Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:59 -0400 (Mon, 18 Oct 2021).

CHECK results for BioQC on riesling1

To the developers/maintainers of the BioQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 187/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.21.4  (landing page)
Jitao David Zhang
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioQC
git_branch: master
git_last_commit: 91a7127
git_last_commit_date: 2021-08-18 08:15:12 -0400 (Wed, 18 Aug 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

Summary

Package: BioQC
Version: 1.21.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioQC_1.21.4.tar.gz
StartedAt: 2021-10-18 00:03:40 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 00:05:34 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 113.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BioQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BioQC_1.21.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BioQC.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 'BioQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioQC' version '1.21.4'
* package encoding: UTF-8
* 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 'BioQC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      2.0Mb
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/BioQC/libs/i386/BioQC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/BioQC/libs/x64/BioQC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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/BioQC.Rcheck/00check.log'
for details.



Installation output

BioQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioQC_1.21.4.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.21.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioQC_1.21.4.zip && rm BioQC_1.21.4.tar.gz BioQC_1.21.4.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
  9 4348k    9  408k    0     0  1470k      0  0:00:02 --:--:--  0:00:02 1464k
100 4348k  100 4348k    0     0  9154k      0 --:--:-- --:--:-- --:--:-- 9135k

install for i386

* installing *source* package 'BioQC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gini.c -o gini.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'wmw_test':
wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioQC'
    finding HTML links ... done
    BaseIndexList-class                     html  
    GmtList-class                           html  
    GmtList                                 html  
    IndexList-class                         html  
    IndexList                               html  
    SignedGenesets-class                    html  
    SignedGenesets                          html  
    SignedIndexList-class                   html  
    SignedIndexList                         html  
    absLog10p                               html  
    appendGmtList                           html  
    as.GmtList                              html  
    entropy                                 html  
    entropyDiversity                        html  
    entropySpecificity                      html  
    filterBySize                            html  
    filterPmat                              html  
    getLeadingEdgeIndexFromVector           html  
    gini                                    html  
    gmtlist2signedGenesets                  html  
    gsDesc                                  html  
    gsGeneCount                             html  
    gsGenes                                 html  
    gsName                                  html  
    gsNamespace                             html  
    hasNamespace                            html  
    isValidBaseIndexList                    html  
    isValidGmtList                          html  
    isValidIndexList                        html  
    isValidSignedGenesets                   html  
    isValidSignedIndexList                  html  
    matchGenes                              html  
    offset-set                              html  
    offset                                  html  
    prettySigNames                          html  
    readCurrentSignatures                   html  
    readGmt                                 html  
    readSignedGmt                           html  
    sampleSpecialization                    html  
    setDescAsNamespace                      html  
    setGsNamespace                          html  
    setNamespace                            html  
    show-GmtList-method                     html  
    show-IndexList-method                   html  
    show-SignedGenesets-method              html  
    show-SignedIndexList-method             html  
    simplifyMatrix                          html  
    sub-.GmtList                            html  
    sub-sub-.GmtList                        html  
    uniqGenesetsByNamespace                 html  
    valTypes                                html  
    wmwLeadingEdge                          html  
    wmwTest                                 html  
    wmwTestInR                              html  
*** copying figures
** 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 'BioQC' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gini.c -o gini.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'wmw_test':
wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.21.4.zip
* DONE (BioQC)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked

Tests output

BioQC.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics

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

Welcome to Bioconductor

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

> 
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
   5.25    0.25    5.53 

BioQC.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics

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

Welcome to Bioconductor

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

> 
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
> 
> proc.time()
   user  system elapsed 
   5.18    0.18    5.37 

Example timings

BioQC.Rcheck/examples_i386/BioQC-Ex.timings

nameusersystemelapsed
GmtList000
IndexList0.010.000.01
SignedGenesets000
SignedIndexList000
absLog10p000
appendGmtList0.020.000.02
as.GmtList000
entropy000
entropyDiversity000
entropySpecificity000
filterPmat000
getLeadingEdgeIndexFromVector000
gini000
gmtlist2signedGenesets0.010.000.01
matchGenes0.040.010.05
offset-set000
offset000
prettySigNames0.030.000.03
readCurrentSignatures0.030.000.03
readGmt0.050.020.06
readSignedGmt000
sampleSpecialization000
setNamespace000
simplifyMatrix000
sub-.GmtList000
sub-sub-.GmtList000
uniqGenesetsByNamespace000
wmwLeadingEdge000
wmwTest0.170.000.17
wmwTestInR000

BioQC.Rcheck/examples_x64/BioQC-Ex.timings

nameusersystemelapsed
GmtList000
IndexList000
SignedGenesets000
SignedIndexList000
absLog10p000
appendGmtList000
as.GmtList000
entropy000
entropyDiversity0.020.000.01
entropySpecificity000
filterPmat000
getLeadingEdgeIndexFromVector000
gini000
gmtlist2signedGenesets000
matchGenes0.060.000.06
offset-set000
offset000
prettySigNames0.030.000.03
readCurrentSignatures0.030.000.03
readGmt0.050.000.05
readSignedGmt0.010.000.02
sampleSpecialization000
setNamespace0.020.000.01
simplifyMatrix000
sub-.GmtList000
sub-sub-.GmtList000
uniqGenesetsByNamespace000
wmwLeadingEdge0.010.000.02
wmwTest0.210.000.20
wmwTestInR000