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CHECK report for mdgsa on tokay2

This page was generated on 2020-10-17 11:57:01 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE mdgsa PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1011/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdgsa 1.20.0
David Montaner
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/mdgsa
Branch: RELEASE_3_11
Last Commit: 581181c
Last Changed Date: 2020-04-27 14:45:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mdgsa
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mdgsa_1.20.0.tar.gz
StartedAt: 2020-10-17 05:44:10 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:47:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 190.9 seconds
RetCode: 0
Status:  OK  
CheckDir: mdgsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings mdgsa_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/mdgsa.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mdgsa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mdgsa' version '1.20.0'
* 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 whether package 'mdgsa' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
getGOnames: no visible global function definition for
  'packageDescription'
getKEGGnames: no visible global function definition for
  'packageDescription'
getOntology: no visible global function definition for
  'packageDescription'
goLeaves: no visible global function definition for
  'packageDescription'
index.normalize: no visible global function definition for 'qqnorm'
index.standardize: no visible global function definition for 'sd'
mdGsa: no visible global function definition for 'quasibinomial'
mdGsa: no visible global function definition for 'glm.fit'
mdGsa: no visible global function definition for 'summary.glm'
mdGsa: no visible global function definition for 'p.adjust'
mdPat: no visible global function definition for 'read.table'
plotMdGsa: no visible global function definition for 'points'
plotMdGsa: no visible global function definition for 'cov'
plotMdGsa: no visible global function definition for 'qchisq'
plotMdGsa: no visible global function definition for 'lines'
plotMdGsa: no visible global function definition for 'abline'
propagateGO.matrix: no visible global function definition for
  'packageDescription'
splitOntologies: no visible global function definition for
  'packageDescription'
uvGsa: no visible global function definition for 'quasibinomial'
uvGsa: no visible global function definition for 'glm.fit'
uvGsa: no visible global function definition for 'summary.glm'
uvGsa: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  abline cov glm.fit lines p.adjust packageDescription points qchisq
  qqnorm quasibinomial read.table sd summary.glm
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "cov", "glm.fit", "p.adjust", "qchisq", "qqnorm",
             "quasibinomial", "sd", "summary.glm")
  importFrom("utils", "packageDescription", "read.table")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/mdgsa.Rcheck/00check.log'
for details.



Installation output

mdgsa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/mdgsa_1.20.0.tar.gz && rm -rf mdgsa.buildbin-libdir && mkdir mdgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mdgsa.buildbin-libdir mdgsa_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL mdgsa_1.20.0.zip && rm mdgsa_1.20.0.tar.gz mdgsa_1.20.0.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
100 33247  100 33247    0     0   507k      0 --:--:-- --:--:-- --:--:--  569k

install for i386

* installing *source* package 'mdgsa' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mdgsa'
    finding HTML links ... done
    annotFilter                             html  
    annotList2mat                           html  
    annotMat2list                           html  
    getGOnames                              html  
    getKEGGnames                            html  
    getOntology                             html  
    goLeaves                                html  
    indexTransform                          html  
    mdGsa                                   html  
    mdPat                                   html  
    plotMdGsa                               html  
    propagateGO                             html  
    pval2index                              html  
    revList                                 html  
    splitOntologies                         html  
    transferIndex                           html  
    uvGsa                                   html  
    uvPat                                   html  
    uvSignif                                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 'mdgsa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mdgsa' as mdgsa_1.20.0.zip
* DONE (mdgsa)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'mdgsa' successfully unpacked and MD5 sums checked

Tests output

mdgsa.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 ("mdgsa")


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

Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Warning: There are genes in the annotation list which are not
part of the gene universe defined by the ranking index;
they will be eliminated form the annotation.
60% of the genes in the index are annotated in the list.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Using GO.db version: 3.11.4
Using GO.db version: 3.11.4
Loading required package: KEGG.db
Using KEGG.db version: 3.2.4
Using GO.db version: 3.11.4
Analyzed blocks:
time in seconds:
   user  system elapsed 
   0.00    0.01    0.01 
Using GO.db version: 3.11.4
  3miRNAs with annotated targets
  2miRNAs without targets
  0miRNAs with targets but not in the ranking index
Analyzed blocks:
time in seconds:
   user  system elapsed 
   0.00    0.01    0.02 
Analyzed blocks:
time in seconds:
   user  system elapsed 
   0.01    0.02    0.03 


RUNIT TEST PROTOCOL -- Sat Oct 17 05:46:56 2020 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mdgsa RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
> 
> proc.time()
   user  system elapsed 
  13.18    0.42   13.57 

mdgsa.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 ("mdgsa")


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

Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Warning: There are genes in the annotation list which are not
part of the gene universe defined by the ranking index;
they will be eliminated form the annotation.
60% of the genes in the index are annotated in the list.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Using GO.db version: 3.11.4
Using GO.db version: 3.11.4
Loading required package: KEGG.db
Using KEGG.db version: 3.2.4
Using GO.db version: 3.11.4
Analyzed blocks:
time in seconds:
   user  system elapsed 
   0.03    0.00    0.03 
Using GO.db version: 3.11.4
  3miRNAs with annotated targets
  2miRNAs without targets
  0miRNAs with targets but not in the ranking index
Analyzed blocks:
time in seconds:
   user  system elapsed 
      0       0       0 
Analyzed blocks:
time in seconds:
   user  system elapsed 
   0.02    0.00    0.01 


RUNIT TEST PROTOCOL -- Sat Oct 17 05:47:07 2020 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mdgsa RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
> 
> proc.time()
   user  system elapsed 
  10.15    0.40   10.56 

Example timings

mdgsa.Rcheck/examples_i386/mdgsa-Ex.timings

nameusersystemelapsed
annotFilter000
annotList2mat000
annotMat2list000
getGOnames0.180.000.18
getKEGGnames0.020.000.02
getOntology0.120.000.12
goLeaves2.460.002.46
indexTransform0.010.000.01
mdGsa0.020.020.03
mdPat0.010.000.02
plotMdGsa000
propagateGO3.210.013.22
pval2index0.010.000.01
revList000
splitOntologies0.320.000.32
transferIndex0.040.000.04
uvGsa0.030.000.04
uvPat0.020.000.01
uvSignif000

mdgsa.Rcheck/examples_x64/mdgsa-Ex.timings

nameusersystemelapsed
annotFilter000
annotList2mat000
annotMat2list000
getGOnames0.170.010.19
getKEGGnames0.060.000.06
getOntology0.130.000.13
goLeaves2.190.022.21
indexTransform0.030.000.03
mdGsa0.470.000.47
mdPat0.020.000.01
plotMdGsa000
propagateGO3.110.063.17
pval2index000
revList000
splitOntologies0.30.00.3
transferIndex0.040.000.04
uvGsa0.040.000.04
uvPat000
uvSignif000