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CHECK report for hapFabia on tokay1

This page was generated on 2020-04-15 12:20:57 -0400 (Wed, 15 Apr 2020).

Package 769/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.28.0
Andreas Mitterecker
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/hapFabia
Branch: RELEASE_3_10
Last Commit: 840df47
Last Changed Date: 2019-10-29 13:08:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hapFabia
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hapFabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hapFabia_1.28.0.tar.gz
StartedAt: 2020-04-15 03:49:20 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:51:05 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 104.9 seconds
RetCode: 0
Status:  OK  
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hapFabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings hapFabia_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/hapFabia.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.28.0'
* 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 '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
* 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
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 shell scripts ... 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-3.10-bioc/R/library/hapFabia/libs/i386/hapFabia.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/hapFabia/libs/x64/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 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
Examples with CPU or elapsed time > 5s
                 user system elapsed
iterateIntervals 5.65   0.46    6.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iterateIntervals 7.89    0.5    8.39
* 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-3.10-bioc/meat/hapFabia.Rcheck/00check.log'
for details.



Installation output

hapFabia.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/hapFabia_1.28.0.tar.gz && rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hapFabia.buildbin-libdir hapFabia_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL hapFabia_1.28.0.zip && rm hapFabia_1.28.0.tar.gz hapFabia_1.28.0.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  956k  100  956k    0     0  4926k      0 --:--:-- --:--:-- --:--:-- 5010k

install for i386

* installing *source* package 'hapFabia' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/hapFabia.buildbin-libdir/00LOCK-hapFabia/00new/hapFabia/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hapFabia'
    finding HTML links ... done
    IBDsegment-class                        html  
    IBDsegmentList-class                    html  
    IBDsegmentList2excel                    html  
    analyzeIBDsegments                      html  
    chr1ASW1000G                            html  
    compareIBDsegmentLists                  html  
    extractIBDsegments                      html  
    findDenseRegions                        html  
    hapFabia                                html  
    hapFabiaVersion                         html  
    hapRes                                  html  
    identifyDuplicates                      html  
    iterateIntervals                        html  
    makePipelineFile                        html  
    matrixPlot                              html  
    mergeIBDsegmentLists                    html  
    mergedIBDsegmentList                    html  
    plotIBDsegment                          html  
    res                                     html  
    setAnnotation                           html  
    setStatistics                           html  
    sim                                     html  
    simu                                    html  
    simulateIBDsegments                     html  
    simulateIBDsegmentsFabia                html  
    split_sparse_matrix                     html  
    toolsFactorizationClass                 html  
    vcftoFABIA                              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 'hapFabia' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hapFabia' as hapFabia_1.28.0.zip
* DONE (hapFabia)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'hapFabia' successfully unpacked and MD5 sums checked

Tests output


Example timings

hapFabia.Rcheck/examples_i386/hapFabia-Ex.timings

nameusersystemelapsed
IBDsegment-class0.360.060.42
IBDsegmentList-class0.020.000.02
IBDsegmentList2excel0.020.000.02
analyzeIBDsegments000
compareIBDsegmentLists0.020.000.01
extractIBDsegments0.040.000.05
findDenseRegions000
hapFabia1.960.192.14
hapFabiaVersion000
identifyDuplicates0.000.010.02
iterateIntervals5.650.466.14
makePipelineFile0.000.010.01
matrixPlot000
mergeIBDsegmentLists0.030.000.04
plotIBDsegment0.350.110.45
setAnnotation0.040.000.05
setStatistics0.030.000.03
sim000
simulateIBDsegments000
simulateIBDsegmentsFabia0.950.030.99
split_sparse_matrix000
toolsFactorizationClass0.740.000.73
vcftoFABIA000

hapFabia.Rcheck/examples_x64/hapFabia-Ex.timings

nameusersystemelapsed
IBDsegment-class0.530.110.64
IBDsegmentList-class0.020.000.02
IBDsegmentList2excel000
analyzeIBDsegments000
compareIBDsegmentLists0.040.000.03
extractIBDsegments0.030.000.03
findDenseRegions0.000.010.02
hapFabia2.280.142.42
hapFabiaVersion000
identifyDuplicates000
iterateIntervals7.890.508.39
makePipelineFile000
matrixPlot0.000.020.01
mergeIBDsegmentLists0.020.000.02
plotIBDsegment0.500.070.58
setAnnotation0.080.020.10
setStatistics0.060.000.06
sim000
simulateIBDsegments000
simulateIBDsegmentsFabia1.220.161.37
split_sparse_matrix000
toolsFactorizationClass1.050.021.06
vcftoFABIA000