GeneticsPed 1.26.0
David Henderson
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GeneticsPed | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | 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 --no-multiarch GeneticsPed_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GeneticsPed.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneticsPed/DESCRIPTION’ ... OK
* this is package ‘GeneticsPed’ version ‘1.26.0’
* 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 ‘GeneticsPed’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Packages in Depends field not imported from:
‘MASS’ ‘gdata’ ‘genetics’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘checkAttributes’ ‘dropLevels’ ‘unusedLevels’
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
gpLong2Wide: warning in expectedGenotypes(allele = allele.names(x[,
genotype])): partial argument match of 'allele' to 'alleles'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.Pedigree':
‘summary.Pedigree’
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 61198 Abort trap: 6 LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'GeneticsPed-Ex.Rout' 2>&1 < GeneticsPed-Ex.R
ERROR
Running examples in ‘GeneticsPed-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geneFlowT
> ### Title: Gene and gamete flow matrices
> ### Aliases: geneFlowT geneFlowTinv gameteFlowM mendelianSamplingD
> ### Keywords: array misc
>
> ### ** Examples
>
> data(Mrode2.1)
> Mrode2.1$dtB <- as.Date(Mrode2.1$dtB)
> x2.1 <- Pedigree(x=Mrode2.1, subject="sub", ascendant=c("fat", "mot"),
+ ascendantSex=c("M", "F"), family="fam", sex="sex",
+ generation="gen", dtBirth="dtB")
>
> fractions(geneFlowT(x2.1))
S1 S2 S3 S4 S5 S6
S1 1 0 0 0 0 0
S2 0 1 0 0 0 0
S3 1 0 1 0 0 0
S4 1 0 0 1 0 0
S5 1 0 0 1 1 0
S6 1 0 0 1 1 1
> fractions(geneFlowTinv(x2.1))
S1 S2 S3 S4 S5 S6
S1 1 0 0 0 0 0
S2 0 1 0 0 0 0
S3 -1/2 0 1 0 0 0
S4 -1/2 0 0 1 0 0
S5 0 0 0 -1/2 1 0
S6 0 0 0 0 -1/2 1
> fractions(gameteFlowM(x2.1))
S1 S2 S3 S4 S5 S6
S1 0 0 0 0 0 0
S2 0 0 0 0 0 0
S3 1/2 0 0 0 0 0
S4 1/2 0 0 0 0 0
S5 0 0 0 1/2 0 0
S6 0 0 0 0 1/2 0
> mendelianSamplingD(x2.1)
R(61198,0x7fff75239310) malloc: *** error for object 0x7f81bb91a030: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
* installing *source* package ‘GeneticsPed’ ...
** 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 ainverse.cc -o ainverse.o
In file included from ainverse.cc:9:
./../include/ainverse.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
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 eibd.cc -o eibd.o
In file included from eibd.cc:15:
./../include/eibd.h:19:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
gfortran-4.8 -fPIC -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran-4.8 -fPIC -g -O2 -Wall -c gpi.f -o gpi.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 inbreed.cc -o inbreed.o
In file included from inbreed.cc:10:
./../include/inbreed.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
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 inverseAdditive.cc -o inverseAdditive.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 meuwissen.cc -o meuwissen.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 pedSort.cc -o pedSort.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 pedtemplate.cc -o pedtemplate.o
In file included from pedtemplate.cc:15:
./../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
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 register.cc -o register.o
In file included from register.cc:8:
./../include/meuwissen.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
1 warning generated.
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 sargolzaei.c -o sargolzaei.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 sortped.cc -o sortped.o
In file included from sortped.cc:1:
./../include/sortped.h:7:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
In file included from sortped.cc:1:
In file included from ./../include/sortped.h:9:
./../include/../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/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 (GeneticsPed)