BioC 2.12: CHECK report for inveRsion on pelham

Package: inveRsion

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch inveRsion_1.8.0.tar.gz

StartedAt: 2013-05-01 07:05:35 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:06:25 -0700 (Wed, 01 May 2013)

EllapsedTime: 49.9 seconds

RetCode: 0

Status: OK

CheckDir: inveRsion.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/inveRsion.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'inveRsion/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'inveRsion' version '1.8.0'
* 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 'inveRsion' can be installed ... [3s/4s] OK
* checking installed package size ... OK
* checking package 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 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 ... NOTE
File 'inveRsion/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Hola!\n")
    packageStartupMessage("welcome to inevRsion package. \n \n \n")
    packageStartupMessage("type: manual() for full manual \n      vignette(\"inveRsion\") for a quick start \n")

See section 'Good practice' in '?.onAttach'.
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [6s/7s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/inveRsion.Rcheck/00check.log'
for details.

* installing *source* package 'inveRsion' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c init_inveRsion.c -o init_inveRsion.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inversionModel.c -o inversionModel.o
inversionModel.c:176:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
   levelleft[*nlev-1]=dat[(*nr)*(c1)+0];
                     ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
inversionModel.c:177:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
   levelright[*nlev-1]=dat[(*nr)*(c2)+0];
                      ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
inversionModel.c:195:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        levelleft[*nlev-1]=dat[(*nr)*(c1)+row];
                          ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
inversionModel.c:196:29: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        levelright[*nlev-1]=dat[(*nr)*(c2)+row];
                           ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
inversionModel.c:167:8: warning: unused variable 'ncol' [-Wunused-variable]
   int ncol, row, level, found, c1, c2;
       ^
inversionModel.c:240:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  double *BB= (double *)malloc(((*nr)*(*nr))*sizeof(*BB));
                                ˜˜˜˜˜^˜˜˜˜˜ ˜
inversionModel.c:316:4: warning: '/*' within block comment [-Wcomment]
   /* compute block  b1b2b3b4, level its haplotypes and get their frequencies*/
   ^
inversionModel.c:237:8: warning: unused variable 'ncol' [-Wunused-variable]
   int ncol, row, level, i;
       ^
inversionModel.c:237:26: warning: unused variable 'i' [-Wunused-variable]
   int ncol, row, level, i;
                         ^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c:36:20: warning: unused variable 'fm' [-Wunused-variable]
   FILE *fg, *fa, *fm;
                   ^
writeGenoDat.c:36:15: warning: unused variable 'fa' [-Wunused-variable]
   FILE *fg, *fa, *fm;
              ^
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/inveRsion.Rcheck/inveRsion/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'inveRsion'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inveRsion)

name	user	system	elapsed
GenoDat-class	0.037	0.004	0.041
GenoDatROI-class	0.023	0.001	0.024
HaploCode-class	0.147	0.009	0.174
ac	0.013	0.002	0.015
accBic	2.476	0.026	2.552
accuracy-class	0.017	0.002	0.019
codeHaplo	0.186	0.003	0.192
gDat	0.018	0.002	0.022
getClassif-methods	0.298	0.008	0.306
getInv-methods	0.010	0.002	0.011
getROIs-methods	0.012	0.002	0.012
hapCode	0.025	0.004	0.030
invList	0.013	0.000	0.014
inveRsion-package	0.008	0.000	0.009
inversionList-class	0.013	0.001	0.014
listInv-methods	1.612	0.040	1.685
scan-class	0.022	0.002	0.025
scanInv	0.171	0.010	0.181
scanRes	0.014	0.001	0.017
setUpGenoDatFile	0.019	0.003	0.024

Summary

Command output