Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-25 14:06:07 -0400 (Mon, 25 Oct 2021).

CHECK results for BLMA on riesling1

To the developers/maintainers of the BLMA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BLMA.git to
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raw results

Package 203/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BLMA 1.17.0  (landing page)
Hung Nguyen
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/BLMA
git_branch: master
git_last_commit: 20a44ab
git_last_commit_date: 2021-05-19 12:27:28 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: BLMA
Version: 1.17.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BLMA.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BLMA_1.17.0.tar.gz
StartedAt: 2021-10-25 00:09:50 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 00:19:09 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 559.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BLMA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BLMA.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BLMA_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BLMA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BLMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BLMA' version '1.17.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
bilevelAnalysisGeneset 77.57   0.06   77.64
getStatistics          46.05   0.82   46.88
bilevelAnalysisPathway 45.63   0.13   45.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
bilevelAnalysisGeneset 64.61   0.15   65.33
getStatistics          50.69   0.72   52.80
bilevelAnalysisPathway 45.56   0.13   45.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/BLMA.Rcheck/00check.log'
for details.



Installation output

BLMA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BLMA_1.17.0.tar.gz && rm -rf BLMA.buildbin-libdir && mkdir BLMA.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BLMA.buildbin-libdir BLMA_1.17.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BLMA_1.17.0.zip && rm BLMA_1.17.0.tar.gz BLMA_1.17.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 42 2575k   42 1091k    0     0  2152k      0  0:00:01 --:--:--  0:00:01 2148k
100 2575k  100 2575k    0     0  2926k      0 --:--:-- --:--:-- --:--:-- 2926k

install for i386

* installing *source* package 'BLMA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BLMA'
    finding HTML links ... done
    GSE17054                                html  
    GSE33223                                html  
    GSE42140                                html  
    GSE57194                                html  
    addCLT                                  html  
    bilevelAnalysisClassic                  html  
    bilevelAnalysisGene                     html  
    bilevelAnalysisGeneset                  html  
    finding level-2 HTML links ... done

    bilevelAnalysisPathway                  html  
    fisherMethod                            html  
    getStatistics                           html  
    intraAnalysisClassic                    html  
    intraAnalysisGene                       html  
    loadKEGGPathways                        html  
    pORACalc                                html  
    stoufferMethod                          html  
** 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

install for x64

* installing *source* package 'BLMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BLMA' as BLMA_1.17.0.zip
* DONE (BLMA)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BLMA' successfully unpacked and MD5 sums checked

Tests output

BLMA.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: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 the 'metafor' package (version 3.0-2). For an
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 -- Mon Oct 25 00:18:09 2021 
*********************************************** 
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 
  18.34    0.45   18.78 

BLMA.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: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 the 'metafor' package (version 3.0-2). For an
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 -- Mon Oct 25 00:18:33 2021 
*********************************************** 
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 
  22.85    0.62   23.50 

Example timings

BLMA.Rcheck/examples_i386/BLMA-Ex.timings

nameusersystemelapsed
addCLT000
bilevelAnalysisClassic0.010.000.02
bilevelAnalysisGene1.490.061.54
bilevelAnalysisGeneset77.57 0.0677.64
bilevelAnalysisPathway45.63 0.1345.75
fisherMethod000
getStatistics46.05 0.8246.88
intraAnalysisClassic000
intraAnalysisGene0.400.000.41
loadKEGGPathways1.580.021.59
stoufferMethod000

BLMA.Rcheck/examples_x64/BLMA-Ex.timings

nameusersystemelapsed
addCLT000
bilevelAnalysisClassic0.000.010.02
bilevelAnalysisGene2.420.072.48
bilevelAnalysisGeneset64.61 0.1565.33
bilevelAnalysisPathway45.56 0.1345.69
fisherMethod000
getStatistics50.69 0.7252.80
intraAnalysisClassic000
intraAnalysisGene0.360.030.39
loadKEGGPathways1.510.001.51
stoufferMethod000