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Package 466/514HostnameOS / ArchBUILDCHECKBUILD BIN
snpStats 1.4.1
David Clayton
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/snpStats
Last Changed Rev: 61454 / Revision: 64395
Last Changed Date: 2011-12-19 07:48:37 -0800 (Mon, 19 Dec 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: snpStats
Version: 1.4.1
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings snpStats_1.4.1.tar.gz
StartedAt: 2012-03-24 02:50:08 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:53:39 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 210.6 seconds
RetCode: 0
Status:  OK 
CheckDir: snpStats.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/snpStats.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.4.1’
* 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 whether package ‘snpStats’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
    doc    2.3Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                     old_size new_size compress
  families.RData         46Kb     26Kb       xz
  for.exercise.RData    5.4Mb    3.5Mb       xz
  ld.example.RData       28Kb     20Kb       xz
  testdata.RData        875Kb    557Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/snpStats.Rcheck/snpStats/libs/snpStats.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

snpStats.Rcheck/00install.out:

* installing *source* package ‘snpStats’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c adler32.c -o adler32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bind.c -o bind.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compress.c -o compress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c count_gt.c -o count_gt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c covwin.c -o covwin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c crc32.c -o crc32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c deflate.c -o deflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c force_hom.c -o force_hom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c fst.c -o fst.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c glm_test.c -o glm_test.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c glm_test_R.c -o glm_test_R.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gzclose.c -o gzclose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gzlib.c -o gzlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gzread.c -o gzread.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gzwrite.c -o gzwrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hash_index.c -o hash_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hphase.c -o hphase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c imputation.c -o imputation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c in.c -o in.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c infback.c -o infback.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inffast.c -o inffast.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inflate.c -o inflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inftrees.c -o inftrees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c invert.c -o invert.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ipf.c -o ipf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ld.c -o ld.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c misc.c -o misc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mla.c -o mla.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mvphenotype.c -o mvphenotype.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c outdata.c -o outdata.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c plink.c -o plink.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c read_uncertain.c -o read_uncertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readped.c -o readped.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c single_snp_tests.c -o single_snp_tests.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c snp_summary.c -o snp_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c snpmpy.c -o snpmpy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c structure.c -o structure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c switch.c -o switch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c tdt.c -o tdt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c trees.c -o trees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c uncertain.c -o uncertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c uncompr.c -o uncompr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c zutil.c -o zutil.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o snpStats.so adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o fst.o glm_test.o glm_test_R.o gzclose.o gzlib.o gzread.o gzwrite.o hash_index.o hphase.o imputation.o in.o infback.o inffast.o inflate.o inftrees.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 trees.o uncertain.o uncompr.o zutil.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘data-input-vignette.Rnw’ 
   ‘differences.Rnw’ 
   ‘imputation-vignette.Rnw’ 
   ‘ld-vignette.Rnw’ 
   ‘pca-vignette.Rnw’ 
   ‘snpStats-vignette.Rnw’ 
   ‘tdt-vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (snpStats)

snpStats.Rcheck/snpStats-Ex.timings:

nameusersystemelapsed
Fst0.5200.0480.579
GlmEstimates-class0.0000.0000.002
GlmTests-class000
ImputationRules-class0.0040.0000.001
SingleSnpTests-class0.0000.0000.002
SnpMatrix-class0.4960.0480.544
XSnpMatrix-class0.0760.0160.088
chi.squared0.0400.0040.045
families0.0320.0000.036
filter.rules000
for.exercise1.4120.0201.529
ibsCount0.9080.0080.916
ibsDist0.3080.0080.348
imputation.maf0.0000.0000.002
impute.snps4.4880.0524.660
ld0.1120.0120.124
misinherits0.2880.0160.305
mvtests000
plotUncertainty000
pool0.1760.0040.181
pp0.0800.0000.082
qq.chisq000
read.beagle0.0000.0000.001
read.impute000
read.long000
read.mach000
read.pedfile000
row.summary0.1200.0080.128
single.snp.tests0.0680.0040.075
sm.compare0.0000.0000.001
snp.cbind0.3400.0680.407
snp.cor0.9640.0001.024
snp.imputation2.9930.1163.156
snp.lhs.estimates0.5240.0240.546
snp.lhs.tests0.0800.0000.082
snp.pre.multiply0.0720.0080.083
snp.rhs.estimates0.0840.0040.088
snp.rhs.tests0.0360.0080.045
switch.alleles0.0760.0120.086
tdt.snp0.0200.0040.023
test.allele.switch0.1400.0040.141
testdata0.1320.0000.136
write.plink0.1080.0040.111
xxt0.8320.0000.832