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BioC 3.6: CHECK report for hapFabia on malbec1

This page was generated on 2017-08-16 13:20:25 -0400 (Wed, 16 Aug 2017).

Package 620/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hapFabia 1.19.0
Sepp Hochreiter
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hapFabia
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hapFabia
Version: 1.19.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings hapFabia_1.19.0.tar.gz
StartedAt: 2017-08-15 23:51:51 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:52:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 53.6 seconds
RetCode: 0
Status:  OK 
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings hapFabia_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/hapFabia.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iterateIntervals 5.432  0.088   5.522
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/hapFabia.Rcheck/00check.log’
for details.


hapFabia.Rcheck/00install.out:

* installing *source* package ‘hapFabia’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c interfaceR.c -o interfaceR.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2  -Wall
gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2  -Wall
gcc ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2  -Wall
gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2  -Wall
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-3.6-bioc/meat/hapFabia.Rcheck/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hapFabia)

hapFabia.Rcheck/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.5160.0120.528
IBDsegmentList-class0.0200.0040.021
IBDsegmentList2excel0.0080.0000.008
analyzeIBDsegments0.0040.0000.003
compareIBDsegmentLists0.0280.0000.027
extractIBDsegments0.0600.0040.064
findDenseRegions0.0120.0000.010
hapFabia2.6840.0202.706
hapFabiaVersion0.0000.0000.001
identifyDuplicates0.0040.0000.004
iterateIntervals5.4320.0885.522
makePipelineFile0.0120.0000.012
matrixPlot0.0040.0000.005
mergeIBDsegmentLists0.0120.0000.011
plotIBDsegment0.2360.0200.253
setAnnotation0.0440.0040.048
setStatistics0.0320.0000.032
sim0.0000.0000.001
simulateIBDsegments0.0040.0000.001
simulateIBDsegmentsFabia0.7640.0080.775
split_sparse_matrix0.0040.0000.004
toolsFactorizationClass0.8920.0080.922
vcftoFABIA0.0040.0000.003