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BioC 3.4: CHECK report for hapFabia on tokay1

This page was generated on 2017-04-15 16:17:25 -0400 (Sat, 15 Apr 2017).

Package 579/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.16.1
Sepp Hochreiter
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/hapFabia
Last Changed Rev: 127306 / Revision: 128728
Last Changed Date: 2017-03-11 04:32:11 -0500 (Sat, 11 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hapFabia
Version: 1.16.1
Command: rm -rf hapFabia.buildbin-libdir hapFabia.Rcheck && mkdir hapFabia.buildbin-libdir hapFabia.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.16.1.tar.gz >hapFabia.Rcheck\00install.out 2>&1 && cp hapFabia.Rcheck\00install.out hapFabia-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=hapFabia.buildbin-libdir --install="check:hapFabia-install.out" --force-multiarch --no-vignettes --timings hapFabia_1.16.1.tar.gz
StartedAt: 2017-04-14 22:55:11 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:57:01 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 109.4 seconds
RetCode: 0
Status:  OK  
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf hapFabia.buildbin-libdir hapFabia.Rcheck && mkdir hapFabia.buildbin-libdir hapFabia.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.16.1.tar.gz >hapFabia.Rcheck\00install.out 2>&1 && cp hapFabia.Rcheck\00install.out hapFabia-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=hapFabia.buildbin-libdir --install="check:hapFabia-install.out" --force-multiarch --no-vignettes --timings hapFabia_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/hapFabia.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hapFabia/DESCRIPTION' ... OK
* this is package 'hapFabia' version '1.16.1'
* 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 'hapFabia' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
File 'hapFabia/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("+--------------------------+          #    #    ##    #####     \n",     "|#.....#...#.......#.#....#|          #    #   #  #   #    #    \n",     "|#.....#...#.......#.#....#|          ######  #    #  #    #    \n",     "|#.....#...#...............|          #    #  ######  #####     \n",     "|#.....#...#.......#.#....#|          #    #  #    #  #         \n",     "|#.....#...#...............|          #    #  #    #  #         \n",     "|#.....#...#.......#.#....#|  #######                           \n",     "|..................#.#....#|  #         ##    #####   #    ##   \n",     "|#.....#...#.......#.#....#|  #        #  #   #    #  #   #  #  \n",     "|..................#.#....#|  #####   #    #  #####   #  #    # \n",     "|#.....#...#.......#.#....#|  #       ######  #    #  #  ###### \n",     "|#.....#...#.......#.#....#|  #       #    #  #    #  #  #    # \n",     "+--------------------------+  #       #    #  #####   #  #    # \n")
    packageStartupMessage("Citation: S. Hochreiter,", "\n", "HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data,",     "\n", "Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt1013.",     "\n", "BibTex: enter 'toBibtex(citation(\"hapFabia\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/index.html",     "\n\n", "hapFabia Package Version ", version, "\n")

See section 'Good practice' in '?.onAttach'.
* 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 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-3.4-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iterateIntervals 6.44   0.39    6.88
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iterateIntervals 6.14   0.41    6.54
* 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-3.4-bioc/meat/hapFabia.Rcheck/00check.log'
for details.


hapFabia.Rcheck/00install.out:


install for i386

* installing *source* package 'hapFabia' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c interfaceR.c -o interfaceR.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vcftoFABIAB.c -o vcftoFABIAB.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'hapFabia' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c interfaceR.c -o interfaceR.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vcftoFABIAB.c -o vcftoFABIAB.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o hapFabia.dll tmp.def interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.16.1.zip
* DONE (hapFabia)

hapFabia.Rcheck/examples_i386/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.370.090.47
IBDsegmentList-class0.020.000.01
IBDsegmentList2excel0.010.000.02
analyzeIBDsegments000
compareIBDsegmentLists0.020.010.03
extractIBDsegments0.040.000.05
findDenseRegions0.020.000.01
hapFabia2.840.082.93
hapFabiaVersion000
identifyDuplicates0.020.000.01
iterateIntervals6.440.396.88
makePipelineFile000
matrixPlot000
mergeIBDsegmentLists0.010.000.02
plotIBDsegment0.330.080.40
setAnnotation0.050.000.05
setStatistics0.040.000.05
sim000
simulateIBDsegments000
simulateIBDsegmentsFabia1.110.091.20
split_sparse_matrix000
toolsFactorizationClass1.320.021.33
vcftoFABIA000

hapFabia.Rcheck/examples_x64/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.450.030.49
IBDsegmentList-class0.030.000.03
IBDsegmentList2excel0.020.000.01
analyzeIBDsegments000
compareIBDsegmentLists0.030.020.05
extractIBDsegments0.080.000.08
findDenseRegions000
hapFabia3.120.083.20
hapFabiaVersion000
identifyDuplicates000
iterateIntervals6.140.416.54
makePipelineFile000
matrixPlot0.020.000.02
mergeIBDsegmentLists0.010.000.02
plotIBDsegment0.270.080.34
setAnnotation0.050.010.06
setStatistics0.040.000.05
sim000
simulateIBDsegments000
simulateIBDsegmentsFabia1.320.031.34
split_sparse_matrix000
toolsFactorizationClass1.090.071.16
vcftoFABIA000