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CHECK report for BioQC on tokay2

This page was generated on 2019-04-09 12:25:22 -0400 (Tue, 09 Apr 2019).

Package 163/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.11.1
Jitao David Zhang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BioQC
Branch: master
Last Commit: 2ebe9fc
Last Changed Date: 2019-01-07 07:44:18 -0400 (Mon, 07 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: BioQC
Version: 1.11.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BioQC_1.11.1.tar.gz
StartedAt: 2019-04-09 01:24:20 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:25:46 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BioQC.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BioQC_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.11.1'
* 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 ... WARNING
Found the following significant warnings:
  Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:6: All text must be in a section
  Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:7: All text must be in a section
  Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:9: All text must be in a section
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck/00install.out' for details.
* 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 ... OK
* checking Rd files ... WARNING
prepare_Rd: IndexList.Rd:6: All text must be in a section
prepare_Rd: IndexList.Rd:7: All text must be in a section
prepare_Rd: IndexList.Rd:9: All text must be in a section
* 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 ... WARNING
Bad \usage lines found in documentation object 'IndexList':
  <<<<<<< HEAD
  =======
  >>>>>>> db884caed21e4f2384482a3834c89b269eaa7cc6

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-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 'C:/Users/biocbuild/bbs-3.9-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: 3 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck/00check.log'
for details.

Installation output

BioQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BioQC_1.11.1.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.11.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BioQC_1.11.1.zip && rm BioQC_1.11.1.tar.gz BioQC_1.11.1.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  590k  100  590k    0     0  6454k      0 --:--:-- --:--:-- --:--:-- 6948k

install for i386

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gini.c -o gini.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'wmw_test':
wmw_test.c:155:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
C:/Rtools/mingw_32/bin/g++ -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 -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:6: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:7: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpsPSrCw/R.INSTALL12684c712d71/BioQC/man/IndexList.Rd:9: All text must be in a section
*** 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  
    as.gmtlist                              html  
    entropy                                 html  
    filterPmat                              html  
    gini                                    html  
    gmtlist2signedGenesets                  html  
    matchGenes                              html  
    offset-BaseIndexList-method             html  
    offset-set                              html  
    readGmt                                 html  
    readSignedGmt                           html  
    simplifyMatrix                          html  
    valTypes                                html  
    wmwTest                                 html  
    wmwTestInR                              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 'BioQC' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gini.c -o gini.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'wmw_test':
wmw_test.c:155:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
C:/Rtools/mingw_64/bin/g++ -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 -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.11.1.zip
* DONE (BioQC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked

Tests output

BioQC.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: Rcpp
Loading required package: Biobase
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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")
== testthat results  ===========================================================
OK: 99 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.60    0.21   10.82

BioQC.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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: Rcpp
Loading required package: Biobase
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, 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")
== testthat results  ===========================================================
OK: 99 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   8.56    0.15    8.76

Example timings

BioQC.Rcheck/examples_i386/BioQC-Ex.timings

nameusersystemelapsed
GmtList000
IndexList000
SignedGenesets000
SignedIndexList000
absLog10p000
as.gmtlist000
entropy0.030.000.03
filterPmat000
gini0.020.000.02
gmtlist2signedGenesets000
offset-BaseIndexList-method000
offset-set0.010.000.01
readGmt0.050.000.24
readSignedGmt0.020.000.01
simplifyMatrix000
wmwTest0.340.020.36
wmwTestInR0.020.000.02

BioQC.Rcheck/examples_x64/BioQC-Ex.timings

nameusersystemelapsed
GmtList000
IndexList0.010.000.01
SignedGenesets0.020.000.02
SignedIndexList000
absLog10p000
as.gmtlist000
entropy0.010.000.02
filterPmat000
gini000
gmtlist2signedGenesets0.020.000.01
offset-BaseIndexList-method000
offset-set000
readGmt0.030.000.03
readSignedGmt000
simplifyMatrix000
wmwTest0.370.000.38
wmwTestInR000