Tin Nguyen
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BLMA |
| Branch: RELEASE_3_8 |
| Last Commit: bb6599e |
| Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:37 -0400 (Tue, 16 Apr 2019).
| Package 169/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BLMA 1.6.0 Tin Nguyen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BLMA |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BLMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BLMA_1.6.0.tar.gz |
| StartedAt: 2019-04-15 22:40:30 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:47:26 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 416.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BLMA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BLMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BLMA_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BLMA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BLMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BLMA’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘ROntoTools’ ‘GSA’ ‘PADOG’ ‘limma’ ‘graph’ ‘parallel’ ‘Biobase’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘BLMA’ 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 ... OK
* checking R code for possible problems ... NOTE
addCLT: warning in pnorm(mean(x), 1/2, sqrt(1/(12 * n)), lower = TRUE):
partial argument match of 'lower' to 'lower.tail'
additiveMethod: warning in pnorm(sum(x), n/2, sqrt(n/12), lower =
TRUE): partial argument match of 'lower' to 'lower.tail'
bilevelAnalysisGeneset : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
bilevelAnalysisPathway : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
fisherMethod: warning in pchisq(-2 * sum(log(x)), df = 2 * length(x),
lower = FALSE): partial argument match of 'lower' to 'lower.tail'
intraAnalysisGene : <anonymous>: warning in topTable(fit2, adjust =
"none", sort.by = "none", number = Inf): partial argument match of
'adjust' to 'adjust.method'
intraAnalysisGene: warning in topTable(fit2, adjust = "none", sort.by =
"none", number = Inf): partial argument match of 'adjust' to
'adjust.method'
bilevelAnalysisPathway : <anonymous>: no visible global function
definition for ‘Summary’
intraAnalysisGene: no visible binding for global variable ‘d’
Undefined global functions or variables:
Summary d
Consider adding
importFrom("methods", "Summary")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
bilevelAnalysisGeneset 127.294 10.523 139.265
bilevelAnalysisPathway 96.251 2.859 99.838
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/BLMA.Rcheck/00check.log’
for details.
BLMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BLMA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘BLMA’ ... ** 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 * DONE (BLMA)
BLMA.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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("BLMA")
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, 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
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Working on dataset GSE17054, 9 samples
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
Working on dataset GSE17054, 9 samples
GSM426404, GSM426405, GSM426406, GSM426407, GSM426412
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
RUNIT TEST PROTOCOL -- Mon Apr 15 22:47:22 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
BLMA RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
38.924 1.722 40.931
BLMA.Rcheck/BLMA-Ex.timings
| name | user | system | elapsed | |
| addCLT | 0.001 | 0.000 | 0.001 | |
| bilevelAnalysisClassic | 0.011 | 0.001 | 0.012 | |
| bilevelAnalysisGene | 4.604 | 0.109 | 4.757 | |
| bilevelAnalysisGeneset | 127.294 | 10.523 | 139.265 | |
| bilevelAnalysisPathway | 96.251 | 2.859 | 99.838 | |
| fisherMethod | 0.001 | 0.000 | 0.001 | |
| intraAnalysisClassic | 0.010 | 0.000 | 0.011 | |
| intraAnalysisGene | 1.002 | 0.025 | 1.029 | |
| loadKEGGPathways | 3.740 | 0.078 | 3.850 | |
| stoufferMethod | 0 | 0 | 0 | |