hapFabia 1.4.2
Sepp Hochreiter
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/hapFabia | | Last Changed Rev: 84166 / Revision: 88450 | | Last Changed Date: 2013-12-11 02:36:25 -0800 (Wed, 11 Dec 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/hapFabia.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.4.2’
* 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 ... [6s/6s] 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘fabia’ which was already attached by Depends.
Please remove these calls from your code.
Namespace in Imports field not imported from: ‘KernSmooth’
All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 ... [16s/17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
iterateIntervals 7.284 0.112 7.554
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/hapFabia.Rcheck/00check.log’
for details.
* installing *source* package ‘hapFabia’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c interfaceR.c -o interfaceR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
split_sparse_matrixB.c: In function ‘split_sparse_matrixB’:
split_sparse_matrixB.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:96:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:163:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:164:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:166:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:167:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:279:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:280:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:335:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -std=gnu99 -shared -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
gcc -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall
./commandLine/split_sparse_matrix.c: In function ‘Rprintf’:
./commandLine/split_sparse_matrix.c:9:3: warning: format not a string literal and no format arguments [-Wformat-security]
gcc -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall
split_sparse_matrixB.c: In function ‘split_sparse_matrixB’:
split_sparse_matrixB.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:96:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:163:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:164:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:166:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:167:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:279:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:280:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:335:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall
./commandLine/vcftoFABIA.c: In function ‘Rprintf’:
./commandLine/vcftoFABIA.c:10:3: warning: format not a string literal and no format arguments [-Wformat-security]
gcc -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall
gcc -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-2.13-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)