Ines de Santiago
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/BaalChIP |
| Branch: RELEASE_3_10 |
| Last Commit: cdb93e0 |
| Last Changed Date: 2019-10-29 13:10:05 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:11:50 -0400 (Wed, 15 Apr 2020).
| Package 101/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BaalChIP 1.12.0 Ines de Santiago
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BaalChIP |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BaalChIP_1.12.0.tar.gz |
| StartedAt: 2020-04-15 04:09:04 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:23:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 838.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BaalChIP.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BaalChIP_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BaalChIP.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 ‘BaalChIP/DESCRIPTION’ ... OK
* this is package ‘BaalChIP’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BaalChIP’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 198.2Mb
sub-directories of 1Mb or more:
data 95.8Mb
test 101.9Mb
* 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
* 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
applyBayes: no visible binding for global variable ‘SNP_id’
plot.filt.barplot: no visible binding for global variable ‘cellname’
plot.filt.barplot: no visible binding for global variable ‘value’
plot.filt.barplot: no visible binding for global variable ‘variable’
plot.filt.boxplot: no visible binding for global variable ‘variable’
plot.filt.boxplot: no visible binding for global variable ‘value’
plot.filt.boxplot: no visible binding for global variable ‘coltype’
plot.filt.pie: no visible binding for global variable ‘variable’
plot.filt.pie: no visible binding for global variable ‘value.mean’
plot.simul: no visible binding for global variable ‘readslen’
plot.simul: no visible binding for global variable ‘perc_right’
plotadjustment: no visible binding for global variable ‘value’
plotadjustment: no visible binding for global variable ‘variable’
Undefined global functions or variables:
SNP_id cellname coltype perc_right readslen value value.mean variable
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.10-bioc/R/library/BaalChIP/test’, resetting
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/BaalChIP.Rcheck/00check.log’
for details.
BaalChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BaalChIP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘BaalChIP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (BaalChIP)
BaalChIP.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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("BaalChIP")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Wed Apr 15 04:22:57 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
BaalChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.508 0.408 12.516
BaalChIP.Rcheck/BaalChIP-Ex.timings
| name | user | system | elapsed | |
| BaalChIP.get | 0.080 | 0.004 | 0.085 | |
| BaalChIP.report | 0.016 | 0.000 | 0.017 | |
| adjustmentBaalPlot | 1.104 | 0.004 | 1.107 | |
| plotQC | 1.248 | 0.004 | 1.336 | |
| plotSimul | 0.280 | 0.000 | 0.286 | |
| summaryASB | 0.004 | 0.000 | 0.004 | |
| summaryQC | 0.080 | 0.000 | 0.082 | |