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CHECK report for BLMA on malbec1

This page was generated on 2020-08-07 11:30:57 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BLMA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 187/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BLMA 1.13.3
Hung Nguyen
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BLMA
Branch: master
Last Commit: 959eb20
Last Changed Date: 2020-06-24 13:42:38 -0400 (Wed, 24 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BLMA
Version: 1.13.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BLMA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BLMA_1.13.3.tar.gz
StartedAt: 2020-08-07 02:59:48 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:07:46 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 478.2 seconds
RetCode: 0
Status:  OK 
CheckDir: BLMA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BLMA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BLMA_1.13.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BLMA.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.13.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ROntoTools', 'GSA', 'PADOG', 'limma', 'graph', 'parallel',
  'Biobase', 'metafor'
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'
getStatistics: warning in topTable(fit2, adjust = "fdr", sort.by = "B",
  number = Inf): partial argument match of 'adjust' to 'adjust.method'
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'
calculateFC: no visible binding for global variable ‘m1i’
calculateFC: no visible binding for global variable ‘sd1i’
calculateFC: no visible binding for global variable ‘n1i’
calculateFC: no visible binding for global variable ‘m2i’
calculateFC: no visible binding for global variable ‘sd2i’
calculateFC: no visible binding for global variable ‘n2i’
calculateFC: no visible binding for global variable ‘yi’
getStatistics: no visible binding for global variable ‘d’
hierClustering: no visible binding for global variable ‘km’
hierClustering: no visible global function definition for ‘clusGap’
hierClustering: no visible global function definition for ‘maxSE’
intraAnalysisGene: no visible binding for global variable ‘d’
Undefined global functions or variables:
  clusGap d km m1i m2i maxSE n1i n2i sd1i sd2i yi
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getStatistics          97.268  0.248  97.730
bilevelAnalysisGeneset 96.060  0.336  96.680
bilevelAnalysisPathway 83.644  0.032  83.836
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BLMA.Rcheck/00check.log’
for details.



Installation output

BLMA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BLMA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BLMA’ ...
** 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 (BLMA)

Tests output

BLMA.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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("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, 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.max, which.min


Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

The following object is masked from 'package:base':

    plot

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.




Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading 'metafor' package (version 2.4-0). For an overview 
and introduction to the package please type: help(metafor).
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 -- Fri Aug  7 03:07:43 2020 
*********************************************** 
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 
 36.296   0.380  36.814 

Example timings

BLMA.Rcheck/BLMA-Ex.timings

nameusersystemelapsed
addCLT0.0000.0000.001
bilevelAnalysisClassic0.0120.0000.011
bilevelAnalysisGene3.7360.0363.779
bilevelAnalysisGeneset96.060 0.33696.680
bilevelAnalysisPathway83.644 0.03283.836
fisherMethod0.0000.0000.001
getStatistics97.268 0.24897.730
intraAnalysisClassic0.0040.0000.005
intraAnalysisGene0.6480.0000.647
loadKEGGPathways3.0280.0003.028
stoufferMethod000