BioC 2.11: CHECK report for CGEN on perceval

Package: CGEN

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGEN_1.10.0.tar.gz

StartedAt: 2013-03-24 22:54:57 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:56:57 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 119.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: CGEN.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CGEN.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.10.0'
* 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 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 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call with 'PACKAGE' argument in a base package:
  .Fortran("hcass2", ..., PACKAGE = "stats")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
snp.scan.logistic : calcEffects: warning in effects.init(temp$parms,
  temp$cov, eff$var1, eff$var2, eff$snp.levels, eff$var.levels, base1 =
  0, base2 = eff$var.base, int.var = eff$int.var, effects = type, sep =
  eff$sep): partial argument match of 'sep' to 'sep1'
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.11-bioc/meat/CGEN.Rcheck/CGEN/libs/i386/CGEN.so':
  Found '_exit', possibly from 'exit' (C)
    Objects: 'ccl.o', 'hcl.o'
  Found '_printf', possibly from 'printf' (C)
    Object: 'CML.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (C)
    Objects: 'CML.o', 'ccl.o', 'hcl.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getMatchedSets 30.692  1.411  34.941
snp.matched    27.885  0.133  29.271
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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-2.11-bioc/meat/CGEN.Rcheck/CGEN/libs/i386
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (CGEN)

name	user	system	elapsed
LocusMapData	0.037	0.008	0.055
QQ.plot	0.007	0.002	0.012
SNPdata	0.013	0.004	0.021
Xdata	0.018	0.005	0.028
chromosome.plot	0.153	0.007	0.179
getMatchedSets	30.692	1.411	34.941
getSummary	0.015	0.002	0.017
getWaldTest	0.008	0.001	0.009
printEffects	0.165	0.020	0.233
recode.geno	0.004	0.000	0.004
snp.effects	0.155	0.009	0.168
snp.list	0.001	0.000	0.000
snp.logistic	0.254	0.019	0.315
snp.matched	27.885	0.133	29.271
snp.scan.logistic	0.003	0.004	0.012

Summary

Command output