | |
| trio.power | 0.020 | 0.000 | 0.019 | |
| trio.prepare | 2.928 | 0.004 | 2.940 | |
| trio.sim | 0.432 | 0.000 | 0.437 | |
| trioFS | 8.568 | 0.036 | 8.621 | |
| trioLR | 2.884 | 0.000 | 2.884 | |