CGEN 1.3.0
William Wheeler
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CGEN | | Last Changed Rev: 50295 / Revision: 53825 | | Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/CGEN.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '1.3.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CGEN' can be installed ... OK
* checking installed package size ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Assignments in \usage in documentation object 'locusMap.list':
locusMap.list <- list(file = , file.type = 3, delimiter = "\t",
header = 0, snp.var = , chrm.var = , loc.var = , sas.list = NULL)
Assignments in \usage in documentation object 'pheno.list':
pheno.list <- list(file = , id.var = , response.var = , strata.var = NULL,
main.vars = NULL, int.vars = NULL, file.type = 3, delimiter = "",
factor.vars = NULL, in.miss = "NA", sas.list = NULL)
Assignments in \usage in documentation object 'sas.list':
sas.list <- list(sas.exe = , sas.file = , shell = "bash")
Assignments in \usage in documentation object 'snp.list':
snp.list <- list(dir = , file = , file.type = 2, delimiter = "\t",
in.miss = " ", heter.codes = NULL, id.var = , sas.list = NULL)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: cluster
* 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'/Users/biocbuild/bbs-2.8-bioc/meat/CGEN.Rcheck/00check.log'
for details
* installing *source* package 'CGEN' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c CML.c -o CML.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c ccl.c -o ccl.o
gfortran -arch i386 -fPIC -g -O2 -Wall -pedantic -c csclust.f -o csclust.o
Warning: Nonconforming tab character in column 1 of line 46
Warning: Nonconforming tab character in column 1 of line 83
Warning: Nonconforming tab character in column 1 of line 190
Warning: Nonconforming tab character in column 1 of line 203
Warning: Nonconforming tab character in column 1 of line 205
Warning: Nonconforming tab character in column 1 of line 207
csclust.f:222.3:
650 RETURN
1
Warning: Label 650 at (1) defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c fsclust.c -o fsclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c hcl.c -o hcl.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c pmatch.c -o pmatch.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o CGEN.so CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/CGEN.Rcheck/CGEN/libs/i386
** R
** data
** exec
** inst
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (CGEN)