snpStats 1.16.0
David Clayton
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/snpStats | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings snpStats_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/snpStats.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.16.0’
* 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 ‘snpStats’ can be installed ... [14s/14s] OK
* checking installed package size ... NOTE
installed size is 8.2Mb
sub-directories of 1Mb or more:
data 4.1Mb
doc 2.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘snpStats/libs/snpStats.so’:
Found non-API call to R: ‘R_data_class’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* 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
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/snpStats.Rcheck/00check.log’
for details.
* installing *source* package ‘snpStats’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bind.c -o bind.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_gt.c -o count_gt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c covwin.c -o covwin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fst.c -o fst.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function ‘glm_fit’:
glm_test.c:261:26: warning: ‘dfr’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function ‘snp_rhs_score’:
glm_test_R.c:370:8: warning: variable ‘testname’ set but not used [-Wunused-but-set-variable]
glm_test_R.c: In function ‘snp_rhs_estimate’:
glm_test_R.c:1520:11: warning: variable ‘Uc’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hphase.c -o hphase.o
hphase.c: In function ‘emhap’:
hphase.c:261:9: warning: variable ‘ipfault’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imputation.c -o imputation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c in.c -o in.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c invert.c -o invert.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ipf.c -o ipf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ld.c -o ld.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c misc.c -o misc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mla.c -o mla.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function ‘mvphen’:
mvphenotype.c:190:7: warning: variable ‘ifX’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outdata.c -o outdata.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plink.c -o plink.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c read_uncertain.c -o read_uncertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readped.c -o readped.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c structure.c -o structure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c switch.c -o switch.o
switch.c: In function ‘test_switch’:
switch.c:52:10: warning: variable ‘fg’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tdt.c -o tdt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o snpStats.so Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o switch.o tdt.o uncertain.o -lz -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/snpStats.Rcheck/snpStats/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘snpStats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snpStats)