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CHECK report for GSReg on tokay1

This page was generated on 2019-04-13 11:24:04 -0400 (Sat, 13 Apr 2019).

Package 695/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSReg 1.16.0
Bahman Afsari , Elana J. Fertig
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GSReg
Branch: RELEASE_3_8
Last Commit: 1286f6e
Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GSReg
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSReg.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GSReg_1.16.0.tar.gz
StartedAt: 2019-04-13 02:56:03 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:00:44 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 281.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GSReg.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GSReg.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GSReg_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GSReg.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSReg/DESCRIPTION' ... OK
* this is package 'GSReg' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'GSReg' 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 ... NOTE
Packages in Depends field not imported from:
  'AnnotationDbi' 'GenomicFeatures' 'Homo.sapiens' 'org.Hs.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSReg.DIRAC.Pathways: no visible global function definition for 'pnorm'
GSReg.DIRAC.mu: no visible global function definition for 'var'
GSReg.Variance: no visible global function definition for 'var'
GSReg.Variance: no visible global function definition for 'pnorm'
GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible
  global function definition for 'as'
GSReg.overlapJunction: no visible binding for global variable
  'TxDb.Hsapiens.UCSC.hg19.knownGene'
GSReg.overlapJunction: no visible binding for global variable
  'org.Hs.eg.db'
GSReg.overlapJunction: no visible global function definition for
  'genes'
GSReg.overlapJunction: no visible global function definition for
  'mapIds'
GSReg.overlapJunction: no visible global function definition for
  'GRanges'
GSReg.overlapJunction: no visible global function definition for 'Rle'
GSReg.overlapJunction: no visible global function definition for
  'IRanges'
GSReg.overlapJunction: no visible global function definition for
  'findOverlaps'
GSReg.overlapJunction: no visible global function definition for
  'queryHits'
GSReg.overlapJunction: no visible global function definition for
  'subjectHits'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'findOverlaps'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'Matrix'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'queryHits'
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for 'subjectHits'
Undefined global functions or variables:
  GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as
  findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits
  var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "pnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GSReg.kendall.tau.distance.template'
Undocumented data sets:
  'geneExrsGSReg' 'junc.RPM.Simulated' 'phenotypes'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'GSReg.GeneSets.DIRAC':
GSReg.GeneSets.DIRAC
  Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0, minGeneNum = 5)
  Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0.05, minGeneNum = 5)
  Mismatches in argument default values:
    Name: 'alpha' Code: 0 Docs: 0.05

Codoc mismatches from documentation object 'GSReg.GeneSets.EVA':
GSReg.GeneSets.EVA
  Code: function(geneexpres, pathways, phenotypes, verbose = T,
                 minGeneNum = 5, distFunc = GSReg.kendall.tau.distance,
                 distparamPathways, ...)
  Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5)
  Argument names in code not in docs:
    verbose distFunc distparamPathways ...
  Mismatches in argument names:
    Position: 4 Code: verbose Docs: minGeneNum

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'GSReg.kendall.tau.distance':
  'GSReg.kendall.tau.distance.template'

Bad \usage lines found in documentation object 'GSReg.overlapJunction':
   GSReg.overlapJunction <- function(juncExprs,
                                    GenestoStudy=NULL,
                                    geneexpr=NULL,
                                    minmeanloggeneexp= 3,
                                    alpha =0,
                                    sparse = F,
                                    genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene, 
                                    geneIDInTxDB = 'ENTREZID', 
                                    geneIDOut = 'SYMBOL',
                                    org=org.Hs.eg.db, ...) 
Bad \usage lines found in documentation object 'GSReg.SEVA':
   function(juncExprs,
  		  phenoVect, 
            verbose=T,
            sparse =F, ...)

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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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-3.8-bioc/R/library/GSReg/libs/i386/GSReg.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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' ... NOTE
The following files look like leftovers/mistakes:
  'Rplots.pdf'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/GSReg.Rcheck/00check.log'
for details.



Installation output

GSReg.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GSReg_1.16.0.tar.gz && rm -rf GSReg.buildbin-libdir && mkdir GSReg.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GSReg.buildbin-libdir GSReg_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GSReg_1.16.0.zip && rm GSReg_1.16.0.tar.gz GSReg_1.16.0.zip
###
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  % 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  204k  100  204k    0     0  2220k      0 --:--:-- --:--:-- --:--:-- 2321k

install for i386

* installing *source* package 'GSReg' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistance.cc -o kendallTauDistance.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nij.cc -o nij.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vect2compC.cc -o vect2compC.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GSReg.dll tmp.def init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GSReg.buildbin-libdir/GSReg/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GSReg'
    finding HTML links ... done
    GSReg-package                           html  
    GSReg_GeneSets_DIRAC                    html  
    GSReg_GeneSets_VReg.                    html  
    GSReg_Kendall                           html  
    GSReg_OverlapJunction                   html  
    GSReg_SEVA                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GSReg' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistance.cc -o kendallTauDistance.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nij.cc -o nij.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vect2compC.cc -o vect2compC.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GSReg.dll tmp.def init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GSReg.buildbin-libdir/GSReg/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GSReg' as GSReg_1.16.0.zip
* DONE (GSReg)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GSReg' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

GSReg.Rcheck/examples_i386/GSReg-Ex.timings

nameusersystemelapsed
GSReg_GeneSets_DIRAC1.580.141.87
GSReg_GeneSets_VReg.1.490.081.56
GSReg_Kendall000
GSReg_OverlapJunction2.390.102.48
GSReg_SEVA2.050.182.24

GSReg.Rcheck/examples_x64/GSReg-Ex.timings

nameusersystemelapsed
GSReg_GeneSets_DIRAC1.420.041.47
GSReg_GeneSets_VReg.1.150.021.18
GSReg_Kendall000
GSReg_OverlapJunction1.980.012.00
GSReg_SEVA2.560.022.58