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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hapFabia_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/hapFabia.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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 6.502 0.912 241.351
hapFabia 3.460 0.213 35.455
simulateIBDsegmentsFabia 1.589 0.137 16.229
IBDsegment-class 0.506 0.091 16.328
plotIBDsegment 0.434 0.085 15.027
* 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
‘/Users/biocbuild/bbs-3.4-bioc/meat/hapFabia.Rcheck/00check.log’
for details.
* installing *source* package ‘hapFabia’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c interfaceR.c -o interfaceR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c split_sparse_matrixB.c -o split_sparse_matrixB.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c vcftoFABIAB.c -o vcftoFABIAB.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -Wall -mtune=core2 -g -O2
clang -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -Wall -mtune=core2 -g -O2
clang ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
clang -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -Wall -mtune=core2 -g -O2
clang -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -Wall -mtune=core2 -g -O2
clang ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /Users/biocbuild/bbs-3.4-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)